make -k und/T0124-1reqA-local.index \
	und/T0124-1reqA-2track-l.index \
	 und/1reqA-T0124-local.index \
	und/1reqA-T0124-fssp-global.index
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
make[1]: `und/T0124-1reqA-local.index' is up to date.
make[1]: `und/T0124-1reqA-2track-l.index' is up to date.
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[1]: [und/1reqA-T0124-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[1]: [und/1reqA-T0124-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1reqA/1reqA-T0124-local.pw.a2m.gz \
	-target T0124 -template 1reqA \
	-out 1reqA-T0124-local -outdir und
Sequence named T0124 has all gap columns.
It will be included anyway.
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[1]: `und/1reqA-T0124-fssp-global.index' is up to date.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
../scripts/fragments-to-indexes
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-119l.85.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-119l.85.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-119l.85.3.a2m \
	-target T0124 -template 119l \
	-out T0124-119l.85.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/119l-orig.a2m
Writing a2m file: tmp/119l-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-24707


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-24707/tmp -alignfile tmp/119l-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/119l-orig.a2m (1 sequences, 164 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-24707/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-24707/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-24707/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24707/tmp.a2m (1 sequences, 164 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-24707/tmp.mod tmp/119l-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-24707 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/119l-align.mod
tmp/119l-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24707/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/119l-orig.a2m tmp/119l-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/119l-align.mod
Running w0.5 tmp/119l-orig.a2m tmp/119l-align.mod
Running align2model tmp/119l-align -i tmp/119l-align.mod -db tmp/119l-orig.a2m -db tmp/119l-pdb.a2m
partial PDB gets fragment 93 through 102 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   15
GLU    3   12
TYR    4    3
HIS    5    4
ASP    6    4
ILE    8    2
ARG    9   27
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.12949
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-119l.85.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-119l.86.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-119l.86.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-119l.86.2.a2m \
	-target T0124 -template 119l \
	-out T0124-119l.86.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/119l-orig.a2m
Writing a2m file: tmp/119l-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23911


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23911/tmp -alignfile tmp/119l-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/119l-orig.a2m (1 sequences, 164 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23911/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23911/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23911/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23911/tmp.a2m (1 sequences, 164 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23911/tmp.mod tmp/119l-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23911 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/119l-align.mod
tmp/119l-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23911/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/119l-orig.a2m tmp/119l-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/119l-align.mod
Running w0.5 tmp/119l-orig.a2m tmp/119l-align.mod
Running align2model tmp/119l-align -i tmp/119l-align.mod -db tmp/119l-orig.a2m -db tmp/119l-pdb.a2m
partial PDB gets fragment 92 through 101 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
GLU    2   12
TYR    3    3
HIS    4    4
ASP    5    4
ILE    7    3
ARG    8   27
ARG    9   26
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-119l.86.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-119l.87.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-119l.87.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-119l.87.1.a2m \
	-target T0124 -template 119l \
	-out T0124-119l.87.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/119l-orig.a2m
Writing a2m file: tmp/119l-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20442


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20442/tmp -alignfile tmp/119l-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/119l-orig.a2m (1 sequences, 164 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20442/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20442/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20442/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20442/tmp.a2m (1 sequences, 164 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20442/tmp.mod tmp/119l-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20442 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/119l-align.mod
tmp/119l-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20442/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/119l-orig.a2m tmp/119l-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/119l-align.mod
Running w0.5 tmp/119l-orig.a2m tmp/119l-align.mod
Running align2model tmp/119l-align -i tmp/119l-align.mod -db tmp/119l-orig.a2m -db tmp/119l-pdb.a2m
partial PDB gets fragment 91 through 100 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
TYR    2    3
HIS    3    3
ASP    4    4
ILE    6    3
ARG    7   27
ARG    8   27
ARG    9   27
LYS   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-119l.87.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-119l.88.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-119l.88.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-119l.88.1.a2m \
	-target T0124 -template 119l \
	-out T0124-119l.88.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/119l-orig.a2m
Writing a2m file: tmp/119l-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22796


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22796/tmp -alignfile tmp/119l-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/119l-orig.a2m (1 sequences, 164 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22796/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22796/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22796/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22796/tmp.a2m (1 sequences, 164 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22796/tmp.mod tmp/119l-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22796 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/119l-align.mod
tmp/119l-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22796/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/119l-orig.a2m tmp/119l-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/119l-align.mod
Running w0.5 tmp/119l-orig.a2m tmp/119l-align.mod
Running align2model tmp/119l-align -i tmp/119l-align.mod -db tmp/119l-orig.a2m -db tmp/119l-pdb.a2m
partial PDB gets fragment 90 through 99 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
HIS    2    4
ASP    3    4
ILE    5    5
ARG    7   28
ARG    8   27
LYS    9   26
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2   10     38.3637
Cluster     1 =   2  10
2 clashing residues after turn 
Residue clashes:
2-10
cluster 1 has 2 members and 5.000e+01 combinations:
 2  10 
Energy     38.3637
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 5.000e+01 - Sending to search
0.000000 < 38.363728: keeping 
Solved cluster 1: residual clashing  0.21
Still clashes at these sidechain pairs:
Residual clashes =    6.94603
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-119l.88.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a34A.19.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a34A.19.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a34A.19.3.a2m \
	-target T0124 -template 1a34A \
	-out T0124-1a34A.19.3 -outdir und
Skipped atom 203, because occupancy 0.4 <= existing 0.600001
Skipped atom 205, because occupancy 0.4 <= existing 0.600001
Skipped atom 564, because occupancy 0.5 <= existing 0.500001
Skipped atom 566, because occupancy 0.5 <= existing 0.500001
Skipped atom 1012, because occupancy 0.45 <= existing 0.550001
Skipped atom 1014, because occupancy 0.45 <= existing 0.550001
Skipped atom 1016, because occupancy 0.45 <= existing 0.550001
Skipped atom 1018, because occupancy 0.45 <= existing 0.550001
Skipped atom 1020, because occupancy 0.45 <= existing 0.550001
Skipped atom 1022, because occupancy 0.45 <= existing 0.550001
Skipped atom 1024, because occupancy 0.45 <= existing 0.550001
Skipped atom 1466, because occupancy 0.45 <= existing 0.550001
Skipped atom 1468, because occupancy 0.45 <= existing 0.550001
Skipped atom 1660, because occupancy 0.4 <= existing 0.600001
Skipped atom 1662, because occupancy 0.4 <= existing 0.600001
Skipped atom 1664, because occupancy 0.4 <= existing 0.600001
Skipped atom 2267, because occupancy 0.25 <= existing 0.750001
Skipped atom 2269, because occupancy 0.25 <= existing 0.750001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a34A-orig.a2m
Writing a2m file: tmp/1a34A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15178


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15178/tmp -alignfile tmp/1a34A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a34A-orig.a2m (1 sequences, 159 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15178/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15178/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15178/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15178/tmp.a2m (1 sequences, 159 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15178/tmp.mod tmp/1a34A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15178 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a34A-align.mod
tmp/1a34A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15178/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a34A-orig.a2m tmp/1a34A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a34A-align.mod
Running w0.5 tmp/1a34A-orig.a2m tmp/1a34A-align.mod
Running align2model tmp/1a34A-align -i tmp/1a34A-align.mod -db tmp/1a34A-orig.a2m -db tmp/1a34A-pdb.a2m
partial PDB gets fragment 137 through 146 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
GLN    2   12
MET    3   10
LYS    4   26
LEU    5    3
PHE    6    3
LEU    7    4
LYS    8   27
LEU    9    3
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a34A.19.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a34A.20.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a34A.20.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a34A.20.3.a2m \
	-target T0124 -template 1a34A \
	-out T0124-1a34A.20.3 -outdir und
Skipped atom 203, because occupancy 0.4 <= existing 0.600001
Skipped atom 205, because occupancy 0.4 <= existing 0.600001
Skipped atom 564, because occupancy 0.5 <= existing 0.500001
Skipped atom 566, because occupancy 0.5 <= existing 0.500001
Skipped atom 1012, because occupancy 0.45 <= existing 0.550001
Skipped atom 1014, because occupancy 0.45 <= existing 0.550001
Skipped atom 1016, because occupancy 0.45 <= existing 0.550001
Skipped atom 1018, because occupancy 0.45 <= existing 0.550001
Skipped atom 1020, because occupancy 0.45 <= existing 0.550001
Skipped atom 1022, because occupancy 0.45 <= existing 0.550001
Skipped atom 1024, because occupancy 0.45 <= existing 0.550001
Skipped atom 1466, because occupancy 0.45 <= existing 0.550001
Skipped atom 1468, because occupancy 0.45 <= existing 0.550001
Skipped atom 1660, because occupancy 0.4 <= existing 0.600001
Skipped atom 1662, because occupancy 0.4 <= existing 0.600001
Skipped atom 1664, because occupancy 0.4 <= existing 0.600001
Skipped atom 2267, because occupancy 0.25 <= existing 0.750001
Skipped atom 2269, because occupancy 0.25 <= existing 0.750001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a34A-orig.a2m
Writing a2m file: tmp/1a34A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26660


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26660/tmp -alignfile tmp/1a34A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a34A-orig.a2m (1 sequences, 159 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26660/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26660/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26660/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26660/tmp.a2m (1 sequences, 159 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26660/tmp.mod tmp/1a34A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26660 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a34A-align.mod
tmp/1a34A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26660/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a34A-orig.a2m tmp/1a34A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a34A-align.mod
Running w0.5 tmp/1a34A-orig.a2m tmp/1a34A-align.mod
Running align2model tmp/1a34A-align -i tmp/1a34A-align.mod -db tmp/1a34A-orig.a2m -db tmp/1a34A-pdb.a2m
partial PDB gets fragment 136 through 145 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    2   10
LYS    3   27
PHE    5    2
LEU    6    3
LYS    7   25
LEU    8    4
LEU    9    3
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a34A.20.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a44.44.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a44.44.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a44.44.3.a2m \
	-target T0124 -template 1a44 \
	-out T0124-1a44.44.3 -outdir und
partial PDB gets fragment 137 through 146 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
ARG    2   20
GLU    4   11
GLU    5   12
LEU    6    3
LEU    7    2
GLN    8   12
LYS    9   24
TYR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    4     11.4315
Cluster     1 =   2   4
2 clashing residues after turn 
Residue clashes:
2-4
cluster 1 has 2 members and 0.000e+00 combinations:
 4  2 
Energy     11.4315
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
0.000000 < 11.431529: keeping 
Solved cluster 1: residual clashing  0.98
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a44.44.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a44.45.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a44.45.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a44.45.3.a2m \
	-target T0124 -template 1a44 \
	-out T0124-1a44.45.3 -outdir und
partial PDB gets fragment 136 through 145 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   28
ARG    2   26
GLU    3   11
GLU    4   11
LEU    5    5
LEU    6    2
GLN    7   12
LYS    8   17
TYR    9    3
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a44.45.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a7cA.43.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a7cA.43.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a7cA.43.3.a2m \
	-target T0124 -template 1a7cA \
	-out T0124-1a7cA.43.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a7cA-orig.a2m
Writing a2m file: tmp/1a7cA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1596


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1596/tmp -alignfile tmp/1a7cA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a7cA-orig.a2m (1 sequences, 379 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1596/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1596/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1596/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1596/tmp.a2m (1 sequences, 379 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1596/tmp.mod tmp/1a7cA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1596 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a7cA-align.mod
tmp/1a7cA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1596/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a7cA-orig.a2m tmp/1a7cA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a7cA-align.mod
Running w0.5 tmp/1a7cA-orig.a2m tmp/1a7cA-align.mod
Running align2model tmp/1a7cA-align -i tmp/1a7cA-align.mod -db tmp/1a7cA-orig.a2m -db tmp/1a7cA-pdb.a2m
partial PDB gets fragment 337 through 346 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
LYS    2   20
ARG    3   20
GLU    5   16
GLU    6   15
LEU    8    3
GLN    9   14
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    7     17.3626
turnclash      7   12    5    0     22.6126
Cluster     1 =   3   5   7
3 clashing residues after turn 
Residue clashes:
3-7
7-5
cluster 1 has 3 members and 0.000e+00 combinations:
 5  7  3 
Energy     17.5866
Searching cluster 3
Combinations for 3 members in cluster 1 OK: 0.000e+00 - Sending to search
5.477870 < 17.586594: keeping 
0.000000 < 6.682556: keeping 
0.000000 < 2.727034: keeping 
0.000000 < 1.507115: keeping 
Solved cluster 1: residual clashing  0.76
Still clashes at these sidechain pairs:
Residual clashes =    2.02870
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a7cA.43.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a7cA.44.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a7cA.44.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a7cA.44.2.a2m \
	-target T0124 -template 1a7cA \
	-out T0124-1a7cA.44.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a7cA-orig.a2m
Writing a2m file: tmp/1a7cA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27002


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27002/tmp -alignfile tmp/1a7cA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a7cA-orig.a2m (1 sequences, 379 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27002/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27002/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27002/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27002/tmp.a2m (1 sequences, 379 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27002/tmp.mod tmp/1a7cA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27002 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a7cA-align.mod
tmp/1a7cA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27002/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a7cA-orig.a2m tmp/1a7cA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a7cA-align.mod
Running w0.5 tmp/1a7cA-orig.a2m tmp/1a7cA-align.mod
Running align2model tmp/1a7cA-align -i tmp/1a7cA-align.mod -db tmp/1a7cA-orig.a2m -db tmp/1a7cA-pdb.a2m
partial PDB gets fragment 336 through 345 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
ARG    2   26
ARG    3   24
GLU    4   14
GLU    5   15
LEU    6    3
LEU    7    5
GLN    8   13
LYS    9   31
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    6.05323
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a7cA.44.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a7cA.46.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a7cA.46.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a7cA.46.5.a2m \
	-target T0124 -template 1a7cA \
	-out T0124-1a7cA.46.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a7cA-orig.a2m
Writing a2m file: tmp/1a7cA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17880


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17880/tmp -alignfile tmp/1a7cA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a7cA-orig.a2m (1 sequences, 379 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17880/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17880/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17880/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17880/tmp.a2m (1 sequences, 379 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17880/tmp.mod tmp/1a7cA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17880 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a7cA-align.mod
tmp/1a7cA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17880/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a7cA-orig.a2m tmp/1a7cA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a7cA-align.mod
Running w0.5 tmp/1a7cA-orig.a2m tmp/1a7cA-align.mod
Running align2model tmp/1a7cA-align -i tmp/1a7cA-align.mod -db tmp/1a7cA-orig.a2m -db tmp/1a7cA-pdb.a2m
partial PDB gets fragment 334 through 343 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   32
GLU    3   11
LEU    4    3
LEU    5    3
GLN    6    9
LYS    7   31
TYR    8    3
SER    9    3
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    7     41.4893
Cluster     1 =   5   7
2 clashing residues after turn 
Residue clashes:
5-7
cluster 1 has 2 members and 1.600e+01 combinations:
 5  7 
Energy     41.4893
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 1.600e+01 - Sending to search
40.223366 < 41.489304: keeping 
15.719720 < 40.331818: keeping 
7.171400 < 15.834189: keeping 
0.000000 < 9.472672: keeping 
Solved cluster 1: residual clashing  0.24
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a7cA.46.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.64.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.64.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.64.4.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.64.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22364


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22364/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22364/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22364/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22364/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22364/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22364/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22364 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22364/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 106 through 115 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
ASP    4    4
SER    5    3
GLN    6   12
VAL    7    2
VAL    8    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.64.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.65.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.65.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.65.5.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.65.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12682


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12682/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12682/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12682/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12682/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12682/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12682/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12682 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12682/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 109 through 118 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    4    3
GLN    5   12
VAL    6    2
VAL    7    2
LEU    9    3
LYS   10   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.65.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.66.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.66.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.66.0.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.66.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-24640


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-24640/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-24640/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-24640/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-24640/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24640/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-24640/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-24640 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24640/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 108 through 120 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
ASP    2    4
SER    3    3
GLN    4   12
VAL    5    2
VAL    6    2
LYS    9   26
ARG   11   29
LEU   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.66.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.67.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.67.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.67.0.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.67.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4418


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4418/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4418/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4418/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4418/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4418/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4418/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4418 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4418/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 107 through 116 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    5
SER    2    2
GLN    3    9
VAL    4    2
VAL    5    1
GLU    6   13
LEU    7    3
LYS    8   26
GLU    9   12
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.06392
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.67.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.67.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.67.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.67.3.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.67.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6775


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6775/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6775/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6775/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6775/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6775/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6775/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6775 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6775/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 111 through 120 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    2    3
GLN    3   12
VAL    4    2
VAL    5    2
LEU    7    3
LYS    8   30
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.67.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.68.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.68.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.68.1.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.68.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26803


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26803/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26803/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26803/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26803/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26803/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26803/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26803 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26803/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 106 through 118 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
VAL    3    2
VAL    4    2
GLU    5   13
LEU    6    3
LYS    7   27
ARG    9   28
MET   12    9
GLU   13   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.68.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.69.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.69.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.69.1.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.69.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14720


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14720/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14720/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14720/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14720/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14720/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14720/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14720 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14720/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 105 through 117 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
VAL    2    2
VAL    3    3
GLU    4   13
LEU    5    2
LYS    6   24
GLU    7   12
ARG    8   29
LEU    9    3
MET   11   10
LEU   13    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.69.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.69.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.69.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.69.2.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.69.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18598


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18598/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18598/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18598/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18598/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18598/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18598/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18598 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18598/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 109 through 119 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1    9
VAL    2    2
VAL    3    1
GLU    4   13
LEU    5    3
LYS    6   26
GLU    7   12
ARG    8   32
LEU    9    3
GLU   10   15
MET   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.69.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.70.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.70.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.70.3.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.70.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8424


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8424/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8424/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8424/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8424/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8424/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8424/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8424 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8424/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 104 through 113 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
VAL    2    3
GLU    3   12
LEU    4    3
LYS    5   22
GLU    6   11
ARG    7   25
LEU    8    3
GLU    9   13
MET   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.70.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.72.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.72.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.72.2.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.72.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27112


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27112/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27112/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27112/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27112/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27112/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27112/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27112 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27112/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 106 through 116 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    2    3
LYS    3   22
GLU    4   11
ARG    5   25
LEU    6    3
GLU    7   13
MET    8   10
ILE   11    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.72.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.73.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.73.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.73.2.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.73.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25075


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25075/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25075/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25075/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25075/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25075/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25075/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25075 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25075/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 105 through 115 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   26
GLU    3   15
ARG    4   24
LEU    5    2
GLU    6   13
MET    7   10
GLU    8   13
LEU    9    3
ILE   10    3
HIS   11    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.73.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8i.74.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8i.74.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8i.74.3.a2m \
	-target T0124 -template 1a8i \
	-out T0124-1a8i.74.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a8i-orig.a2m
Writing a2m file: tmp/1a8i-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-19363


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-19363/tmp -alignfile tmp/1a8i-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a8i-orig.a2m (1 sequences, 842 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-19363/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-19363/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-19363/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19363/tmp.a2m (1 sequences, 842 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-19363/tmp.mod tmp/1a8i-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-19363 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a8i-align.mod
tmp/1a8i-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19363/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a8i-orig.a2m tmp/1a8i-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a8i-align.mod
Running w0.5 tmp/1a8i-orig.a2m tmp/1a8i-align.mod
Running align2model tmp/1a8i-align -i tmp/1a8i-align.mod -db tmp/1a8i-orig.a2m -db tmp/1a8i-pdb.a2m
partial PDB gets fragment 104 through 114 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
GLU    2   15
ARG    3   27
LEU    4    3
GLU    5   13
MET    6    6
GLU    7   13
LEU    8    3
ILE    9    4
HIS   10    4
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3   10     20.0000
Cluster     1 =   3  10
2 clashing residues after turn 
Residue clashes:
3-10
cluster 1 has 2 members and 2.100e+01 combinations:
 10  3 
Energy     20.0000
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 2.100e+01 - Sending to search
10.000000 < 20.000000: keeping 
0.000000 < 10.647597: keeping 
Solved cluster 1: residual clashing  0.76
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8i.74.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.10.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.10.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.10.0.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.10.0 -outdir und
partial PDB gets fragment 211 through 221 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
GLN    2   15
THR    3    1
SER    5    3
LEU    6    3
LEU    9    3
GLN   10   12
GLN   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.10.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.11.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.11.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.11.0.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.11.0 -outdir und
partial PDB gets fragment 210 through 220 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
THR    2    2
SER    4    3
LEU    5    3
GLU    7   12
GLN    9   11
GLN   10   11
MET   11   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.11.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.12.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.12.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.12.0.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.12.0 -outdir und
partial PDB gets fragment 209 through 219 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
SER    3    3
LEU    4    3
GLU    6   12
LEU    7    3
GLN    8   11
GLN    9   11
MET   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.12.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.12.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.12.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.12.1.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.12.1 -outdir und
partial PDB gets fragment 203 through 217 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
17 residues read 
Measuring phi and psi 
Getting chi values
THR    1    3
SER    3    3
LEU    4    3
LEU    7    2
GLN    8   12
GLN    9   14
MET   10   10
LYS   11   25
LEU   12    3
PHE   13    3
LEU   14    3
LYS   15   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7    8     11.5029
keepclash    10   14     61.9599
Cluster     1 =   7   8  10  14
4 clashing residues after turn 
Residue clashes:
7-8
8-10
10-14
cluster 1 has 4 members and 0.000e+00 combinations:
 7  14  8  10 
Energy     87.7325
Searching cluster 7
Combinations for 4 members in cluster 1 OK: 0.000e+00 - Sending to search
77.685547 < 87.732529: keeping 
67.349258 < 82.010033: keeping 
62.123375 < 71.733490: keeping 
21.502853 < 67.565643: keeping 
Solved cluster 1: residual clashing 21.87
Still clashes at these sidechain pairs:
ires=    7 irot=    1 jres=    8 jrot=    1      11.5029
Residual clashes =   21.50285
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.12.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.13.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.13.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.13.0.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.13.0 -outdir und
partial PDB gets fragment 208 through 219 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
SER    2    3
LEU    3    3
GLU    5   16
LEU    6    3
GLN    7   11
GLN    8   12
MET    9   10
LYS   10   24
LEU   11    3
PHE   12    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.13.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.13.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.13.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.13.2.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.13.2 -outdir und
partial PDB gets fragment 206 through 218 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
SER    2    2
LEU    3    3
GLU    5   12
LEU    6    3
GLN    7   15
GLN    8   12
MET    9   10
LYS   10   26
LEU   11    3
PHE   12    2
LEU   13    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.13.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.16.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.16.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.16.0.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.16.0 -outdir und
partial PDB gets fragment 205 through 216 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LEU    3    2
GLN    4   14
GLN    5   14
MET    6   10
LYS    7   25
LEU    8    3
PHE    9    2
LEU   10    3
LYS   11   26
LEU   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.16.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.16.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.16.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.16.4.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.16.4 -outdir und
partial PDB gets fragment 203 through 214 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   13
LEU    3    4
GLN    4   13
GLN    5   15
MET    6   11
LYS    7   30
LEU    8    3
PHE    9    3
LEU   10    3
LYS   11   25
LEU   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    8.13274
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.16.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.17.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.17.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.17.5.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.17.5 -outdir und
partial PDB gets fragment 202 through 213 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    4
GLN    3   13
GLN    4   15
MET    5   11
LYS    6   28
LEU    7    3
PHE    8    3
LEU    9    3
LYS   10   25
LEU   11    3
LEU   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.17.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.19.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.19.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.19.0.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.19.0 -outdir und
partial PDB gets fragment 202 through 212 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
GLN    2   14
MET    3   12
LYS    4   31
LEU    5    3
LEU    7    3
LYS    8   30
LEU    9    3
LEU   10    3
LYS   11   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.19.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.20.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.20.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.20.1.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.20.1 -outdir und
partial PDB gets fragment 201 through 211 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
MET    2   10
LYS    3   30
LEU    4    3
PHE    5    3
LEU    6    3
LYS    7   28
LEU    8    3
LEU    9    3
LYS   10   24
LYS   11   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    8     11.7223
turnclash      8    4   12    0     39.8830
Cluster     1 =   6   8  12
3 clashing residues after turn 
Residue clashes:
6-8
8-12
cluster 1 has 3 members and 1.716e+03 combinations:
 12  6  8 
Energy     11.7223
Searching cluster 6
Combinations for 3 members in cluster 1 OK: 1.716e+03 - Sending to search
9.312034 < 11.722328: keeping 
0.000000 < 10.391275: keeping 
0.000000 < 2.930875: keeping 
Solved cluster 1: residual clashing  0.40
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.20.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.21.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.21.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.21.1.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.21.1 -outdir und
partial PDB gets fragment 200 through 210 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
MET    1    6
LYS    2   20
LEU    3    3
PHE    4    3
LEU    5    3
LYS    6   31
LEU    7    3
LEU    8    4
LYS    9   28
LYS   10   30
GLN   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.21.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.22.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.22.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.22.1.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.22.1 -outdir und
partial PDB gets fragment 199 through 209 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LEU    2    2
PHE    3    2
LEU    4    3
LYS    5   30
LEU    6    3
LEU    7    4
LYS    8   29
LYS    9   28
GLN   10   14
GLU   11   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    9     46.6434
Cluster     1 =   6   9
2 clashing residues after turn 
Residue clashes:
6-9
cluster 1 has 2 members and 8.120e+02 combinations:
 9  6 
Energy     46.6434
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 8.120e+02 - Sending to search
0.000000 < 46.643410: keeping 
0.000000 < 0.089592: keeping 
Solved cluster 1: residual clashing  0.02
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.22.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.23.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.23.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.23.1.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.23.1 -outdir und
partial PDB gets fragment 198 through 208 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
PHE    2    3
LEU    3    2
LYS    4   20
LEU    5    3
LEU    6    3
LYS    7   29
LYS    8   31
GLN    9   13
GLU   10   14
LYS   11   28
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.13977
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.23.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.24.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.24.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.24.1.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.24.1 -outdir und
partial PDB gets fragment 197 through 207 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
PHE    1    3
LEU    2    3
LYS    3   26
LEU    4    2
LEU    5    3
LYS    6   27
LYS    7   30
GLN    8   13
GLU    9   16
LYS   10   29
GLU   11   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   11     46.6434
Cluster     1 =   8  11
2 clashing residues after turn 
Residue clashes:
8-11
cluster 1 has 2 members and 6.720e+02 combinations:
 11  8 
Energy     46.6434
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 6.720e+02 - Sending to search
0.000000 < 46.643410: keeping 
0.000000 < 0.089592: keeping 
Solved cluster 1: residual clashing  0.02
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.24.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.25.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.25.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.25.3.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.25.3 -outdir und
partial PDB gets fragment 196 through 205 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   27
LEU    3    3
LEU    4    3
LYS    5   19
LYS    6   20
GLN    7   13
GLU    8   15
LYS    9   29
GLU   10   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.99493
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.25.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a8l.9.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a8l.9.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a8l.9.1.a2m \
	-target T0124 -template 1a8l \
	-out T0124-1a8l.9.1 -outdir und
partial PDB gets fragment 212 through 221 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   16
PRO    2    2
GLN    3   11
THR    4    2
SER    6    3
LEU    7    3
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a8l.9.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1a9xA.102.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1a9xA.102.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1a9xA.102.5.a2m \
	-target T0124 -template 1a9xA \
	-out T0124-1a9xA.102.5 -outdir und
Skipped atom 3749, because occupancy 0.5 <= existing 0.500001
Skipped atom 3751, because occupancy 0.5 <= existing 0.500001
Skipped atom 3753, because occupancy 0.5 <= existing 0.500001
Skipped atom 3755, because occupancy 0.5 <= existing 0.500001
Skipped atom 3757, because occupancy 0.5 <= existing 0.500001
Skipped atom 3759, because occupancy 0.5 <= existing 0.500001
Skipped atom 3761, because occupancy 0.5 <= existing 0.500001
Skipped atom 3984, because occupancy 0.5 <= existing 0.500001
Skipped atom 3986, because occupancy 0.5 <= existing 0.500001
Skipped atom 3988, because occupancy 0.5 <= existing 0.500001
Skipped atom 3990, because occupancy 0.5 <= existing 0.500001
Skipped atom 4283, because occupancy 0.5 <= existing 0.500001
Skipped atom 4285, because occupancy 0.5 <= existing 0.500001
Skipped atom 4287, because occupancy 0.5 <= existing 0.500001
Skipped atom 4289, because occupancy 0.5 <= existing 0.500001
Skipped atom 5865, because occupancy 0.5 <= existing 0.500001
Skipped atom 5867, because occupancy 0.5 <= existing 0.500001
Skipped atom 5869, because occupancy 0.5 <= existing 0.500001
Skipped atom 5871, because occupancy 0.5 <= existing 0.500001
Skipped atom 6242, because occupancy 0.5 <= existing 0.500001
Skipped atom 6244, because occupancy 0.5 <= existing 0.500001
Skipped atom 6246, because occupancy 0.5 <= existing 0.500001
Skipped atom 6248, because occupancy 0.5 <= existing 0.500001
Skipped atom 6250, because occupancy 0.5 <= existing 0.500001
Skipped atom 7199, because occupancy 0.5 <= existing 0.500001
Skipped atom 7201, because occupancy 0.5 <= existing 0.500001
Skipped atom 7203, because occupancy 0.5 <= existing 0.500001
Skipped atom 7205, because occupancy 0.5 <= existing 0.500001
Skipped atom 7680, because occupancy 0.5 <= existing 0.500001
Skipped atom 7682, because occupancy 0.5 <= existing 0.500001
Skipped atom 7684, because occupancy 0.5 <= existing 0.500001
Skipped atom 7686, because occupancy 0.5 <= existing 0.500001
Skipped atom 7688, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1a9xA-orig.a2m
Writing a2m file: tmp/1a9xA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8173


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8173/tmp -alignfile tmp/1a9xA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1a9xA-orig.a2m (1 sequences, 1024 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8173/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8173/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8173/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8173/tmp.a2m (1 sequences, 1024 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8173/tmp.mod tmp/1a9xA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8173 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1a9xA-align.mod
tmp/1a9xA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8173/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1a9xA-orig.a2m tmp/1a9xA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1a9xA-align.mod
Running w0.5 tmp/1a9xA-orig.a2m tmp/1a9xA-align.mod
Running align2model tmp/1a9xA-align -i tmp/1a9xA-align.mod -db tmp/1a9xA-orig.a2m -db tmp/1a9xA-pdb.a2m
partial PDB gets fragment 85 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
GLN    2   11
THR    3    1
LYS    5   20
ILE    6    3
THR    7    3
GLU    8   15
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1a9xA.102.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1adoA.127.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1adoA.127.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1adoA.127.3.a2m \
	-target T0124 -template 1adoA \
	-out T0124-1adoA.127.3 -outdir und
partial PDB gets fragment 87 through 96 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
SER    2    2
ASN    3    5
ILE    4    3
LYS    5   30
ASP    6    4
ILE    7    5
LYS    8   26
LYS    9   26
LYS   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1adoA.127.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1adoA.128.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1adoA.128.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1adoA.128.3.a2m \
	-target T0124 -template 1adoA \
	-out T0124-1adoA.128.3 -outdir und
partial PDB gets fragment 86 through 95 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
ASN    2    4
ILE    3    2
LYS    4   15
ASP    5    5
ILE    6    5
LYS    7   27
LYS    8   30
LYS    9   26
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    6     16.9627
Cluster     1 =   4   6
2 clashing residues after turn 
Residue clashes:
4-6
cluster 1 has 2 members and 3.000e+00 combinations:
 4  6 
Energy     16.9627
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 3.000e+00 - Sending to search
0.000000 < 16.962729: keeping 
Solved cluster 1: residual clashing  0.12
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1adoA.128.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1adoA.129.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1adoA.129.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1adoA.129.2.a2m \
	-target T0124 -template 1adoA \
	-out T0124-1adoA.129.2 -outdir und
partial PDB gets fragment 85 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    5
ILE    2    5
LYS    3   31
ILE    5    2
LYS    6   27
LYS    7   30
LYS    8   27
LEU    9    3
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    6     14.4049
Cluster     1 =   5   6
2 clashing residues after turn 
Residue clashes:
5-6
cluster 1 has 2 members and 0.000e+00 combinations:
 5  6 
Energy     14.4049
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
Solved cluster 1: residual clashing 14.40
Still clashes at these sidechain pairs:
ires=    5 irot=    1 jres=    6 jrot=    1      14.4049
Residual clashes =   14.40489
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1adoA.129.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1adoA.130.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1adoA.130.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1adoA.130.4.a2m \
	-target T0124 -template 1adoA \
	-out T0124-1adoA.130.4 -outdir und
partial PDB gets fragment 84 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    5
ASP    3    5
ILE    4    5
LYS    5   17
LYS    6   15
LYS    7   27
LEU    8    3
GLU    9   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.69220
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1adoA.130.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1adoA.131.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1adoA.131.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1adoA.131.3.a2m \
	-target T0124 -template 1adoA \
	-out T0124-1adoA.131.3 -outdir und
partial PDB gets fragment 83 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   20
ASP    2    5
ILE    3    5
LYS    4   24
LYS    5   31
LYS    6   17
LEU    7    2
GLU    8   12
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1adoA.131.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1adoA.212.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1adoA.212.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1adoA.212.4.a2m \
	-target T0124 -template 1adoA \
	-out T0124-1adoA.212.4 -outdir und
partial PDB gets fragment 12 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
VAL    3    1
GLU    5   12
TYR    6    2
GLU    7   12
GLU    8   12
LYS    9   26
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1adoA.212.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1adoA.213.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1adoA.213.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1adoA.213.1.a2m \
	-target T0124 -template 1adoA \
	-out T0124-1adoA.213.1 -outdir und
partial PDB gets fragment 11 through 20 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    2    1
GLU    4   12
TYR    5    3
GLU    6   12
GLU    7   12
LYS    8   26
LEU    9    3
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   10     10.1979
Cluster     1 =   6  10
2 clashing residues after turn 
Residue clashes:
6-10
cluster 1 has 2 members and 4.000e+00 combinations:
 6  10 
Energy     10.1979
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
0.000000 < 10.197873: keeping 
Solved cluster 1: residual clashing  0.65
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1adoA.213.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1adoA.214.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1adoA.214.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1adoA.214.2.a2m \
	-target T0124 -template 1adoA \
	-out T0124-1adoA.214.2 -outdir und
partial PDB gets fragment 10 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
GLU    3   12
TYR    4    2
GLU    5   12
GLU    6   12
LYS    7   26
LEU    8    3
LYS    9   26
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1adoA.214.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1adoA.215.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1adoA.215.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1adoA.215.3.a2m \
	-target T0124 -template 1adoA \
	-out T0124-1adoA.215.3 -outdir und
partial PDB gets fragment 9 through 18 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   12
TYR    3    2
GLU    4   12
LYS    6   29
LEU    7    3
LYS    8   26
THR    9    1
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    8     21.9748
Cluster     1 =   4   8
2 clashing residues after turn 
Residue clashes:
4-8
cluster 1 has 2 members and 4.000e+00 combinations:
 4  8 
Energy     21.9748
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
0.000000 < 21.974804: keeping 
Solved cluster 1: residual clashing  0.42
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1adoA.215.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1adoA.216.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1adoA.216.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1adoA.216.4.a2m \
	-target T0124 -template 1adoA \
	-out T0124-1adoA.216.4 -outdir und
partial PDB gets fragment 8 through 17 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
TYR    2    3
GLU    3   12
GLU    4   12
LEU    6    3
LYS    7   26
THR    8    2
LEU    9    3
THR   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1adoA.216.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ads.222.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ads.222.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ads.222.5.a2m \
	-target T0124 -template 1ads \
	-out T0124-1ads.222.5 -outdir und
partial PDB gets fragment 6 through 15 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   28
THR    2    1
LEU    3    3
THR    4    2
VAL    5    1
GLU    6   13
VAL    7    2
GLN    8   15
GLU    9   12
MET   10    9
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ads.222.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1af7.13.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1af7.13.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1af7.13.5.a2m \
	-target T0124 -template 1af7 \
	-out T0124-1af7.13.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1af7-orig.a2m
Writing a2m file: tmp/1af7-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17867


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17867/tmp -alignfile tmp/1af7-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1af7-orig.a2m (1 sequences, 275 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17867/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17867/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17867/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17867/tmp.a2m (1 sequences, 275 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17867/tmp.mod tmp/1af7-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17867 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1af7-align.mod
tmp/1af7-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17867/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1af7-orig.a2m tmp/1af7-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1af7-align.mod
Running w0.5 tmp/1af7-orig.a2m tmp/1af7-align.mod
Running align2model tmp/1af7-align -i tmp/1af7-align.mod -db tmp/1af7-orig.a2m -db tmp/1af7-pdb.a2m
partial PDB gets fragment 261 through 272 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
SER    2    3
LEU    3    4
GLU    5   12
LEU    6    4
GLN    8    7
MET    9   11
LYS   10   23
LEU   11    5
PHE   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   12     20.7909
Cluster     1 =   6  12
2 clashing residues after turn 
Residue clashes:
6-12
cluster 1 has 2 members and 2.000e+01 combinations:
 12  6 
Energy     21.5498
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 2.000e+01 - Sending to search
0.000000 < 21.549803: keeping 
Solved cluster 1: residual clashing  2.69
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1af7.13.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1af7.16.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1af7.16.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1af7.16.5.a2m \
	-target T0124 -template 1af7 \
	-out T0124-1af7.16.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1af7-orig.a2m
Writing a2m file: tmp/1af7-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-24342


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-24342/tmp -alignfile tmp/1af7-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1af7-orig.a2m (1 sequences, 275 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-24342/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-24342/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-24342/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24342/tmp.a2m (1 sequences, 275 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-24342/tmp.mod tmp/1af7-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-24342 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1af7-align.mod
tmp/1af7-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24342/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1af7-orig.a2m tmp/1af7-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1af7-align.mod
Running w0.5 tmp/1af7-orig.a2m tmp/1af7-align.mod
Running align2model tmp/1af7-align -i tmp/1af7-align.mod -db tmp/1af7-orig.a2m -db tmp/1af7-pdb.a2m
partial PDB gets fragment 262 through 271 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   16
GLN    4   14
GLN    5   13
MET    6   10
LYS    7   18
LEU    8    3
PHE    9    3
LEU   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   11     19.4745
Cluster     1 =   5  11
2 clashing residues after turn 
Residue clashes:
5-11
cluster 1 has 2 members and 3.600e+01 combinations:
 11  5 
Energy     19.5890
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 3.600e+01 - Sending to search
11.485100 < 19.589003: keeping 
0.000000 < 12.850040: keeping 
0.000000 < 2.221744: keeping 
Solved cluster 1: residual clashing  2.21
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1af7.16.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1af7.6.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1af7.6.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1af7.6.4.a2m \
	-target T0124 -template 1af7 \
	-out T0124-1af7.6.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1af7-orig.a2m
Writing a2m file: tmp/1af7-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26568


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26568/tmp -alignfile tmp/1af7-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1af7-orig.a2m (1 sequences, 275 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26568/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26568/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26568/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26568/tmp.a2m (1 sequences, 275 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26568/tmp.mod tmp/1af7-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26568 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1af7-align.mod
tmp/1af7-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26568/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1af7-orig.a2m tmp/1af7-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1af7-align.mod
Running w0.5 tmp/1af7-orig.a2m tmp/1af7-align.mod
Running align2model tmp/1af7-align -i tmp/1af7-align.mod -db tmp/1af7-orig.a2m -db tmp/1af7-pdb.a2m
partial PDB gets fragment 264 through 273 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
LEU    2    3
PRO    3    2
GLU    4   12
PRO    5    2
GLN    6   13
THR    7    2
SER    9    3
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   12.22436
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1af7.6.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1af7.8.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1af7.8.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1af7.8.4.a2m \
	-target T0124 -template 1af7 \
	-out T0124-1af7.8.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1af7-orig.a2m
Writing a2m file: tmp/1af7-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-16437


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-16437/tmp -alignfile tmp/1af7-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1af7-orig.a2m (1 sequences, 275 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-16437/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16437/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16437/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16437/tmp.a2m (1 sequences, 275 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16437/tmp.mod tmp/1af7-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16437 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1af7-align.mod
tmp/1af7-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16437/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1af7-orig.a2m tmp/1af7-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1af7-align.mod
Running w0.5 tmp/1af7-orig.a2m tmp/1af7-align.mod
Running align2model tmp/1af7-align -i tmp/1af7-align.mod -db tmp/1af7-orig.a2m -db tmp/1af7-pdb.a2m
partial PDB gets fragment 264 through 273 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
GLU    2   12
PRO    3    2
SER    7    3
LEU    8    5
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    9     20.7909
Cluster     1 =   3   9
2 clashing residues after turn 
Residue clashes:
3-9
cluster 1 has 2 members and 2.000e+01 combinations:
 9  3 
Energy     21.5498
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 2.000e+01 - Sending to search
0.000000 < 21.549803: keeping 
Solved cluster 1: residual clashing  2.69
Still clashes at these sidechain pairs:
ires=    3 irot=    5 jres=    4 jrot=    1      12.7169
Residual clashes =   12.71690
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1af7.8.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1af7.9.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1af7.9.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1af7.9.3.a2m \
	-target T0124 -template 1af7 \
	-out T0124-1af7.9.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1af7-orig.a2m
Writing a2m file: tmp/1af7-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26587


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26587/tmp -alignfile tmp/1af7-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1af7-orig.a2m (1 sequences, 275 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26587/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26587/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26587/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26587/tmp.a2m (1 sequences, 275 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26587/tmp.mod tmp/1af7-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26587 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1af7-align.mod
tmp/1af7-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26587/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1af7-orig.a2m tmp/1af7-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1af7-align.mod
Running w0.5 tmp/1af7-orig.a2m tmp/1af7-align.mod
Running align2model tmp/1af7-align -i tmp/1af7-align.mod -db tmp/1af7-orig.a2m -db tmp/1af7-pdb.a2m
partial PDB gets fragment 263 through 272 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   16
PRO    2    2
GLN    3   14
THR    4    2
SER    6    2
LEU    7    3
GLU    9   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue T 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4   10     20.1018
keepclash     5    8     20.0000
Cluster     1 =   4  10
Cluster     2 =   5   8
4 clashing residues after turn 
Residue clashes:
4-10
5-8
cluster 1 has 2 members and 1.100e+02 combinations:
 4  10 
Energy     20.2162
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 1.100e+02 - Sending to search
7.856421 < 20.216240: keeping 
0.000000 < 8.729784: keeping 
Solved cluster 1: residual clashing  1.45
cluster 2 has 2 members and 4.000e+00 combinations:
 5  8 
Energy     30.0000
Searching cluster 5
Combinations for 2 members in cluster 2 OK: 4.000e+00 - Sending to search
2.927569 < 30.000000: keeping 
0.000000 < 13.085799: keeping 
Solved cluster 2: residual clashing  8.62
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1af7.9.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1afwA.134.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1afwA.134.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1afwA.134.3.a2m \
	-target T0124 -template 1afwA \
	-out T0124-1afwA.134.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1afwA-orig.a2m
Writing a2m file: tmp/1afwA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29176


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29176/tmp -alignfile tmp/1afwA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1afwA-orig.a2m (1 sequences, 393 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29176/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29176/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29176/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29176/tmp.a2m (1 sequences, 393 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29176/tmp.mod tmp/1afwA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29176 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1afwA-align.mod
tmp/1afwA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29176/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1afwA-orig.a2m tmp/1afwA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1afwA-align.mod
Running w0.5 tmp/1afwA-orig.a2m tmp/1afwA-align.mod
Running align2model tmp/1afwA-align -i tmp/1afwA-align.mod -db tmp/1afwA-orig.a2m -db tmp/1afwA-pdb.a2m
partial PDB gets fragment 43 through 52 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
LYS    2   25
LYS    3   25
LEU    4    3
GLU    5   12
LYS    7   21
ARG    8   27
LEU    9    3
ASP   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    8     19.4520
Cluster     1 =   5   8
2 clashing residues after turn 
Residue clashes:
5-8
cluster 1 has 2 members and 2.800e+01 combinations:
 5  8 
Energy     20.0444
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 2.800e+01 - Sending to search
0.000000 < 20.044353: keeping 
Solved cluster 1: residual clashing  0.98
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1afwA.134.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1alq.140.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1alq.140.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1alq.140.1.a2m \
	-target T0124 -template 1alq \
	-out T0124-1alq.140.1 -outdir und
Skipped atom 298 because residue number 31  < previous residue 298 
Skipped atom 299 because residue number 31  < previous residue 298 
Skipped atom 300 because residue number 31  < previous residue 298 
Skipped atom 301 because residue number 31  < previous residue 298 
Skipped atom 302 because residue number 31  < previous residue 298 
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Skipped atom 306 because residue number 31  < previous residue 298 
Skipped atom 307 because residue number 32  < previous residue 298 
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Skipped atom 311 because residue number 32  < previous residue 298 
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Skipped atom 315 because residue number 32  < previous residue 298 
Skipped atom 316 because residue number 33  < previous residue 298 
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Skipped atom 324 because residue number 34  < previous residue 298 
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Skipped atom 332 because residue number 35  < previous residue 298 
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Skipped atom 340 because residue number 36  < previous residue 298 
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Skipped atom 348 because residue number 37  < previous residue 298 
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Skipped atom 372 because residue number 39  < previous residue 298 
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Skipped atom 375 because residue number 40  < previous residue 298 
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Skipped atom 379 because residue number 40  < previous residue 298 
Skipped atom 380 because residue number 40  < previous residue 298 
Skipped atom 381 because residue number 40  < previous residue 298 
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Skipped atom 387 because residue number 41  < previous residue 298 
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Skipped atom 391 because residue number 41  < previous residue 298 
Skipped atom 392 because residue number 41  < previous residue 298 
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Skipped atom 394 because residue number 41  < previous residue 298 
Skipped atom 395 because residue number 42  < previous residue 298 
Skipped atom 396 because residue number 42  < previous residue 298 
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Skipped atom 399 because residue number 42  < previous residue 298 
Skipped atom 400 because residue number 43  < previous residue 298 
Skipped atom 401 because residue number 43  < previous residue 298 
Skipped atom 402 because residue number 43  < previous residue 298 
Skipped atom 403 because residue number 43  < previous residue 298 
Skipped atom 404 because residue number 43  < previous residue 298 
Skipped atom 405 because residue number 43  < previous residue 298 
Skipped atom 406 because residue number 43  < previous residue 298 
Skipped atom 407 because residue number 43  < previous residue 298 
Skipped atom 408 because residue number 43  < previous residue 298 
Skipped atom 409 because residue number 43  < previous residue 298 
Skipped atom 410 because residue number 44  < previous residue 298 
Skipped atom 411 because residue number 44  < previous residue 298 
Skipped atom 412 because residue number 44  < previous residue 298 
Skipped atom 413 because residue number 44  < previous residue 298 
Skipped atom 414 because residue number 44  < previous residue 298 
Skipped atom 415 because residue number 44  < previous residue 298 
Skipped atom 416 because residue number 44  < previous residue 298 
Skipped atom 417 because residue number 44  < previous residue 298 
Skipped atom 418 because residue number 45  < previous residue 298 
Skipped atom 419 because residue number 45  < previous residue 298 
Skipped atom 420 because residue number 45  < previous residue 298 
Skipped atom 421 because residue number 45  < previous residue 298 
Skipped atom 422 because residue number 46  < previous residue 298 
Skipped atom 423 because residue number 46  < previous residue 298 
Skipped atom 424 because residue number 46  < previous residue 298 
Skipped atom 425 because residue number 46  < previous residue 298 
Skipped atom 426 because residue number 46  < previous residue 298 
Skipped atom 427 because residue number 46  < previous residue 298 
Skipped atom 428 because residue number 46  < previous residue 298 
Skipped atom 429 because residue number 47  < previous residue 298 
Skipped atom 430 because residue number 47  < previous residue 298 
Skipped atom 431 because residue number 47  < previous residue 298 
Skipped atom 432 because residue number 47  < previous residue 298 
Skipped atom 433 because residue number 47  < previous residue 298 
Skipped atom 434 because residue number 47  < previous residue 298 
Skipped atom 435 because residue number 47  < previous residue 298 
Skipped atom 436 because residue number 47  < previous residue 298 
Skipped atom 437 because residue number 47  < previous residue 298 
Skipped atom 438 because residue number 47  < previous residue 298 
Skipped atom 439 because residue number 47  < previous residue 298 
Skipped atom 440 because residue number 47  < previous residue 298 
Skipped atom 441 because residue number 48  < previous residue 298 
Skipped atom 442 because residue number 48  < previous residue 298 
Skipped atom 443 because residue number 48  < previous residue 298 
Skipped atom 444 because residue number 48  < previous residue 298 
Skipped atom 445 because residue number 48  < previous residue 298 
Skipped atom 446 because residue number 49  < previous residue 298 
Skipped atom 447 because residue number 49  < previous residue 298 
Skipped atom 448 because residue number 49  < previous residue 298 
Skipped atom 449 because residue number 49  < previous residue 298 
Skipped atom 450 because residue number 49  < previous residue 298 
Skipped atom 451 because residue number 49  < previous residue 298 
Skipped atom 452 because residue number 49  < previous residue 298 
Skipped atom 453 because residue number 49  < previous residue 298 
Skipped atom 454 because residue number 50  < previous residue 298 
Skipped atom 455 because residue number 50  < previous residue 298 
Skipped atom 456 because residue number 50  < previous residue 298 
Skipped atom 457 because residue number 50  < previous residue 298 
Skipped atom 458 because residue number 50  < previous residue 298 
Skipped atom 459 because residue number 50  < previous residue 298 
Skipped atom 460 because residue number 50  < previous residue 298 
Skipped atom 461 because residue number 50  < previous residue 298 
Skipped atom 462 because residue number 51  < previous residue 298 
Skipped atom 463 because residue number 51  < previous residue 298 
Skipped atom 464 because residue number 51  < previous residue 298 
Skipped atom 465 because residue number 51  < previous residue 298 
Skipped atom 466 because residue number 51  < previous residue 298 
Skipped atom 467 because residue number 51  < previous residue 298 
Skipped atom 468 because residue number 51  < previous residue 298 
Skipped atom 469 because residue number 52  < previous residue 298 
Skipped atom 470 because residue number 52  < previous residue 298 
Skipped atom 471 because residue number 52  < previous residue 298 
Skipped atom 472 because residue number 52  < previous residue 298 
Skipped atom 473 because residue number 52  < previous residue 298 
Skipped atom 474 because residue number 52  < previous residue 298 
Skipped atom 475 because residue number 52  < previous residue 298 
Skipped atom 476 because residue number 52  < previous residue 298 
Skipped atom 477 because residue number 52  < previous residue 298 
Skipped atom 478 because residue number 53  < previous residue 298 
Skipped atom 479 because residue number 53  < previous residue 298 
Skipped atom 480 because residue number 53  < previous residue 298 
Skipped atom 481 because residue number 53  < previous residue 298 
Skipped atom 482 because residue number 53  < previous residue 298 
Skipped atom 483 because residue number 53  < previous residue 298 
Skipped atom 484 because residue number 54  < previous residue 298 
Skipped atom 485 because residue number 54  < previous residue 298 
Skipped atom 486 because residue number 54  < previous residue 298 
Skipped atom 487 because residue number 54  < previous residue 298 
Skipped atom 488 because residue number 55  < previous residue 298 
Skipped atom 489 because residue number 55  < previous residue 298 
Skipped atom 490 because residue number 55  < previous residue 298 
Skipped atom 491 because residue number 55  < previous residue 298 
Skipped atom 492 because residue number 55  < previous residue 298 
Skipped atom 493 because residue number 55  < previous residue 298 
Skipped atom 494 because residue number 55  < previous residue 298 
Skipped atom 495 because residue number 55  < previous residue 298 
Skipped atom 496 because residue number 55  < previous residue 298 
Skipped atom 497 because residue number 56  < previous residue 298 
Skipped atom 498 because residue number 56  < previous residue 298 
Skipped atom 499 because residue number 56  < previous residue 298 
Skipped atom 500 because residue number 56  < previous residue 298 
Skipped atom 501 because residue number 56  < previous residue 298 
Skipped atom 502 because residue number 56  < previous residue 298 
Skipped atom 503 because residue number 56  < previous residue 298 
Skipped atom 504 because residue number 56  < previous residue 298 
Skipped atom 505 because residue number 56  < previous residue 298 
Skipped atom 506 because residue number 57  < previous residue 298 
Skipped atom 507 because residue number 57  < previous residue 298 
Skipped atom 508 because residue number 57  < previous residue 298 
Skipped atom 509 because residue number 57  < previous residue 298 
Skipped atom 510 because residue number 57  < previous residue 298 
Skipped atom 511 because residue number 57  < previous residue 298 
Skipped atom 512 because residue number 57  < previous residue 298 
Skipped atom 513 because residue number 59  < previous residue 298 
Skipped atom 514 because residue number 59  < previous residue 298 
Skipped atom 515 because residue number 59  < previous residue 298 
Skipped atom 516 because residue number 59  < previous residue 298 
Skipped atom 517 because residue number 59  < previous residue 298 
Skipped atom 518 because residue number 59  < previous residue 298 
Skipped atom 519 because residue number 59  < previous residue 298 
Skipped atom 520 because residue number 59  < previous residue 298 
Skipped atom 521 because residue number 59  < previous residue 298 
Skipped atom 522 because residue number 60  < previous residue 298 
Skipped atom 523 because residue number 60  < previous residue 298 
Skipped atom 524 because residue number 60  < previous residue 298 
Skipped atom 525 because residue number 60  < previous residue 298 
Skipped atom 526 because residue number 60  < previous residue 298 
Skipped atom 527 because residue number 60  < previous residue 298 
Skipped atom 528 because residue number 60  < previous residue 298 
Skipped atom 529 because residue number 60  < previous residue 298 
Skipped atom 530 because residue number 60  < previous residue 298 
Skipped atom 531 because residue number 60  < previous residue 298 
Skipped atom 532 because residue number 60  < previous residue 298 
Skipped atom 533 because residue number 61  < previous residue 298 
Skipped atom 534 because residue number 61  < previous residue 298 
Skipped atom 535 because residue number 61  < previous residue 298 
Skipped atom 536 because residue number 61  < previous residue 298 
Skipped atom 537 because residue number 61  < previous residue 298 
Skipped atom 538 because residue number 61  < previous residue 298 
Skipped atom 539 because residue number 61  < previous residue 298 
Skipped atom 540 because residue number 61  < previous residue 298 
Skipped atom 541 because residue number 62  < previous residue 298 
Skipped atom 542 because residue number 62  < previous residue 298 
Skipped atom 543 because residue number 62  < previous residue 298 
Skipped atom 544 because residue number 62  < previous residue 298 
Skipped atom 545 because residue number 62  < previous residue 298 
Skipped atom 546 because residue number 62  < previous residue 298 
Skipped atom 547 because residue number 63  < previous residue 298 
Skipped atom 548 because residue number 63  < previous residue 298 
Skipped atom 549 because residue number 63  < previous residue 298 
Skipped atom 550 because residue number 63  < previous residue 298 
Skipped atom 551 because residue number 63  < previous residue 298 
Skipped atom 552 because residue number 63  < previous residue 298 
Skipped atom 553 because residue number 63  < previous residue 298 
Skipped atom 554 because residue number 63  < previous residue 298 
Skipped atom 555 because residue number 64  < previous residue 298 
Skipped atom 556 because residue number 64  < previous residue 298 
Skipped atom 557 because residue number 64  < previous residue 298 
Skipped atom 558 because residue number 64  < previous residue 298 
Skipped atom 559 because residue number 64  < previous residue 298 
Skipped atom 560 because residue number 64  < previous residue 298 
Skipped atom 561 because residue number 64  < previous residue 298 
Skipped atom 562 because residue number 64  < previous residue 298 
Skipped atom 563 because residue number 64  < previous residue 298 
Skipped atom 564 because residue number 65  < previous residue 298 
Skipped atom 565 because residue number 65  < previous residue 298 
Skipped atom 566 because residue number 65  < previous residue 298 
Skipped atom 567 because residue number 65  < previous residue 298 
Skipped atom 568 because residue number 65  < previous residue 298 
Skipped atom 569 because residue number 65  < previous residue 298 
Skipped atom 570 because residue number 65  < previous residue 298 
Skipped atom 571 because residue number 65  < previous residue 298 
Skipped atom 572 because residue number 65  < previous residue 298 
Skipped atom 573 because residue number 65  < previous residue 298 
Skipped atom 574 because residue number 65  < previous residue 298 
Skipped atom 575 because residue number 66  < previous residue 298 
Skipped atom 576 because residue number 66  < previous residue 298 
Skipped atom 577 because residue number 66  < previous residue 298 
Skipped atom 578 because residue number 66  < previous residue 298 
Skipped atom 579 because residue number 66  < previous residue 298 
Skipped atom 580 because residue number 66  < previous residue 298 
Skipped atom 581 because residue number 66  < previous residue 298 
Skipped atom 582 because residue number 66  < previous residue 298 
Skipped atom 583 because residue number 66  < previous residue 298 
Skipped atom 584 because residue number 66  < previous residue 298 
Skipped atom 585 because residue number 66  < previous residue 298 
Skipped atom 586 because residue number 67  < previous residue 298 
Skipped atom 587 because residue number 67  < previous residue 298 
Skipped atom 588 because residue number 67  < previous residue 298 
Skipped atom 589 because residue number 67  < previous residue 298 
Skipped atom 590 because residue number 67  < previous residue 298 
Skipped atom 591 because residue number 68  < previous residue 298 
Skipped atom 592 because residue number 68  < previous residue 298 
Skipped atom 593 because residue number 68  < previous residue 298 
Skipped atom 594 because residue number 68  < previous residue 298 
Skipped atom 595 because residue number 68  < previous residue 298 
Skipped atom 596 because residue number 68  < previous residue 298 
Skipped atom 597 because residue number 68  < previous residue 298 
Skipped atom 598 because residue number 68  < previous residue 298 
Skipped atom 599 because residue number 68  < previous residue 298 
Skipped atom 600 because residue number 68  < previous residue 298 
Skipped atom 601 because residue number 68  < previous residue 298 
Skipped atom 602 because residue number 68  < previous residue 298 
Skipped atom 603 because residue number 69  < previous residue 298 
Skipped atom 604 because residue number 69  < previous residue 298 
Skipped atom 605 because residue number 69  < previous residue 298 
Skipped atom 606 because residue number 69  < previous residue 298 
Skipped atom 607 because residue number 69  < previous residue 298 
Skipped atom 608 because residue number 70  < previous residue 298 
Skipped atom 609 because residue number 70  < previous residue 298 
Skipped atom 610 because residue number 70  < previous residue 298 
Skipped atom 611 because residue number 70  < previous residue 298 
Skipped atom 612 because residue number 70  < previous residue 298 
Skipped atom 613 because residue number 70  < previous residue 298 
Skipped atom 614 because residue number 71  < previous residue 298 
Skipped atom 615 because residue number 71  < previous residue 298 
Skipped atom 616 because residue number 71  < previous residue 298 
Skipped atom 617 because residue number 71  < previous residue 298 
Skipped atom 618 because residue number 71  < previous residue 298 
Skipped atom 619 because residue number 71  < previous residue 298 
Skipped atom 620 because residue number 71  < previous residue 298 
Skipped atom 621 because residue number 72  < previous residue 298 
Skipped atom 622 because residue number 72  < previous residue 298 
Skipped atom 623 because residue number 72  < previous residue 298 
Skipped atom 624 because residue number 72  < previous residue 298 
Skipped atom 625 because residue number 72  < previous residue 298 
Skipped atom 626 because residue number 72  < previous residue 298 
Skipped atom 627 because residue number 73  < previous residue 298 
Skipped atom 628 because residue number 73  < previous residue 298 
Skipped atom 629 because residue number 73  < previous residue 298 
Skipped atom 630 because residue number 73  < previous residue 298 
Skipped atom 631 because residue number 73  < previous residue 298 
Skipped atom 632 because residue number 73  < previous residue 298 
Skipped atom 633 because residue number 73  < previous residue 298 
Skipped atom 634 because residue number 73  < previous residue 298 
Skipped atom 635 because residue number 73  < previous residue 298 
Skipped atom 636 because residue number 74  < previous residue 298 
Skipped atom 637 because residue number 74  < previous residue 298 
Skipped atom 638 because residue number 74  < previous residue 298 
Skipped atom 639 because residue number 74  < previous residue 298 
Skipped atom 640 because residue number 74  < previous residue 298 
Skipped atom 641 because residue number 75  < previous residue 298 
Skipped atom 642 because residue number 75  < previous residue 298 
Skipped atom 643 because residue number 75  < previous residue 298 
Skipped atom 644 because residue number 75  < previous residue 298 
Skipped atom 645 because residue number 75  < previous residue 298 
Skipped atom 646 because residue number 75  < previous residue 298 
Skipped atom 647 because residue number 75  < previous residue 298 
Skipped atom 648 because residue number 75  < previous residue 298 
Skipped atom 649 because residue number 76  < previous residue 298 
Skipped atom 650 because residue number 76  < previous residue 298 
Skipped atom 651 because residue number 76  < previous residue 298 
Skipped atom 652 because residue number 76  < previous residue 298 
Skipped atom 653 because residue number 76  < previous residue 298 
Skipped atom 654 because residue number 76  < previous residue 298 
Skipped atom 655 because residue number 76  < previous residue 298 
Skipped atom 656 because residue number 76  < previous residue 298 
Skipped atom 657 because residue number 77  < previous residue 298 
Skipped atom 658 because residue number 77  < previous residue 298 
Skipped atom 659 because residue number 77  < previous residue 298 
Skipped atom 660 because residue number 77  < previous residue 298 
Skipped atom 661 because residue number 77  < previous residue 298 
Skipped atom 662 because residue number 77  < previous residue 298 
Skipped atom 663 because residue number 78  < previous residue 298 
Skipped atom 664 because residue number 78  < previous residue 298 
Skipped atom 665 because residue number 78  < previous residue 298 
Skipped atom 666 because residue number 78  < previous residue 298 
Skipped atom 667 because residue number 78  < previous residue 298 
Skipped atom 668 because residue number 79  < previous residue 298 
Skipped atom 669 because residue number 79  < previous residue 298 
Skipped atom 670 because residue number 79  < previous residue 298 
Skipped atom 671 because residue number 79  < previous residue 298 
Skipped atom 672 because residue number 79  < previous residue 298 
Skipped atom 673 because residue number 79  < previous residue 298 
Skipped atom 674 because residue number 79  < previous residue 298 
Skipped atom 675 because residue number 79  < previous residue 298 
Skipped atom 676 because residue number 80  < previous residue 298 
Skipped atom 677 because residue number 80  < previous residue 298 
Skipped atom 678 because residue number 80  < previous residue 298 
Skipped atom 679 because residue number 80  < previous residue 298 
Skipped atom 680 because residue number 80  < previous residue 298 
Skipped atom 681 because residue number 80  < previous residue 298 
Skipped atom 682 because residue number 80  < previous residue 298 
Skipped atom 683 because residue number 80  < previous residue 298 
Skipped atom 684 because residue number 81  < previous residue 298 
Skipped atom 685 because residue number 81  < previous residue 298 
Skipped atom 686 because residue number 81  < previous residue 298 
Skipped atom 687 because residue number 81  < previous residue 298 
Skipped atom 688 because residue number 81  < previous residue 298 
Skipped atom 689 because residue number 81  < previous residue 298 
Skipped atom 690 because residue number 81  < previous residue 298 
Skipped atom 691 because residue number 81  < previous residue 298 
Skipped atom 692 because residue number 82  < previous residue 298 
Skipped atom 693 because residue number 82  < previous residue 298 
Skipped atom 694 because residue number 82  < previous residue 298 
Skipped atom 695 because residue number 82  < previous residue 298 
Skipped atom 696 because residue number 82  < previous residue 298 
Skipped atom 697 because residue number 82  < previous residue 298 
Skipped atom 698 because residue number 82  < previous residue 298 
Skipped atom 699 because residue number 82  < previous residue 298 
Skipped atom 700 because residue number 82  < previous residue 298 
Skipped atom 701 because residue number 83  < previous residue 298 
Skipped atom 702 because residue number 83  < previous residue 298 
Skipped atom 703 because residue number 83  < previous residue 298 
Skipped atom 704 because residue number 83  < previous residue 298 
Skipped atom 705 because residue number 83  < previous residue 298 
Skipped atom 706 because residue number 83  < previous residue 298 
Skipped atom 707 because residue number 83  < previous residue 298 
Skipped atom 708 because residue number 83  < previous residue 298 
Skipped atom 709 because residue number 83  < previous residue 298 
Skipped atom 710 because residue number 84  < previous residue 298 
Skipped atom 711 because residue number 84  < previous residue 298 
Skipped atom 712 because residue number 84  < previous residue 298 
Skipped atom 713 because residue number 84  < previous residue 298 
Skipped atom 714 because residue number 84  < previous residue 298 
Skipped atom 715 because residue number 84  < previous residue 298 
Skipped atom 716 because residue number 84  < previous residue 298 
Skipped atom 717 because residue number 87  < previous residue 298 
Skipped atom 718 because residue number 87  < previous residue 298 
Skipped atom 719 because residue number 87  < previous residue 298 
Skipped atom 720 because residue number 87  < previous residue 298 
Skipped atom 721 because residue number 87  < previous residue 298 
Skipped atom 722 because residue number 87  < previous residue 298 
Skipped atom 723 because residue number 87  < previous residue 298 
Skipped atom 724 because residue number 88  < previous residue 298 
Skipped atom 725 because residue number 88  < previous residue 298 
Skipped atom 726 because residue number 88  < previous residue 298 
Skipped atom 727 because residue number 88  < previous residue 298 
Skipped atom 728 because residue number 88  < previous residue 298 
Skipped atom 729 because residue number 88  < previous residue 298 
Skipped atom 730 because residue number 88  < previous residue 298 
Skipped atom 731 because residue number 88  < previous residue 298 
Skipped atom 732 because residue number 88  < previous residue 298 
Skipped atom 733 because residue number 88  < previous residue 298 
Skipped atom 734 because residue number 88  < previous residue 298 
Skipped atom 735 because residue number 88  < previous residue 298 
Skipped atom 736 because residue number 89  < previous residue 298 
Skipped atom 737 because residue number 89  < previous residue 298 
Skipped atom 738 because residue number 89  < previous residue 298 
Skipped atom 739 because residue number 89  < previous residue 298 
Skipped atom 740 because residue number 89  < previous residue 298 
Skipped atom 741 because residue number 89  < previous residue 298 
Skipped atom 742 because residue number 89  < previous residue 298 
Skipped atom 743 because residue number 89  < previous residue 298 
Skipped atom 744 because residue number 90  < previous residue 298 
Skipped atom 745 because residue number 90  < previous residue 298 
Skipped atom 746 because residue number 90  < previous residue 298 
Skipped atom 747 because residue number 90  < previous residue 298 
Skipped atom 748 because residue number 90  < previous residue 298 
Skipped atom 749 because residue number 90  < previous residue 298 
Skipped atom 750 because residue number 90  < previous residue 298 
Skipped atom 751 because residue number 90  < previous residue 298 
Skipped atom 752 because residue number 90  < previous residue 298 
Skipped atom 753 because residue number 91  < previous residue 298 
Skipped atom 754 because residue number 91  < previous residue 298 
Skipped atom 755 because residue number 91  < previous residue 298 
Skipped atom 756 because residue number 91  < previous residue 298 
Skipped atom 757 because residue number 91  < previous residue 298 
Skipped atom 758 because residue number 91  < previous residue 298 
Skipped atom 759 because residue number 91  < previous residue 298 
Skipped atom 760 because residue number 91  < previous residue 298 
Skipped atom 761 because residue number 92  < previous residue 298 
Skipped atom 762 because residue number 92  < previous residue 298 
Skipped atom 763 because residue number 92  < previous residue 298 
Skipped atom 764 because residue number 92  < previous residue 298 
Skipped atom 765 because residue number 92  < previous residue 298 
Skipped atom 766 because residue number 92  < previous residue 298 
Skipped atom 767 because residue number 92  < previous residue 298 
Skipped atom 768 because residue number 92  < previous residue 298 
Skipped atom 769 because residue number 93  < previous residue 298 
Skipped atom 770 because residue number 93  < previous residue 298 
Skipped atom 771 because residue number 93  < previous residue 298 
Skipped atom 772 because residue number 93  < previous residue 298 
Skipped atom 773 because residue number 93  < previous residue 298 
Skipped atom 774 because residue number 93  < previous residue 298 
Skipped atom 775 because residue number 93  < previous residue 298 
Skipped atom 776 because residue number 93  < previous residue 298 
Skipped atom 777 because residue number 93  < previous residue 298 
Skipped atom 778 because residue number 94  < previous residue 298 
Skipped atom 779 because residue number 94  < previous residue 298 
Skipped atom 780 because residue number 94  < previous residue 298 
Skipped atom 781 because residue number 94  < previous residue 298 
Skipped atom 782 because residue number 94  < previous residue 298 
Skipped atom 783 because residue number 94  < previous residue 298 
Skipped atom 784 because residue number 94  < previous residue 298 
Skipped atom 785 because residue number 94  < previous residue 298 
Skipped atom 786 because residue number 94  < previous residue 298 
Skipped atom 787 because residue number 95  < previous residue 298 
Skipped atom 788 because residue number 95  < previous residue 298 
Skipped atom 789 because residue number 95  < previous residue 298 
Skipped atom 790 because residue number 95  < previous residue 298 
Skipped atom 791 because residue number 95  < previous residue 298 
Skipped atom 792 because residue number 95  < previous residue 298 
Skipped atom 793 because residue number 95  < previous residue 298 
Skipped atom 794 because residue number 96  < previous residue 298 
Skipped atom 795 because residue number 96  < previous residue 298 
Skipped atom 796 because residue number 96  < previous residue 298 
Skipped atom 797 because residue number 96  < previous residue 298 
Skipped atom 798 because residue number 96  < previous residue 298 
Skipped atom 799 because residue number 96  < previous residue 298 
Skipped atom 800 because residue number 96  < previous residue 298 
Skipped atom 801 because residue number 96  < previous residue 298 
Skipped atom 802 because residue number 96  < previous residue 298 
Skipped atom 803 because residue number 96  < previous residue 298 
Skipped atom 804 because residue number 97  < previous residue 298 
Skipped atom 805 because residue number 97  < previous residue 298 
Skipped atom 806 because residue number 97  < previous residue 298 
Skipped atom 807 because residue number 97  < previous residue 298 
Skipped atom 808 because residue number 97  < previous residue 298 
Skipped atom 809 because residue number 97  < previous residue 298 
Skipped atom 810 because residue number 97  < previous residue 298 
Skipped atom 811 because residue number 97  < previous residue 298 
Skipped atom 812 because residue number 98  < previous residue 298 
Skipped atom 813 because residue number 98  < previous residue 298 
Skipped atom 814 because residue number 98  < previous residue 298 
Skipped atom 815 because residue number 98  < previous residue 298 
Skipped atom 816 because residue number 98  < previous residue 298 
Skipped atom 817 because residue number 98  < previous residue 298 
Skipped atom 818 because residue number 98  < previous residue 298 
Skipped atom 819 because residue number 98  < previous residue 298 
Skipped atom 820 because residue number 99  < previous residue 298 
Skipped atom 821 because residue number 99  < previous residue 298 
Skipped atom 822 because residue number 99  < previous residue 298 
Skipped atom 823 because residue number 99  < previous residue 298 
Skipped atom 824 because residue number 99  < previous residue 298 
Skipped atom 825 because residue number 99  < previous residue 298 
Skipped atom 826 because residue number 99  < previous residue 298 
Skipped atom 827 because residue number 99  < previous residue 298 
Skipped atom 828 because residue number 99  < previous residue 298 
Skipped atom 829 because residue number 100  < previous residue 298 
Skipped atom 830 because residue number 100  < previous residue 298 
Skipped atom 831 because residue number 100  < previous residue 298 
Skipped atom 832 because residue number 100  < previous residue 298 
Skipped atom 833 because residue number 100  < previous residue 298 
Skipped atom 834 because residue number 100  < previous residue 298 
Skipped atom 835 because residue number 100  < previous residue 298 
Skipped atom 836 because residue number 100  < previous residue 298 
Skipped atom 837 because residue number 101  < previous residue 298 
Skipped atom 838 because residue number 101  < previous residue 298 
Skipped atom 839 because residue number 101  < previous residue 298 
Skipped atom 840 because residue number 101  < previous residue 298 
Skipped atom 841 because residue number 101  < previous residue 298 
Skipped atom 842 because residue number 101  < previous residue 298 
Skipped atom 843 because residue number 101  < previous residue 298 
Skipped atom 844 because residue number 101  < previous residue 298 
Skipped atom 845 because residue number 102  < previous residue 298 
Skipped atom 846 because residue number 102  < previous residue 298 
Skipped atom 847 because residue number 102  < previous residue 298 
Skipped atom 848 because residue number 102  < previous residue 298 
Skipped atom 849 because residue number 102  < previous residue 298 
Skipped atom 850 because residue number 102  < previous residue 298 
Skipped atom 851 because residue number 102  < previous residue 298 
Skipped atom 852 because residue number 102  < previous residue 298 
Skipped atom 853 because residue number 103  < previous residue 298 
Skipped atom 854 because residue number 103  < previous residue 298 
Skipped atom 855 because residue number 103  < previous residue 298 
Skipped atom 856 because residue number 103  < previous residue 298 
Skipped atom 857 because residue number 103  < previous residue 298 
Skipped atom 858 because residue number 103  < previous residue 298 
Skipped atom 859 because residue number 103  < previous residue 298 
Skipped atom 860 because residue number 104  < previous residue 298 
Skipped atom 861 because residue number 104  < previous residue 298 
Skipped atom 862 because residue number 104  < previous residue 298 
Skipped atom 863 because residue number 104  < previous residue 298 
Skipped atom 864 because residue number 104  < previous residue 298 
Skipped atom 865 because residue number 105  < previous residue 298 
Skipped atom 866 because residue number 105  < previous residue 298 
Skipped atom 867 because residue number 105  < previous residue 298 
Skipped atom 868 because residue number 105  < previous residue 298 
Skipped atom 869 because residue number 105  < previous residue 298 
Skipped atom 870 because residue number 105  < previous residue 298 
Skipped atom 871 because residue number 105  < previous residue 298 
Skipped atom 872 because residue number 105  < previous residue 298 
Skipped atom 873 because residue number 105  < previous residue 298 
Skipped atom 874 because residue number 105  < previous residue 298 
Skipped atom 875 because residue number 105  < previous residue 298 
Skipped atom 876 because residue number 105  < previous residue 298 
Skipped atom 877 because residue number 106  < previous residue 298 
Skipped atom 878 because residue number 106  < previous residue 298 
Skipped atom 879 because residue number 106  < previous residue 298 
Skipped atom 880 because residue number 106  < previous residue 298 
Skipped atom 881 because residue number 106  < previous residue 298 
Skipped atom 882 because residue number 106  < previous residue 298 
Skipped atom 883 because residue number 107  < previous residue 298 
Skipped atom 884 because residue number 107  < previous residue 298 
Skipped atom 885 because residue number 107  < previous residue 298 
Skipped atom 886 because residue number 107  < previous residue 298 
Skipped atom 887 because residue number 107  < previous residue 298 
Skipped atom 888 because residue number 107  < previous residue 298 
Skipped atom 889 because residue number 107  < previous residue 298 
Skipped atom 890 because residue number 108  < previous residue 298 
Skipped atom 891 because residue number 108  < previous residue 298 
Skipped atom 892 because residue number 108  < previous residue 298 
Skipped atom 893 because residue number 108  < previous residue 298 
Skipped atom 894 because residue number 108  < previous residue 298 
Skipped atom 895 because residue number 108  < previous residue 298 
Skipped atom 896 because residue number 108  < previous residue 298 
Skipped atom 897 because residue number 108  < previous residue 298 
Skipped atom 898 because residue number 109  < previous residue 298 
Skipped atom 899 because residue number 109  < previous residue 298 
Skipped atom 900 because residue number 109  < previous residue 298 
Skipped atom 901 because residue number 109  < previous residue 298 
Skipped atom 902 because residue number 109  < previous residue 298 
Skipped atom 903 because residue number 109  < previous residue 298 
Skipped atom 904 because residue number 109  < previous residue 298 
Skipped atom 905 because residue number 109  < previous residue 298 
Skipped atom 906 because residue number 110  < previous residue 298 
Skipped atom 907 because residue number 110  < previous residue 298 
Skipped atom 908 because residue number 110  < previous residue 298 
Skipped atom 909 because residue number 110  < previous residue 298 
Skipped atom 910 because residue number 110  < previous residue 298 
Skipped atom 911 because residue number 110  < previous residue 298 
Skipped atom 912 because residue number 110  < previous residue 298 
Skipped atom 913 because residue number 110  < previous residue 298 
Skipped atom 914 because residue number 110  < previous residue 298 
Skipped atom 915 because residue number 111  < previous residue 298 
Skipped atom 916 because residue number 111  < previous residue 298 
Skipped atom 917 because residue number 111  < previous residue 298 
Skipped atom 918 because residue number 111  < previous residue 298 
Skipped atom 919 because residue number 111  < previous residue 298 
Skipped atom 920 because residue number 111  < previous residue 298 
Skipped atom 921 because residue number 111  < previous residue 298 
Skipped atom 922 because residue number 111  < previous residue 298 
Skipped atom 923 because residue number 111  < previous residue 298 
Skipped atom 924 because residue number 112  < previous residue 298 
Skipped atom 925 because residue number 112  < previous residue 298 
Skipped atom 926 because residue number 112  < previous residue 298 
Skipped atom 927 because residue number 112  < previous residue 298 
Skipped atom 928 because residue number 112  < previous residue 298 
Skipped atom 929 because residue number 112  < previous residue 298 
Skipped atom 930 because residue number 112  < previous residue 298 
Skipped atom 931 because residue number 112  < previous residue 298 
Skipped atom 932 because residue number 112  < previous residue 298 
Skipped atom 933 because residue number 112  < previous residue 298 
Skipped atom 934 because residue number 112  < previous residue 298 
Skipped atom 935 because residue number 112  < previous residue 298 
Skipped atom 936 because residue number 113  < previous residue 298 
Skipped atom 937 because residue number 113  < previous residue 298 
Skipped atom 938 because residue number 113  < previous residue 298 
Skipped atom 939 because residue number 113  < previous residue 298 
Skipped atom 940 because residue number 113  < previous residue 298 
Skipped atom 941 because residue number 113  < previous residue 298 
Skipped atom 942 because residue number 113  < previous residue 298 
Skipped atom 943 because residue number 114  < previous residue 298 
Skipped atom 944 because residue number 114  < previous residue 298 
Skipped atom 945 because residue number 114  < previous residue 298 
Skipped atom 946 because residue number 114  < previous residue 298 
Skipped atom 947 because residue number 115  < previous residue 298 
Skipped atom 948 because residue number 115  < previous residue 298 
Skipped atom 949 because residue number 115  < previous residue 298 
Skipped atom 950 because residue number 115  < previous residue 298 
Skipped atom 951 because residue number 115  < previous residue 298 
Skipped atom 952 because residue number 115  < previous residue 298 
Skipped atom 953 because residue number 115  < previous residue 298 
Skipped atom 954 because residue number 115  < previous residue 298 
Skipped atom 955 because residue number 115  < previous residue 298 
Skipped atom 956 because residue number 116  < previous residue 298 
Skipped atom 957 because residue number 116  < previous residue 298 
Skipped atom 958 because residue number 116  < previous residue 298 
Skipped atom 959 because residue number 116  < previous residue 298 
Skipped atom 960 because residue number 116  < previous residue 298 
Skipped atom 961 because residue number 116  < previous residue 298 
Skipped atom 962 because residue number 116  < previous residue 298 
Skipped atom 963 because residue number 116  < previous residue 298 
Skipped atom 964 because residue number 117  < previous residue 298 
Skipped atom 965 because residue number 117  < previous residue 298 
Skipped atom 966 because residue number 117  < previous residue 298 
Skipped atom 967 because residue number 117  < previous residue 298 
Skipped atom 968 because residue number 117  < previous residue 298 
Skipped atom 969 because residue number 117  < previous residue 298 
Skipped atom 970 because residue number 117  < previous residue 298 
Skipped atom 971 because residue number 117  < previous residue 298 
Skipped atom 972 because residue number 118  < previous residue 298 
Skipped atom 973 because residue number 118  < previous residue 298 
Skipped atom 974 because residue number 118  < previous residue 298 
Skipped atom 975 because residue number 118  < previous residue 298 
Skipped atom 976 because residue number 118  < previous residue 298 
Skipped atom 977 because residue number 118  < previous residue 298 
Skipped atom 978 because residue number 118  < previous residue 298 
Skipped atom 979 because residue number 119  < previous residue 298 
Skipped atom 980 because residue number 119  < previous residue 298 
Skipped atom 981 because residue number 119  < previous residue 298 
Skipped atom 982 because residue number 119  < previous residue 298 
Skipped atom 983 because residue number 119  < previous residue 298 
Skipped atom 984 because residue number 119  < previous residue 298 
Skipped atom 985 because residue number 119  < previous residue 298 
Skipped atom 986 because residue number 119  < previous residue 298 
Skipped atom 987 because residue number 120  < previous residue 298 
Skipped atom 988 because residue number 120  < previous residue 298 
Skipped atom 989 because residue number 120  < previous residue 298 
Skipped atom 990 because residue number 120  < previous residue 298 
Skipped atom 991 because residue number 120  < previous residue 298 
Skipped atom 992 because residue number 120  < previous residue 298 
Skipped atom 993 because residue number 120  < previous residue 298 
Skipped atom 994 because residue number 120  < previous residue 298 
Skipped atom 995 because residue number 120  < previous residue 298 
Skipped atom 996 because residue number 121  < previous residue 298 
Skipped atom 997 because residue number 121  < previous residue 298 
Skipped atom 998 because residue number 121  < previous residue 298 
Skipped atom 999 because residue number 121  < previous residue 298 
Skipped atom 1000 because residue number 121  < previous residue 298 
Skipped atom 1001 because residue number 122  < previous residue 298 
Skipped atom 1002 because residue number 122  < previous residue 298 
Skipped atom 1003 because residue number 122  < previous residue 298 
Skipped atom 1004 because residue number 122  < previous residue 298 
Skipped atom 1005 because residue number 122  < previous residue 298 
Skipped atom 1006 because residue number 122  < previous residue 298 
Skipped atom 1007 because residue number 122  < previous residue 298 
Skipped atom 1008 because residue number 122  < previous residue 298 
Skipped atom 1009 because residue number 123  < previous residue 298 
Skipped atom 1010 because residue number 123  < previous residue 298 
Skipped atom 1011 because residue number 123  < previous residue 298 
Skipped atom 1012 because residue number 123  < previous residue 298 
Skipped atom 1013 because residue number 123  < previous residue 298 
Skipped atom 1014 because residue number 123  < previous residue 298 
Skipped atom 1015 because residue number 123  < previous residue 298 
Skipped atom 1016 because residue number 123  < previous residue 298 
Skipped atom 1017 because residue number 124  < previous residue 298 
Skipped atom 1018 because residue number 124  < previous residue 298 
Skipped atom 1019 because residue number 124  < previous residue 298 
Skipped atom 1020 because residue number 124  < previous residue 298 
Skipped atom 1021 because residue number 124  < previous residue 298 
Skipped atom 1022 because residue number 124  < previous residue 298 
Skipped atom 1023 because residue number 124  < previous residue 298 
Skipped atom 1024 because residue number 124  < previous residue 298 
Skipped atom 1025 because residue number 124  < previous residue 298 
Skipped atom 1026 because residue number 125  < previous residue 298 
Skipped atom 1027 because residue number 125  < previous residue 298 
Skipped atom 1028 because residue number 125  < previous residue 298 
Skipped atom 1029 because residue number 125  < previous residue 298 
Skipped atom 1030 because residue number 125  < previous residue 298 
Skipped atom 1031 because residue number 126  < previous residue 298 
Skipped atom 1032 because residue number 126  < previous residue 298 
Skipped atom 1033 because residue number 126  < previous residue 298 
Skipped atom 1034 because residue number 126  < previous residue 298 
Skipped atom 1035 because residue number 126  < previous residue 298 
Skipped atom 1036 because residue number 126  < previous residue 298 
Skipped atom 1037 because residue number 127  < previous residue 298 
Skipped atom 1038 because residue number 127  < previous residue 298 
Skipped atom 1039 because residue number 127  < previous residue 298 
Skipped atom 1040 because residue number 127  < previous residue 298 
Skipped atom 1041 because residue number 127  < previous residue 298 
Skipped atom 1042 because residue number 127  < previous residue 298 
Skipped atom 1043 because residue number 127  < previous residue 298 
Skipped atom 1044 because residue number 127  < previous residue 298 
Skipped atom 1045 because residue number 128  < previous residue 298 
Skipped atom 1046 because residue number 128  < previous residue 298 
Skipped atom 1047 because residue number 128  < previous residue 298 
Skipped atom 1048 because residue number 128  < previous residue 298 
Skipped atom 1049 because residue number 128  < previous residue 298 
Skipped atom 1050 because residue number 128  < previous residue 298 
Skipped atom 1051 because residue number 128  < previous residue 298 
Skipped atom 1052 because residue number 129  < previous residue 298 
Skipped atom 1053 because residue number 129  < previous residue 298 
Skipped atom 1054 because residue number 129  < previous residue 298 
Skipped atom 1055 because residue number 129  < previous residue 298 
Skipped atom 1056 because residue number 129  < previous residue 298 
Skipped atom 1057 because residue number 129  < previous residue 298 
Skipped atom 1058 because residue number 129  < previous residue 298 
Skipped atom 1059 because residue number 129  < previous residue 298 
Skipped atom 1060 because residue number 129  < previous residue 298 
Skipped atom 1061 because residue number 129  < previous residue 298 
Skipped atom 1062 because residue number 129  < previous residue 298 
Skipped atom 1063 because residue number 129  < previous residue 298 
Skipped atom 1064 because residue number 130  < previous residue 298 
Skipped atom 1065 because residue number 130  < previous residue 298 
Skipped atom 1066 because residue number 130  < previous residue 298 
Skipped atom 1067 because residue number 130  < previous residue 298 
Skipped atom 1068 because residue number 130  < previous residue 298 
Skipped atom 1069 because residue number 130  < previous residue 298 
Skipped atom 1070 because residue number 131  < previous residue 298 
Skipped atom 1071 because residue number 131  < previous residue 298 
Skipped atom 1072 because residue number 131  < previous residue 298 
Skipped atom 1073 because residue number 131  < previous residue 298 
Skipped atom 1074 because residue number 131  < previous residue 298 
Skipped atom 1075 because residue number 131  < previous residue 298 
Skipped atom 1076 because residue number 131  < previous residue 298 
Skipped atom 1077 because residue number 131  < previous residue 298 
Skipped atom 1078 because residue number 132  < previous residue 298 
Skipped atom 1079 because residue number 132  < previous residue 298 
Skipped atom 1080 because residue number 132  < previous residue 298 
Skipped atom 1081 because residue number 132  < previous residue 298 
Skipped atom 1082 because residue number 132  < previous residue 298 
Skipped atom 1083 because residue number 132  < previous residue 298 
Skipped atom 1084 because residue number 132  < previous residue 298 
Skipped atom 1085 because residue number 132  < previous residue 298 
Skipped atom 1086 because residue number 133  < previous residue 298 
Skipped atom 1087 because residue number 133  < previous residue 298 
Skipped atom 1088 because residue number 133  < previous residue 298 
Skipped atom 1089 because residue number 133  < previous residue 298 
Skipped atom 1090 because residue number 133  < previous residue 298 
Skipped atom 1091 because residue number 133  < previous residue 298 
Skipped atom 1092 because residue number 133  < previous residue 298 
Skipped atom 1093 because residue number 134  < previous residue 298 
Skipped atom 1094 because residue number 134  < previous residue 298 
Skipped atom 1095 because residue number 134  < previous residue 298 
Skipped atom 1096 because residue number 134  < previous residue 298 
Skipped atom 1097 because residue number 134  < previous residue 298 
Skipped atom 1098 because residue number 135  < previous residue 298 
Skipped atom 1099 because residue number 135  < previous residue 298 
Skipped atom 1100 because residue number 135  < previous residue 298 
Skipped atom 1101 because residue number 135  < previous residue 298 
Skipped atom 1102 because residue number 135  < previous residue 298 
Skipped atom 1103 because residue number 135  < previous residue 298 
Skipped atom 1104 because residue number 135  < previous residue 298 
Skipped atom 1105 because residue number 135  < previous residue 298 
Skipped atom 1106 because residue number 136  < previous residue 298 
Skipped atom 1107 because residue number 136  < previous residue 298 
Skipped atom 1108 because residue number 136  < previous residue 298 
Skipped atom 1109 because residue number 136  < previous residue 298 
Skipped atom 1110 because residue number 136  < previous residue 298 
Skipped atom 1111 because residue number 136  < previous residue 298 
Skipped atom 1112 because residue number 136  < previous residue 298 
Skipped atom 1113 because residue number 136  < previous residue 298 
Skipped atom 1114 because residue number 137  < previous residue 298 
Skipped atom 1115 because residue number 137  < previous residue 298 
Skipped atom 1116 because residue number 137  < previous residue 298 
Skipped atom 1117 because residue number 137  < previous residue 298 
Skipped atom 1118 because residue number 137  < previous residue 298 
Skipped atom 1119 because residue number 137  < previous residue 298 
Skipped atom 1120 because residue number 137  < previous residue 298 
Skipped atom 1121 because residue number 137  < previous residue 298 
Skipped atom 1122 because residue number 137  < previous residue 298 
Skipped atom 1123 because residue number 138  < previous residue 298 
Skipped atom 1124 because residue number 138  < previous residue 298 
Skipped atom 1125 because residue number 138  < previous residue 298 
Skipped atom 1126 because residue number 138  < previous residue 298 
Skipped atom 1127 because residue number 138  < previous residue 298 
Skipped atom 1128 because residue number 138  < previous residue 298 
Skipped atom 1129 because residue number 138  < previous residue 298 
Skipped atom 1130 because residue number 138  < previous residue 298 
Skipped atom 1131 because residue number 139  < previous residue 298 
Skipped atom 1132 because residue number 139  < previous residue 298 
Skipped atom 1133 because residue number 139  < previous residue 298 
Skipped atom 1134 because residue number 139  < previous residue 298 
Skipped atom 1135 because residue number 139  < previous residue 298 
Skipped atom 1136 because residue number 139  < previous residue 298 
Skipped atom 1137 because residue number 139  < previous residue 298 
Skipped atom 1138 because residue number 139  < previous residue 298 
Skipped atom 1139 because residue number 140  < previous residue 298 
Skipped atom 1140 because residue number 140  < previous residue 298 
Skipped atom 1141 because residue number 140  < previous residue 298 
Skipped atom 1142 because residue number 140  < previous residue 298 
Skipped atom 1143 because residue number 140  < previous residue 298 
Skipped atom 1144 because residue number 140  < previous residue 298 
Skipped atom 1145 because residue number 140  < previous residue 298 
Skipped atom 1146 because residue number 140  < previous residue 298 
Skipped atom 1147 because residue number 140  < previous residue 298 
Skipped atom 1148 because residue number 141  < previous residue 298 
Skipped atom 1149 because residue number 141  < previous residue 298 
Skipped atom 1150 because residue number 141  < previous residue 298 
Skipped atom 1151 because residue number 141  < previous residue 298 
Skipped atom 1152 because residue number 141  < previous residue 298 
Skipped atom 1153 because residue number 141  < previous residue 298 
Skipped atom 1154 because residue number 141  < previous residue 298 
Skipped atom 1155 because residue number 141  < previous residue 298 
Skipped atom 1156 because residue number 141  < previous residue 298 
Skipped atom 1157 because residue number 142  < previous residue 298 
Skipped atom 1158 because residue number 142  < previous residue 298 
Skipped atom 1159 because residue number 142  < previous residue 298 
Skipped atom 1160 because residue number 142  < previous residue 298 
Skipped atom 1161 because residue number 142  < previous residue 298 
Skipped atom 1162 because residue number 142  < previous residue 298 
Skipped atom 1163 because residue number 142  < previous residue 298 
Skipped atom 1164 because residue number 142  < previous residue 298 
Skipped atom 1165 because residue number 143  < previous residue 298 
Skipped atom 1166 because residue number 143  < previous residue 298 
Skipped atom 1167 because residue number 143  < previous residue 298 
Skipped atom 1168 because residue number 143  < previous residue 298 
Skipped atom 1169 because residue number 144  < previous residue 298 
Skipped atom 1170 because residue number 144  < previous residue 298 
Skipped atom 1171 because residue number 144  < previous residue 298 
Skipped atom 1172 because residue number 144  < previous residue 298 
Skipped atom 1173 because residue number 145  < previous residue 298 
Skipped atom 1174 because residue number 145  < previous residue 298 
Skipped atom 1175 because residue number 145  < previous residue 298 
Skipped atom 1176 because residue number 145  < previous residue 298 
Skipped atom 1177 because residue number 145  < previous residue 298 
Skipped atom 1178 because residue number 145  < previous residue 298 
Skipped atom 1179 because residue number 145  < previous residue 298 
Skipped atom 1180 because residue number 145  < previous residue 298 
Skipped atom 1181 because residue number 146  < previous residue 298 
Skipped atom 1182 because residue number 146  < previous residue 298 
Skipped atom 1183 because residue number 146  < previous residue 298 
Skipped atom 1184 because residue number 146  < previous residue 298 
Skipped atom 1185 because residue number 146  < previous residue 298 
Skipped atom 1186 because residue number 146  < previous residue 298 
Skipped atom 1187 because residue number 146  < previous residue 298 
Skipped atom 1188 because residue number 146  < previous residue 298 
Skipped atom 1189 because residue number 146  < previous residue 298 
Skipped atom 1190 because residue number 147  < previous residue 298 
Skipped atom 1191 because residue number 147  < previous residue 298 
Skipped atom 1192 because residue number 147  < previous residue 298 
Skipped atom 1193 because residue number 147  < previous residue 298 
Skipped atom 1194 because residue number 147  < previous residue 298 
Skipped atom 1195 because residue number 147  < previous residue 298 
Skipped atom 1196 because residue number 147  < previous residue 298 
Skipped atom 1197 because residue number 147  < previous residue 298 
Skipped atom 1198 because residue number 147  < previous residue 298 
Skipped atom 1199 because residue number 148  < previous residue 298 
Skipped atom 1200 because residue number 148  < previous residue 298 
Skipped atom 1201 because residue number 148  < previous residue 298 
Skipped atom 1202 because residue number 148  < previous residue 298 
Skipped atom 1203 because residue number 148  < previous residue 298 
Skipped atom 1204 because residue number 148  < previous residue 298 
Skipped atom 1205 because residue number 148  < previous residue 298 
Skipped atom 1206 because residue number 149  < previous residue 298 
Skipped atom 1207 because residue number 149  < previous residue 298 
Skipped atom 1208 because residue number 149  < previous residue 298 
Skipped atom 1209 because residue number 149  < previous residue 298 
Skipped atom 1210 because residue number 149  < previous residue 298 
Skipped atom 1211 because residue number 149  < previous residue 298 
Skipped atom 1212 because residue number 149  < previous residue 298 
Skipped atom 1213 because residue number 149  < previous residue 298 
Skipped atom 1214 because residue number 149  < previous residue 298 
Skipped atom 1215 because residue number 150  < previous residue 298 
Skipped atom 1216 because residue number 150  < previous residue 298 
Skipped atom 1217 because residue number 150  < previous residue 298 
Skipped atom 1218 because residue number 150  < previous residue 298 
Skipped atom 1219 because residue number 150  < previous residue 298 
Skipped atom 1220 because residue number 150  < previous residue 298 
Skipped atom 1221 because residue number 150  < previous residue 298 
Skipped atom 1222 because residue number 150  < previous residue 298 
Skipped atom 1223 because residue number 150  < previous residue 298 
Skipped atom 1224 because residue number 151  < previous residue 298 
Skipped atom 1225 because residue number 151  < previous residue 298 
Skipped atom 1226 because residue number 151  < previous residue 298 
Skipped atom 1227 because residue number 151  < previous residue 298 
Skipped atom 1228 because residue number 151  < previous residue 298 
Skipped atom 1229 because residue number 151  < previous residue 298 
Skipped atom 1230 because residue number 151  < previous residue 298 
Skipped atom 1231 because residue number 151  < previous residue 298 
Skipped atom 1232 because residue number 151  < previous residue 298 
Skipped atom 1233 because residue number 151  < previous residue 298 
Skipped atom 1234 because residue number 151  < previous residue 298 
Skipped atom 1235 because residue number 152  < previous residue 298 
Skipped atom 1236 because residue number 152  < previous residue 298 
Skipped atom 1237 because residue number 152  < previous residue 298 
Skipped atom 1238 because residue number 152  < previous residue 298 
Skipped atom 1239 because residue number 152  < previous residue 298 
Skipped atom 1240 because residue number 152  < previous residue 298 
Skipped atom 1241 because residue number 152  < previous residue 298 
Skipped atom 1242 because residue number 152  < previous residue 298 
Skipped atom 1243 because residue number 153  < previous residue 298 
Skipped atom 1244 because residue number 153  < previous residue 298 
Skipped atom 1245 because residue number 153  < previous residue 298 
Skipped atom 1246 because residue number 153  < previous residue 298 
Skipped atom 1247 because residue number 153  < previous residue 298 
Skipped atom 1248 because residue number 153  < previous residue 298 
Skipped atom 1249 because residue number 153  < previous residue 298 
Skipped atom 1250 because residue number 153  < previous residue 298 
Skipped atom 1251 because residue number 153  < previous residue 298 
Skipped atom 1252 because residue number 154  < previous residue 298 
Skipped atom 1253 because residue number 154  < previous residue 298 
Skipped atom 1254 because residue number 154  < previous residue 298 
Skipped atom 1255 because residue number 154  < previous residue 298 
Skipped atom 1256 because residue number 154  < previous residue 298 
Skipped atom 1257 because residue number 154  < previous residue 298 
Skipped atom 1258 because residue number 154  < previous residue 298 
Skipped atom 1259 because residue number 154  < previous residue 298 
Skipped atom 1260 because residue number 154  < previous residue 298 
Skipped atom 1261 because residue number 155  < previous residue 298 
Skipped atom 1262 because residue number 155  < previous residue 298 
Skipped atom 1263 because residue number 155  < previous residue 298 
Skipped atom 1264 because residue number 155  < previous residue 298 
Skipped atom 1265 because residue number 155  < previous residue 298 
Skipped atom 1266 because residue number 155  < previous residue 298 
Skipped atom 1267 because residue number 155  < previous residue 298 
Skipped atom 1268 because residue number 155  < previous residue 298 
Skipped atom 1269 because residue number 156  < previous residue 298 
Skipped atom 1270 because residue number 156  < previous residue 298 
Skipped atom 1271 because residue number 156  < previous residue 298 
Skipped atom 1272 because residue number 156  < previous residue 298 
Skipped atom 1273 because residue number 157  < previous residue 298 
Skipped atom 1274 because residue number 157  < previous residue 298 
Skipped atom 1275 because residue number 157  < previous residue 298 
Skipped atom 1276 because residue number 157  < previous residue 298 
Skipped atom 1277 because residue number 157  < previous residue 298 
Skipped atom 1278 because residue number 157  < previous residue 298 
Skipped atom 1279 because residue number 157  < previous residue 298 
Skipped atom 1280 because residue number 157  < previous residue 298 
Skipped atom 1281 because residue number 158  < previous residue 298 
Skipped atom 1282 because residue number 158  < previous residue 298 
Skipped atom 1283 because residue number 158  < previous residue 298 
Skipped atom 1284 because residue number 158  < previous residue 298 
Skipped atom 1285 because residue number 158  < previous residue 298 
Skipped atom 1286 because residue number 158  < previous residue 298 
Skipped atom 1287 because residue number 158  < previous residue 298 
Skipped atom 1288 because residue number 158  < previous residue 298 
Skipped atom 1289 because residue number 158  < previous residue 298 
Skipped atom 1290 because residue number 159  < previous residue 298 
Skipped atom 1291 because residue number 159  < previous residue 298 
Skipped atom 1292 because residue number 159  < previous residue 298 
Skipped atom 1293 because residue number 159  < previous residue 298 
Skipped atom 1294 because residue number 159  < previous residue 298 
Skipped atom 1295 because residue number 159  < previous residue 298 
Skipped atom 1296 because residue number 159  < previous residue 298 
Skipped atom 1297 because residue number 160  < previous residue 298 
Skipped atom 1298 because residue number 160  < previous residue 298 
Skipped atom 1299 because residue number 160  < previous residue 298 
Skipped atom 1300 because residue number 160  < previous residue 298 
Skipped atom 1301 because residue number 160  < previous residue 298 
Skipped atom 1302 because residue number 160  < previous residue 298 
Skipped atom 1303 because residue number 160  < previous residue 298 
Skipped atom 1304 because residue number 161  < previous residue 298 
Skipped atom 1305 because residue number 161  < previous residue 298 
Skipped atom 1306 because residue number 161  < previous residue 298 
Skipped atom 1307 because residue number 161  < previous residue 298 
Skipped atom 1308 because residue number 161  < previous residue 298 
Skipped atom 1309 because residue number 161  < previous residue 298 
Skipped atom 1310 because residue number 161  < previous residue 298 
Skipped atom 1311 because residue number 161  < previous residue 298 
Skipped atom 1312 because residue number 162  < previous residue 298 
Skipped atom 1313 because residue number 162  < previous residue 298 
Skipped atom 1314 because residue number 162  < previous residue 298 
Skipped atom 1315 because residue number 162  < previous residue 298 
Skipped atom 1316 because residue number 162  < previous residue 298 
Skipped atom 1317 because residue number 162  < previous residue 298 
Skipped atom 1318 because residue number 162  < previous residue 298 
Skipped atom 1319 because residue number 163  < previous residue 298 
Skipped atom 1320 because residue number 163  < previous residue 298 
Skipped atom 1321 because residue number 163  < previous residue 298 
Skipped atom 1322 because residue number 163  < previous residue 298 
Skipped atom 1323 because residue number 163  < previous residue 298 
Skipped atom 1324 because residue number 163  < previous residue 298 
Skipped atom 1325 because residue number 163  < previous residue 298 
Skipped atom 1326 because residue number 164  < previous residue 298 
Skipped atom 1327 because residue number 164  < previous residue 298 
Skipped atom 1328 because residue number 164  < previous residue 298 
Skipped atom 1329 because residue number 164  < previous residue 298 
Skipped atom 1330 because residue number 164  < previous residue 298 
Skipped atom 1331 because residue number 164  < previous residue 298 
Skipped atom 1332 because residue number 164  < previous residue 298 
Skipped atom 1333 because residue number 164  < previous residue 298 
Skipped atom 1334 because residue number 164  < previous residue 298 
Skipped atom 1335 because residue number 164  < previous residue 298 
Skipped atom 1336 because residue number 164  < previous residue 298 
Skipped atom 1337 because residue number 165  < previous residue 298 
Skipped atom 1338 because residue number 165  < previous residue 298 
Skipped atom 1339 because residue number 165  < previous residue 298 
Skipped atom 1340 because residue number 165  < previous residue 298 
Skipped atom 1341 because residue number 165  < previous residue 298 
Skipped atom 1342 because residue number 165  < previous residue 298 
Skipped atom 1343 because residue number 165  < previous residue 298 
Skipped atom 1344 because residue number 165  < previous residue 298 
Skipped atom 1345 because residue number 165  < previous residue 298 
Skipped atom 1346 because residue number 165  < previous residue 298 
Skipped atom 1347 because residue number 165  < previous residue 298 
Skipped atom 1348 because residue number 165  < previous residue 298 
Skipped atom 1349 because residue number 166  < previous residue 298 
Skipped atom 1350 because residue number 166  < previous residue 298 
Skipped atom 1351 because residue number 166  < previous residue 298 
Skipped atom 1352 because residue number 166  < previous residue 298 
Skipped atom 1353 because residue number 166  < previous residue 298 
Skipped atom 1354 because residue number 166  < previous residue 298 
Skipped atom 1355 because residue number 166  < previous residue 298 
Skipped atom 1356 because residue number 166  < previous residue 298 
Skipped atom 1357 because residue number 166  < previous residue 298 
Skipped atom 1358 because residue number 167  < previous residue 298 
Skipped atom 1359 because residue number 167  < previous residue 298 
Skipped atom 1360 because residue number 167  < previous residue 298 
Skipped atom 1361 because residue number 167  < previous residue 298 
Skipped atom 1362 because residue number 167  < previous residue 298 
Skipped atom 1363 because residue number 167  < previous residue 298 
Skipped atom 1364 because residue number 167  < previous residue 298 
Skipped atom 1365 because residue number 167  < previous residue 298 
Skipped atom 1366 because residue number 168  < previous residue 298 
Skipped atom 1367 because residue number 168  < previous residue 298 
Skipped atom 1368 because residue number 168  < previous residue 298 
Skipped atom 1369 because residue number 168  < previous residue 298 
Skipped atom 1370 because residue number 168  < previous residue 298 
Skipped atom 1371 because residue number 168  < previous residue 298 
Skipped atom 1372 because residue number 168  < previous residue 298 
Skipped atom 1373 because residue number 168  < previous residue 298 
Skipped atom 1374 because residue number 168  < previous residue 298 
Skipped atom 1375 because residue number 169  < previous residue 298 
Skipped atom 1376 because residue number 169  < previous residue 298 
Skipped atom 1377 because residue number 169  < previous residue 298 
Skipped atom 1378 because residue number 169  < previous residue 298 
Skipped atom 1379 because residue number 169  < previous residue 298 
Skipped atom 1380 because residue number 169  < previous residue 298 
Skipped atom 1381 because residue number 169  < previous residue 298 
Skipped atom 1382 because residue number 169  < previous residue 298 
Skipped atom 1383 because residue number 170  < previous residue 298 
Skipped atom 1384 because residue number 170  < previous residue 298 
Skipped atom 1385 because residue number 170  < previous residue 298 
Skipped atom 1386 because residue number 170  < previous residue 298 
Skipped atom 1387 because residue number 170  < previous residue 298 
Skipped atom 1388 because residue number 170  < previous residue 298 
Skipped atom 1389 because residue number 170  < previous residue 298 
Skipped atom 1390 because residue number 170  < previous residue 298 
Skipped atom 1391 because residue number 171  < previous residue 298 
Skipped atom 1392 because residue number 171  < previous residue 298 
Skipped atom 1393 because residue number 171  < previous residue 298 
Skipped atom 1394 because residue number 171  < previous residue 298 
Skipped atom 1395 because residue number 171  < previous residue 298 
Skipped atom 1396 because residue number 171  < previous residue 298 
Skipped atom 1397 because residue number 171  < previous residue 298 
Skipped atom 1398 because residue number 171  < previous residue 298 
Skipped atom 1399 because residue number 171  < previous residue 298 
Skipped atom 1400 because residue number 171  < previous residue 298 
Skipped atom 1401 because residue number 171  < previous residue 298 
Skipped atom 1402 because residue number 171  < previous residue 298 
Skipped atom 1403 because residue number 172  < previous residue 298 
Skipped atom 1404 because residue number 172  < previous residue 298 
Skipped atom 1405 because residue number 172  < previous residue 298 
Skipped atom 1406 because residue number 172  < previous residue 298 
Skipped atom 1407 because residue number 172  < previous residue 298 
Skipped atom 1408 because residue number 172  < previous residue 298 
Skipped atom 1409 because residue number 172  < previous residue 298 
Skipped atom 1410 because residue number 172  < previous residue 298 
Skipped atom 1411 because residue number 172  < previous residue 298 
Skipped atom 1412 because residue number 172  < previous residue 298 
Skipped atom 1413 because residue number 172  < previous residue 298 
Skipped atom 1414 because residue number 172  < previous residue 298 
Skipped atom 1415 because residue number 173  < previous residue 298 
Skipped atom 1416 because residue number 173  < previous residue 298 
Skipped atom 1417 because residue number 173  < previous residue 298 
Skipped atom 1418 because residue number 173  < previous residue 298 
Skipped atom 1419 because residue number 173  < previous residue 298 
Skipped atom 1420 because residue number 173  < previous residue 298 
Skipped atom 1421 because residue number 174  < previous residue 298 
Skipped atom 1422 because residue number 174  < previous residue 298 
Skipped atom 1423 because residue number 174  < previous residue 298 
Skipped atom 1424 because residue number 174  < previous residue 298 
Skipped atom 1425 because residue number 174  < previous residue 298 
Skipped atom 1426 because residue number 174  < previous residue 298 
Skipped atom 1427 because residue number 174  < previous residue 298 
Skipped atom 1428 because residue number 175  < previous residue 298 
Skipped atom 1429 because residue number 175  < previous residue 298 
Skipped atom 1430 because residue number 175  < previous residue 298 
Skipped atom 1431 because residue number 175  < previous residue 298 
Skipped atom 1432 because residue number 175  < previous residue 298 
Skipped atom 1433 because residue number 175  < previous residue 298 
Skipped atom 1434 because residue number 175  < previous residue 298 
Skipped atom 1435 because residue number 175  < previous residue 298 
Skipped atom 1436 because residue number 175  < previous residue 298 
Skipped atom 1437 because residue number 176  < previous residue 298 
Skipped atom 1438 because residue number 176  < previous residue 298 
Skipped atom 1439 because residue number 176  < previous residue 298 
Skipped atom 1440 because residue number 176  < previous residue 298 
Skipped atom 1441 because residue number 176  < previous residue 298 
Skipped atom 1442 because residue number 176  < previous residue 298 
Skipped atom 1443 because residue number 177  < previous residue 298 
Skipped atom 1444 because residue number 177  < previous residue 298 
Skipped atom 1445 because residue number 177  < previous residue 298 
Skipped atom 1446 because residue number 177  < previous residue 298 
Skipped atom 1447 because residue number 177  < previous residue 298 
Skipped atom 1448 because residue number 177  < previous residue 298 
Skipped atom 1449 because residue number 177  < previous residue 298 
Skipped atom 1450 because residue number 177  < previous residue 298 
Skipped atom 1451 because residue number 177  < previous residue 298 
Skipped atom 1452 because residue number 178  < previous residue 298 
Skipped atom 1453 because residue number 178  < previous residue 298 
Skipped atom 1454 because residue number 178  < previous residue 298 
Skipped atom 1455 because residue number 178  < previous residue 298 
Skipped atom 1456 because residue number 178  < previous residue 298 
Skipped atom 1457 because residue number 178  < previous residue 298 
Skipped atom 1458 because residue number 178  < previous residue 298 
Skipped atom 1459 because residue number 178  < previous residue 298 
Skipped atom 1460 because residue number 178  < previous residue 298 
Skipped atom 1461 because residue number 179  < previous residue 298 
Skipped atom 1462 because residue number 179  < previous residue 298 
Skipped atom 1463 because residue number 179  < previous residue 298 
Skipped atom 1464 because residue number 179  < previous residue 298 
Skipped atom 1465 because residue number 179  < previous residue 298 
Skipped atom 1466 because residue number 179  < previous residue 298 
Skipped atom 1467 because residue number 179  < previous residue 298 
Skipped atom 1468 because residue number 179  < previous residue 298 
Skipped atom 1469 because residue number 180  < previous residue 298 
Skipped atom 1470 because residue number 180  < previous residue 298 
Skipped atom 1471 because residue number 180  < previous residue 298 
Skipped atom 1472 because residue number 180  < previous residue 298 
Skipped atom 1473 because residue number 180  < previous residue 298 
Skipped atom 1474 because residue number 180  < previous residue 298 
Skipped atom 1475 because residue number 180  < previous residue 298 
Skipped atom 1476 because residue number 181  < previous residue 298 
Skipped atom 1477 because residue number 181  < previous residue 298 
Skipped atom 1478 because residue number 181  < previous residue 298 
Skipped atom 1479 because residue number 181  < previous residue 298 
Skipped atom 1480 because residue number 181  < previous residue 298 
Skipped atom 1481 because residue number 181  < previous residue 298 
Skipped atom 1482 because residue number 182  < previous residue 298 
Skipped atom 1483 because residue number 182  < previous residue 298 
Skipped atom 1484 because residue number 182  < previous residue 298 
Skipped atom 1485 because residue number 182  < previous residue 298 
Skipped atom 1486 because residue number 182  < previous residue 298 
Skipped atom 1487 because residue number 182  < previous residue 298 
Skipped atom 1488 because residue number 182  < previous residue 298 
Skipped atom 1489 because residue number 183  < previous residue 298 
Skipped atom 1490 because residue number 183  < previous residue 298 
Skipped atom 1491 because residue number 183  < previous residue 298 
Skipped atom 1492 because residue number 183  < previous residue 298 
Skipped atom 1493 because residue number 183  < previous residue 298 
Skipped atom 1494 because residue number 183  < previous residue 298 
Skipped atom 1495 because residue number 183  < previous residue 298 
Skipped atom 1496 because residue number 184  < previous residue 298 
Skipped atom 1497 because residue number 184  < previous residue 298 
Skipped atom 1498 because residue number 184  < previous residue 298 
Skipped atom 1499 because residue number 184  < previous residue 298 
Skipped atom 1500 because residue number 184  < previous residue 298 
Skipped atom 1501 because residue number 185  < previous residue 298 
Skipped atom 1502 because residue number 185  < previous residue 298 
Skipped atom 1503 because residue number 185  < previous residue 298 
Skipped atom 1504 because residue number 185  < previous residue 298 
Skipped atom 1505 because residue number 185  < previous residue 298 
Skipped atom 1506 because residue number 186  < previous residue 298 
Skipped atom 1507 because residue number 186  < previous residue 298 
Skipped atom 1508 because residue number 186  < previous residue 298 
Skipped atom 1509 because residue number 186  < previous residue 298 
Skipped atom 1510 because residue number 186  < previous residue 298 
Skipped atom 1511 because residue number 186  < previous residue 298 
Skipped atom 1512 because residue number 186  < previous residue 298 
Skipped atom 1513 because residue number 186  < previous residue 298 
Skipped atom 1514 because residue number 186  < previous residue 298 
Skipped atom 1515 because residue number 186  < previous residue 298 
Skipped atom 1516 because residue number 186  < previous residue 298 
Skipped atom 1517 because residue number 187  < previous residue 298 
Skipped atom 1518 because residue number 187  < previous residue 298 
Skipped atom 1519 because residue number 187  < previous residue 298 
Skipped atom 1520 because residue number 187  < previous residue 298 
Skipped atom 1521 because residue number 188  < previous residue 298 
Skipped atom 1522 because residue number 188  < previous residue 298 
Skipped atom 1523 because residue number 188  < previous residue 298 
Skipped atom 1524 because residue number 188  < previous residue 298 
Skipped atom 1525 because residue number 188  < previous residue 298 
Skipped atom 1526 because residue number 188  < previous residue 298 
Skipped atom 1527 because residue number 188  < previous residue 298 
Skipped atom 1528 because residue number 188  < previous residue 298 
Skipped atom 1529 because residue number 188  < previous residue 298 
Skipped atom 1530 because residue number 189  < previous residue 298 
Skipped atom 1531 because residue number 189  < previous residue 298 
Skipped atom 1532 because residue number 189  < previous residue 298 
Skipped atom 1533 because residue number 189  < previous residue 298 
Skipped atom 1534 because residue number 189  < previous residue 298 
Skipped atom 1535 because residue number 189  < previous residue 298 
Skipped atom 1536 because residue number 189  < previous residue 298 
Skipped atom 1537 because residue number 190  < previous residue 298 
Skipped atom 1538 because residue number 190  < previous residue 298 
Skipped atom 1539 because residue number 190  < previous residue 298 
Skipped atom 1540 because residue number 190  < previous residue 298 
Skipped atom 1541 because residue number 190  < previous residue 298 
Skipped atom 1542 because residue number 190  < previous residue 298 
Skipped atom 1543 because residue number 190  < previous residue 298 
Skipped atom 1544 because residue number 190  < previous residue 298 
Skipped atom 1545 because residue number 191  < previous residue 298 
Skipped atom 1546 because residue number 191  < previous residue 298 
Skipped atom 1547 because residue number 191  < previous residue 298 
Skipped atom 1548 because residue number 191  < previous residue 298 
Skipped atom 1549 because residue number 191  < previous residue 298 
Skipped atom 1550 because residue number 191  < previous residue 298 
Skipped atom 1551 because residue number 191  < previous residue 298 
Skipped atom 1552 because residue number 191  < previous residue 298 
Skipped atom 1553 because residue number 192  < previous residue 298 
Skipped atom 1554 because residue number 192  < previous residue 298 
Skipped atom 1555 because residue number 192  < previous residue 298 
Skipped atom 1556 because residue number 192  < previous residue 298 
Skipped atom 1557 because residue number 192  < previous residue 298 
Skipped atom 1558 because residue number 192  < previous residue 298 
Skipped atom 1559 because residue number 192  < previous residue 298 
Skipped atom 1560 because residue number 192  < previous residue 298 
Skipped atom 1561 because residue number 192  < previous residue 298 
Skipped atom 1562 because residue number 193  < previous residue 298 
Skipped atom 1563 because residue number 193  < previous residue 298 
Skipped atom 1564 because residue number 193  < previous residue 298 
Skipped atom 1565 because residue number 193  < previous residue 298 
Skipped atom 1566 because residue number 193  < previous residue 298 
Skipped atom 1567 because residue number 193  < previous residue 298 
Skipped atom 1568 because residue number 193  < previous residue 298 
Skipped atom 1569 because residue number 193  < previous residue 298 
Skipped atom 1570 because residue number 194  < previous residue 298 
Skipped atom 1571 because residue number 194  < previous residue 298 
Skipped atom 1572 because residue number 194  < previous residue 298 
Skipped atom 1573 because residue number 194  < previous residue 298 
Skipped atom 1574 because residue number 194  < previous residue 298 
Skipped atom 1575 because residue number 194  < previous residue 298 
Skipped atom 1576 because residue number 194  < previous residue 298 
Skipped atom 1577 because residue number 194  < previous residue 298 
Skipped atom 1578 because residue number 195  < previous residue 298 
Skipped atom 1579 because residue number 195  < previous residue 298 
Skipped atom 1580 because residue number 195  < previous residue 298 
Skipped atom 1581 because residue number 195  < previous residue 298 
Skipped atom 1582 because residue number 195  < previous residue 298 
Skipped atom 1583 because residue number 196  < previous residue 298 
Skipped atom 1584 because residue number 196  < previous residue 298 
Skipped atom 1585 because residue number 196  < previous residue 298 
Skipped atom 1586 because residue number 196  < previous residue 298 
Skipped atom 1587 because residue number 196  < previous residue 298 
Skipped atom 1588 because residue number 196  < previous residue 298 
Skipped atom 1589 because residue number 196  < previous residue 298 
Skipped atom 1590 because residue number 196  < previous residue 298 
Skipped atom 1591 because residue number 197  < previous residue 298 
Skipped atom 1592 because residue number 197  < previous residue 298 
Skipped atom 1593 because residue number 197  < previous residue 298 
Skipped atom 1594 because residue number 197  < previous residue 298 
Skipped atom 1595 because residue number 198  < previous residue 298 
Skipped atom 1596 because residue number 198  < previous residue 298 
Skipped atom 1597 because residue number 198  < previous residue 298 
Skipped atom 1598 because residue number 198  < previous residue 298 
Skipped atom 1599 because residue number 198  < previous residue 298 
Skipped atom 1600 because residue number 198  < previous residue 298 
Skipped atom 1601 because residue number 198  < previous residue 298 
Skipped atom 1602 because residue number 198  < previous residue 298 
Skipped atom 1603 because residue number 198  < previous residue 298 
Skipped atom 1604 because residue number 199  < previous residue 298 
Skipped atom 1605 because residue number 199  < previous residue 298 
Skipped atom 1606 because residue number 199  < previous residue 298 
Skipped atom 1607 because residue number 199  < previous residue 298 
Skipped atom 1608 because residue number 199  < previous residue 298 
Skipped atom 1609 because residue number 199  < previous residue 298 
Skipped atom 1610 because residue number 199  < previous residue 298 
Skipped atom 1611 because residue number 199  < previous residue 298 
Skipped atom 1612 because residue number 200  < previous residue 298 
Skipped atom 1613 because residue number 200  < previous residue 298 
Skipped atom 1614 because residue number 200  < previous residue 298 
Skipped atom 1615 because residue number 200  < previous residue 298 
Skipped atom 1616 because residue number 200  < previous residue 298 
Skipped atom 1617 because residue number 200  < previous residue 298 
Skipped atom 1618 because residue number 201  < previous residue 298 
Skipped atom 1619 because residue number 201  < previous residue 298 
Skipped atom 1620 because residue number 201  < previous residue 298 
Skipped atom 1621 because residue number 201  < previous residue 298 
Skipped atom 1622 because residue number 201  < previous residue 298 
Skipped atom 1623 because residue number 201  < previous residue 298 
Skipped atom 1624 because residue number 201  < previous residue 298 
Skipped atom 1625 because residue number 201  < previous residue 298 
Skipped atom 1626 because residue number 201  < previous residue 298 
Skipped atom 1627 because residue number 202  < previous residue 298 
Skipped atom 1628 because residue number 202  < previous residue 298 
Skipped atom 1629 because residue number 202  < previous residue 298 
Skipped atom 1630 because residue number 202  < previous residue 298 
Skipped atom 1631 because residue number 202  < previous residue 298 
Skipped atom 1632 because residue number 202  < previous residue 298 
Skipped atom 1633 because residue number 202  < previous residue 298 
Skipped atom 1634 because residue number 202  < previous residue 298 
Skipped atom 1635 because residue number 202  < previous residue 298 
Skipped atom 1636 because residue number 203  < previous residue 298 
Skipped atom 1637 because residue number 203  < previous residue 298 
Skipped atom 1638 because residue number 203  < previous residue 298 
Skipped atom 1639 because residue number 203  < previous residue 298 
Skipped atom 1640 because residue number 203  < previous residue 298 
Skipped atom 1641 because residue number 203  < previous residue 298 
Skipped atom 1642 because residue number 203  < previous residue 298 
Skipped atom 1643 because residue number 203  < previous residue 298 
Skipped atom 1644 because residue number 204  < previous residue 298 
Skipped atom 1645 because residue number 204  < previous residue 298 
Skipped atom 1646 because residue number 204  < previous residue 298 
Skipped atom 1647 because residue number 204  < previous residue 298 
Skipped atom 1648 because residue number 204  < previous residue 298 
Skipped atom 1649 because residue number 204  < previous residue 298 
Skipped atom 1650 because residue number 204  < previous residue 298 
Skipped atom 1651 because residue number 204  < previous residue 298 
Skipped atom 1652 because residue number 204  < previous residue 298 
Skipped atom 1653 because residue number 205  < previous residue 298 
Skipped atom 1654 because residue number 205  < previous residue 298 
Skipped atom 1655 because residue number 205  < previous residue 298 
Skipped atom 1656 because residue number 205  < previous residue 298 
Skipped atom 1657 because residue number 205  < previous residue 298 
Skipped atom 1658 because residue number 205  < previous residue 298 
Skipped atom 1659 because residue number 205  < previous residue 298 
Skipped atom 1660 because residue number 205  < previous residue 298 
Skipped atom 1661 because residue number 205  < previous residue 298 
Skipped atom 1662 because residue number 206  < previous residue 298 
Skipped atom 1663 because residue number 206  < previous residue 298 
Skipped atom 1664 because residue number 206  < previous residue 298 
Skipped atom 1665 because residue number 206  < previous residue 298 
Skipped atom 1666 because residue number 206  < previous residue 298 
Skipped atom 1667 because residue number 206  < previous residue 298 
Skipped atom 1668 because residue number 206  < previous residue 298 
Skipped atom 1669 because residue number 206  < previous residue 298 
Skipped atom 1670 because residue number 206  < previous residue 298 
Skipped atom 1671 because residue number 206  < previous residue 298 
Skipped atom 1672 because residue number 206  < previous residue 298 
Skipped atom 1673 because residue number 207  < previous residue 298 
Skipped atom 1674 because residue number 207  < previous residue 298 
Skipped atom 1675 because residue number 207  < previous residue 298 
Skipped atom 1676 because residue number 207  < previous residue 298 
Skipped atom 1677 because residue number 207  < previous residue 298 
Skipped atom 1678 because residue number 207  < previous residue 298 
Skipped atom 1679 because residue number 207  < previous residue 298 
Skipped atom 1680 because residue number 207  < previous residue 298 
Skipped atom 1681 because residue number 208  < previous residue 298 
Skipped atom 1682 because residue number 208  < previous residue 298 
Skipped atom 1683 because residue number 208  < previous residue 298 
Skipped atom 1684 because residue number 208  < previous residue 298 
Skipped atom 1685 because residue number 208  < previous residue 298 
Skipped atom 1686 because residue number 208  < previous residue 298 
Skipped atom 1687 because residue number 208  < previous residue 298 
Skipped atom 1688 because residue number 208  < previous residue 298 
Skipped atom 1689 because residue number 209  < previous residue 298 
Skipped atom 1690 because residue number 209  < previous residue 298 
Skipped atom 1691 because residue number 209  < previous residue 298 
Skipped atom 1692 because residue number 209  < previous residue 298 
Skipped atom 1693 because residue number 209  < previous residue 298 
Skipped atom 1694 because residue number 209  < previous residue 298 
Skipped atom 1695 because residue number 209  < previous residue 298 
Skipped atom 1696 because residue number 209  < previous residue 298 
Skipped atom 1697 because residue number 210  < previous residue 298 
Skipped atom 1698 because residue number 210  < previous residue 298 
Skipped atom 1699 because residue number 210  < previous residue 298 
Skipped atom 1700 because residue number 210  < previous residue 298 
Skipped atom 1701 because residue number 210  < previous residue 298 
Skipped atom 1702 because residue number 210  < previous residue 298 
Skipped atom 1703 because residue number 210  < previous residue 298 
Skipped atom 1704 because residue number 210  < previous residue 298 
Skipped atom 1705 because residue number 211  < previous residue 298 
Skipped atom 1706 because residue number 211  < previous residue 298 
Skipped atom 1707 because residue number 211  < previous residue 298 
Skipped atom 1708 because residue number 211  < previous residue 298 
Skipped atom 1709 because residue number 211  < previous residue 298 
Skipped atom 1710 because residue number 211  < previous residue 298 
Skipped atom 1711 because residue number 211  < previous residue 298 
Skipped atom 1712 because residue number 211  < previous residue 298 
Skipped atom 1713 because residue number 212  < previous residue 298 
Skipped atom 1714 because residue number 212  < previous residue 298 
Skipped atom 1715 because residue number 212  < previous residue 298 
Skipped atom 1716 because residue number 212  < previous residue 298 
Skipped atom 1717 because residue number 212  < previous residue 298 
Skipped atom 1718 because residue number 212  < previous residue 298 
Skipped atom 1719 because residue number 212  < previous residue 298 
Skipped atom 1720 because residue number 212  < previous residue 298 
Skipped atom 1721 because residue number 213  < previous residue 298 
Skipped atom 1722 because residue number 213  < previous residue 298 
Skipped atom 1723 because residue number 213  < previous residue 298 
Skipped atom 1724 because residue number 213  < previous residue 298 
Skipped atom 1725 because residue number 213  < previous residue 298 
Skipped atom 1726 because residue number 213  < previous residue 298 
Skipped atom 1727 because residue number 213  < previous residue 298 
Skipped atom 1728 because residue number 213  < previous residue 298 
Skipped atom 1729 because residue number 214  < previous residue 298 
Skipped atom 1730 because residue number 214  < previous residue 298 
Skipped atom 1731 because residue number 214  < previous residue 298 
Skipped atom 1732 because residue number 214  < previous residue 298 
Skipped atom 1733 because residue number 214  < previous residue 298 
Skipped atom 1734 because residue number 214  < previous residue 298 
Skipped atom 1735 because residue number 214  < previous residue 298 
Skipped atom 1736 because residue number 214  < previous residue 298 
Skipped atom 1737 because residue number 215  < previous residue 298 
Skipped atom 1738 because residue number 215  < previous residue 298 
Skipped atom 1739 because residue number 215  < previous residue 298 
Skipped atom 1740 because residue number 215  < previous residue 298 
Skipped atom 1741 because residue number 215  < previous residue 298 
Skipped atom 1742 because residue number 215  < previous residue 298 
Skipped atom 1743 because residue number 215  < previous residue 298 
Skipped atom 1744 because residue number 215  < previous residue 298 
Skipped atom 1745 because residue number 215  < previous residue 298 
Skipped atom 1746 because residue number 216  < previous residue 298 
Skipped atom 1747 because residue number 216  < previous residue 298 
Skipped atom 1748 because residue number 216  < previous residue 298 
Skipped atom 1749 because residue number 216  < previous residue 298 
Skipped atom 1750 because residue number 216  < previous residue 298 
Skipped atom 1751 because residue number 216  < previous residue 298 
Skipped atom 1752 because residue number 217  < previous residue 298 
Skipped atom 1753 because residue number 217  < previous residue 298 
Skipped atom 1754 because residue number 217  < previous residue 298 
Skipped atom 1755 because residue number 217  < previous residue 298 
Skipped atom 1756 because residue number 218  < previous residue 298 
Skipped atom 1757 because residue number 218  < previous residue 298 
Skipped atom 1758 because residue number 218  < previous residue 298 
Skipped atom 1759 because residue number 218  < previous residue 298 
Skipped atom 1760 because residue number 218  < previous residue 298 
Skipped atom 1761 because residue number 218  < previous residue 298 
Skipped atom 1762 because residue number 218  < previous residue 298 
Skipped atom 1763 because residue number 218  < previous residue 298 
Skipped atom 1764 because residue number 219  < previous residue 298 
Skipped atom 1765 because residue number 219  < previous residue 298 
Skipped atom 1766 because residue number 219  < previous residue 298 
Skipped atom 1767 because residue number 219  < previous residue 298 
Skipped atom 1768 because residue number 219  < previous residue 298 
Skipped atom 1769 because residue number 219  < previous residue 298 
Skipped atom 1770 because residue number 219  < previous residue 298 
Skipped atom 1771 because residue number 220  < previous residue 298 
Skipped atom 1772 because residue number 220  < previous residue 298 
Skipped atom 1773 because residue number 220  < previous residue 298 
Skipped atom 1774 because residue number 220  < previous residue 298 
Skipped atom 1775 because residue number 220  < previous residue 298 
Skipped atom 1776 because residue number 220  < previous residue 298 
Skipped atom 1777 because residue number 220  < previous residue 298 
Skipped atom 1778 because residue number 220  < previous residue 298 
Skipped atom 1779 because residue number 221  < previous residue 298 
Skipped atom 1780 because residue number 221  < previous residue 298 
Skipped atom 1781 because residue number 221  < previous residue 298 
Skipped atom 1782 because residue number 221  < previous residue 298 
Skipped atom 1783 because residue number 221  < previous residue 298 
Skipped atom 1784 because residue number 221  < previous residue 298 
Skipped atom 1785 because residue number 221  < previous residue 298 
Skipped atom 1786 because residue number 221  < previous residue 298 
Skipped atom 1787 because residue number 222  < previous residue 298 
Skipped atom 1788 because residue number 222  < previous residue 298 
Skipped atom 1789 because residue number 222  < previous residue 298 
Skipped atom 1790 because residue number 222  < previous residue 298 
Skipped atom 1791 because residue number 222  < previous residue 298 
Skipped atom 1792 because residue number 222  < previous residue 298 
Skipped atom 1793 because residue number 222  < previous residue 298 
Skipped atom 1794 because residue number 222  < previous residue 298 
Skipped atom 1795 because residue number 222  < previous residue 298 
Skipped atom 1796 because residue number 223  < previous residue 298 
Skipped atom 1797 because residue number 223  < previous residue 298 
Skipped atom 1798 because residue number 223  < previous residue 298 
Skipped atom 1799 because residue number 223  < previous residue 298 
Skipped atom 1800 because residue number 223  < previous residue 298 
Skipped atom 1801 because residue number 223  < previous residue 298 
Skipped atom 1802 because residue number 223  < previous residue 298 
Skipped atom 1803 because residue number 223  < previous residue 298 
Skipped atom 1804 because residue number 224  < previous residue 298 
Skipped atom 1805 because residue number 224  < previous residue 298 
Skipped atom 1806 because residue number 224  < previous residue 298 
Skipped atom 1807 because residue number 224  < previous residue 298 
Skipped atom 1808 because residue number 225  < previous residue 298 
Skipped atom 1809 because residue number 225  < previous residue 298 
Skipped atom 1810 because residue number 225  < previous residue 298 
Skipped atom 1811 because residue number 225  < previous residue 298 
Skipped atom 1812 because residue number 225  < previous residue 298 
Skipped atom 1813 because residue number 225  < previous residue 298 
Skipped atom 1814 because residue number 225  < previous residue 298 
Skipped atom 1815 because residue number 226  < previous residue 298 
Skipped atom 1816 because residue number 226  < previous residue 298 
Skipped atom 1817 because residue number 226  < previous residue 298 
Skipped atom 1818 because residue number 226  < previous residue 298 
Skipped atom 1819 because residue number 226  < previous residue 298 
Skipped atom 1820 because residue number 226  < previous residue 298 
Skipped atom 1821 because residue number 226  < previous residue 298 
Skipped atom 1822 because residue number 227  < previous residue 298 
Skipped atom 1823 because residue number 227  < previous residue 298 
Skipped atom 1824 because residue number 227  < previous residue 298 
Skipped atom 1825 because residue number 227  < previous residue 298 
Skipped atom 1826 because residue number 227  < previous residue 298 
Skipped atom 1827 because residue number 227  < previous residue 298 
Skipped atom 1828 because residue number 228  < previous residue 298 
Skipped atom 1829 because residue number 228  < previous residue 298 
Skipped atom 1830 because residue number 228  < previous residue 298 
Skipped atom 1831 because residue number 228  < previous residue 298 
Skipped atom 1832 because residue number 228  < previous residue 298 
Skipped atom 1833 because residue number 228  < previous residue 298 
Skipped atom 1834 because residue number 228  < previous residue 298 
Skipped atom 1835 because residue number 228  < previous residue 298 
Skipped atom 1836 because residue number 229  < previous residue 298 
Skipped atom 1837 because residue number 229  < previous residue 298 
Skipped atom 1838 because residue number 229  < previous residue 298 
Skipped atom 1839 because residue number 229  < previous residue 298 
Skipped atom 1840 because residue number 229  < previous residue 298 
Skipped atom 1841 because residue number 229  < previous residue 298 
Skipped atom 1842 because residue number 229  < previous residue 298 
Skipped atom 1843 because residue number 229  < previous residue 298 
Skipped atom 1844 because residue number 229  < previous residue 298 
Skipped atom 1845 because residue number 229  < previous residue 298 
Skipped atom 1846 because residue number 229  < previous residue 298 
Skipped atom 1847 because residue number 229  < previous residue 298 
Skipped atom 1848 because residue number 230  < previous residue 298 
Skipped atom 1849 because residue number 230  < previous residue 298 
Skipped atom 1850 because residue number 230  < previous residue 298 
Skipped atom 1851 because residue number 230  < previous residue 298 
Skipped atom 1852 because residue number 230  < previous residue 298 
Skipped atom 1853 because residue number 230  < previous residue 298 
Skipped atom 1854 because residue number 230  < previous residue 298 
Skipped atom 1855 because residue number 230  < previous residue 298 
Skipped atom 1856 because residue number 230  < previous residue 298 
Skipped atom 1857 because residue number 231  < previous residue 298 
Skipped atom 1858 because residue number 231  < previous residue 298 
Skipped atom 1859 because residue number 231  < previous residue 298 
Skipped atom 1860 because residue number 231  < previous residue 298 
Skipped atom 1861 because residue number 231  < previous residue 298 
Skipped atom 1862 because residue number 231  < previous residue 298 
Skipped atom 1863 because residue number 231  < previous residue 298 
Skipped atom 1864 because residue number 232  < previous residue 298 
Skipped atom 1865 because residue number 232  < previous residue 298 
Skipped atom 1866 because residue number 232  < previous residue 298 
Skipped atom 1867 because residue number 232  < previous residue 298 
Skipped atom 1868 because residue number 232  < previous residue 298 
Skipped atom 1869 because residue number 233  < previous residue 298 
Skipped atom 1870 because residue number 233  < previous residue 298 
Skipped atom 1871 because residue number 233  < previous residue 298 
Skipped atom 1872 because residue number 233  < previous residue 298 
Skipped atom 1873 because residue number 233  < previous residue 298 
Skipped atom 1874 because residue number 233  < previous residue 298 
Skipped atom 1875 because residue number 233  < previous residue 298 
Skipped atom 1876 because residue number 233  < previous residue 298 
Skipped atom 1877 because residue number 234  < previous residue 298 
Skipped atom 1878 because residue number 234  < previous residue 298 
Skipped atom 1879 because residue number 234  < previous residue 298 
Skipped atom 1880 because residue number 234  < previous residue 298 
Skipped atom 1881 because residue number 234  < previous residue 298 
Skipped atom 1882 because residue number 234  < previous residue 298 
Skipped atom 1883 because residue number 234  < previous residue 298 
Skipped atom 1884 because residue number 234  < previous residue 298 
Skipped atom 1885 because residue number 234  < previous residue 298 
Skipped atom 1886 because residue number 235  < previous residue 298 
Skipped atom 1887 because residue number 235  < previous residue 298 
Skipped atom 1888 because residue number 235  < previous residue 298 
Skipped atom 1889 because residue number 235  < previous residue 298 
Skipped atom 1890 because residue number 235  < previous residue 298 
Skipped atom 1891 because residue number 235  < previous residue 298 
Skipped atom 1892 because residue number 236  < previous residue 298 
Skipped atom 1893 because residue number 236  < previous residue 298 
Skipped atom 1894 because residue number 236  < previous residue 298 
Skipped atom 1895 because residue number 236  < previous residue 298 
Skipped atom 1896 because residue number 237  < previous residue 298 
Skipped atom 1897 because residue number 237  < previous residue 298 
Skipped atom 1898 because residue number 237  < previous residue 298 
Skipped atom 1899 because residue number 237  < previous residue 298 
Skipped atom 1900 because residue number 237  < previous residue 298 
Skipped atom 1901 because residue number 237  < previous residue 298 
Skipped atom 1902 because residue number 237  < previous residue 298 
Skipped atom 1903 because residue number 237  < previous residue 298 
Skipped atom 1904 because residue number 237  < previous residue 298 
Skipped atom 1905 because residue number 238  < previous residue 298 
Skipped atom 1906 because residue number 238  < previous residue 298 
Skipped atom 1907 because residue number 238  < previous residue 298 
Skipped atom 1908 because residue number 238  < previous residue 298 
Skipped atom 1909 because residue number 238  < previous residue 298 
Skipped atom 1910 because residue number 239  < previous residue 298 
Skipped atom 1911 because residue number 239  < previous residue 298 
Skipped atom 1912 because residue number 239  < previous residue 298 
Skipped atom 1913 because residue number 239  < previous residue 298 
Skipped atom 1914 because residue number 239  < previous residue 298 
Skipped atom 1915 because residue number 239  < previous residue 298 
Skipped atom 1916 because residue number 239  < previous residue 298 
Skipped atom 1917 because residue number 239  < previous residue 298 
Skipped atom 1918 because residue number 240  < previous residue 298 
Skipped atom 1919 because residue number 240  < previous residue 298 
Skipped atom 1920 because residue number 240  < previous residue 298 
Skipped atom 1921 because residue number 240  < previous residue 298 
Skipped atom 1922 because residue number 240  < previous residue 298 
Skipped atom 1923 because residue number 240  < previous residue 298 
Skipped atom 1924 because residue number 240  < previous residue 298 
Skipped atom 1925 because residue number 241  < previous residue 298 
Skipped atom 1926 because residue number 241  < previous residue 298 
Skipped atom 1927 because residue number 241  < previous residue 298 
Skipped atom 1928 because residue number 241  < previous residue 298 
Skipped atom 1929 because residue number 241  < previous residue 298 
Skipped atom 1930 because residue number 241  < previous residue 298 
Skipped atom 1931 because residue number 241  < previous residue 298 
Skipped atom 1932 because residue number 241  < previous residue 298 
Skipped atom 1933 because residue number 241  < previous residue 298 
Skipped atom 1934 because residue number 241  < previous residue 298 
Skipped atom 1935 because residue number 241  < previous residue 298 
Skipped atom 1936 because residue number 241  < previous residue 298 
Skipped atom 1937 because residue number 242  < previous residue 298 
Skipped atom 1938 because residue number 242  < previous residue 298 
Skipped atom 1939 because residue number 242  < previous residue 298 
Skipped atom 1940 because residue number 242  < previous residue 298 
Skipped atom 1941 because residue number 242  < previous residue 298 
Skipped atom 1942 because residue number 243  < previous residue 298 
Skipped atom 1943 because residue number 243  < previous residue 298 
Skipped atom 1944 because residue number 243  < previous residue 298 
Skipped atom 1945 because residue number 243  < previous residue 298 
Skipped atom 1946 because residue number 243  < previous residue 298 
Skipped atom 1947 because residue number 243  < previous residue 298 
Skipped atom 1948 because residue number 244  < previous residue 298 
Skipped atom 1949 because residue number 244  < previous residue 298 
Skipped atom 1950 because residue number 244  < previous residue 298 
Skipped atom 1951 because residue number 244  < previous residue 298 
Skipped atom 1952 because residue number 244  < previous residue 298 
Skipped atom 1953 because residue number 244  < previous residue 298 
Skipped atom 1954 because residue number 244  < previous residue 298 
Skipped atom 1955 because residue number 244  < previous residue 298 
Skipped atom 1956 because residue number 244  < previous residue 298 
Skipped atom 1957 because residue number 244  < previous residue 298 
Skipped atom 1958 because residue number 244  < previous residue 298 
Skipped atom 1959 because residue number 245  < previous residue 298 
Skipped atom 1960 because residue number 245  < previous residue 298 
Skipped atom 1961 because residue number 245  < previous residue 298 
Skipped atom 1962 because residue number 245  < previous residue 298 
Skipped atom 1963 because residue number 245  < previous residue 298 
Skipped atom 1964 because residue number 245  < previous residue 298 
Skipped atom 1965 because residue number 245  < previous residue 298 
Skipped atom 1966 because residue number 245  < previous residue 298 
Skipped atom 1967 because residue number 246  < previous residue 298 
Skipped atom 1968 because residue number 246  < previous residue 298 
Skipped atom 1969 because residue number 246  < previous residue 298 
Skipped atom 1970 because residue number 246  < previous residue 298 
Skipped atom 1971 because residue number 246  < previous residue 298 
Skipped atom 1972 because residue number 246  < previous residue 298 
Skipped atom 1973 because residue number 246  < previous residue 298 
Skipped atom 1974 because residue number 246  < previous residue 298 
Skipped atom 1975 because residue number 247  < previous residue 298 
Skipped atom 1976 because residue number 247  < previous residue 298 
Skipped atom 1977 because residue number 247  < previous residue 298 
Skipped atom 1978 because residue number 247  < previous residue 298 
Skipped atom 1979 because residue number 247  < previous residue 298 
Skipped atom 1980 because residue number 247  < previous residue 298 
Skipped atom 1981 because residue number 247  < previous residue 298 
Skipped atom 1982 because residue number 248  < previous residue 298 
Skipped atom 1983 because residue number 248  < previous residue 298 
Skipped atom 1984 because residue number 248  < previous residue 298 
Skipped atom 1985 because residue number 248  < previous residue 298 
Skipped atom 1986 because residue number 248  < previous residue 298 
Skipped atom 1987 because residue number 249  < previous residue 298 
Skipped atom 1988 because residue number 249  < previous residue 298 
Skipped atom 1989 because residue number 249  < previous residue 298 
Skipped atom 1990 because residue number 249  < previous residue 298 
Skipped atom 1991 because residue number 249  < previous residue 298 
Skipped atom 1992 because residue number 249  < previous residue 298 
Skipped atom 1993 because residue number 249  < previous residue 298 
Skipped atom 1994 because residue number 249  < previous residue 298 
Skipped atom 1995 because residue number 249  < previous residue 298 
Skipped atom 1996 because residue number 249  < previous residue 298 
Skipped atom 1997 because residue number 249  < previous residue 298 
Skipped atom 1998 because residue number 250  < previous residue 298 
Skipped atom 1999 because residue number 250  < previous residue 298 
Skipped atom 2000 because residue number 250  < previous residue 298 
Skipped atom 2001 because residue number 250  < previous residue 298 
Skipped atom 2002 because residue number 250  < previous residue 298 
Skipped atom 2003 because residue number 250  < previous residue 298 
Skipped atom 2004 because residue number 250  < previous residue 298 
Skipped atom 2005 because residue number 251  < previous residue 298 
Skipped atom 2006 because residue number 251  < previous residue 298 
Skipped atom 2007 because residue number 251  < previous residue 298 
Skipped atom 2008 because residue number 251  < previous residue 298 
Skipped atom 2009 because residue number 251  < previous residue 298 
Skipped atom 2010 because residue number 251  < previous residue 298 
Skipped atom 2011 because residue number 251  < previous residue 298 
Skipped atom 2012 because residue number 251  < previous residue 298 
Skipped atom 2013 because residue number 251  < previous residue 298 
Skipped atom 2014 because residue number 251  < previous residue 298 
Skipped atom 2015 because residue number 251  < previous residue 298 
Skipped atom 2016 because residue number 251  < previous residue 298 
Skipped atom 2017 because residue number 252  < previous residue 298 
Skipped atom 2018 because residue number 252  < previous residue 298 
Skipped atom 2019 because residue number 252  < previous residue 298 
Skipped atom 2020 because residue number 252  < previous residue 298 
Skipped atom 2021 because residue number 252  < previous residue 298 
Skipped atom 2022 because residue number 252  < previous residue 298 
Skipped atom 2023 because residue number 252  < previous residue 298 
Skipped atom 2024 because residue number 253  < previous residue 298 
Skipped atom 2025 because residue number 253  < previous residue 298 
Skipped atom 2026 because residue number 253  < previous residue 298 
Skipped atom 2027 because residue number 253  < previous residue 298 
Skipped atom 2028 because residue number 253  < previous residue 298 
Skipped atom 2029 because residue number 253  < previous residue 298 
Skipped atom 2030 because residue number 253  < previous residue 298 
Skipped atom 2031 because residue number 253  < previous residue 298 
Skipped atom 2032 because residue number 253  < previous residue 298 
Skipped atom 2033 because residue number 253  < previous residue 298 
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1alq-orig.a2m
Writing a2m file: tmp/1alq-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1098


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1098/tmp -alignfile tmp/1alq-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1alq-orig.a2m (1 sequences, 266 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1098/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1098/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1098/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1098/tmp.a2m (1 sequences, 266 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1098/tmp.mod tmp/1alq-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1098 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1alq-align.mod
tmp/1alq-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1098/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1alq-orig.a2m tmp/1alq-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1alq-align.mod
Running w0.5 tmp/1alq-orig.a2m tmp/1alq-align.mod
Running align2model tmp/1alq-align -i tmp/1alq-align.mod -db tmp/1alq-orig.a2m -db tmp/1alq-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1alq.140.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1alq.141.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1alq.141.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1alq.141.3.a2m \
	-target T0124 -template 1alq \
	-out T0124-1alq.141.3 -outdir und
Skipped atom 298 because residue number 31  < previous residue 298 
Skipped atom 299 because residue number 31  < previous residue 298 
Skipped atom 300 because residue number 31  < previous residue 298 
Skipped atom 301 because residue number 31  < previous residue 298 
Skipped atom 302 because residue number 31  < previous residue 298 
Skipped atom 303 because residue number 31  < previous residue 298 
Skipped atom 304 because residue number 31  < previous residue 298 
Skipped atom 305 because residue number 31  < previous residue 298 
Skipped atom 306 because residue number 31  < previous residue 298 
Skipped atom 307 because residue number 32  < previous residue 298 
Skipped atom 308 because residue number 32  < previous residue 298 
Skipped atom 309 because residue number 32  < previous residue 298 
Skipped atom 310 because residue number 32  < previous residue 298 
Skipped atom 311 because residue number 32  < previous residue 298 
Skipped atom 312 because residue number 32  < previous residue 298 
Skipped atom 313 because residue number 32  < previous residue 298 
Skipped atom 314 because residue number 32  < previous residue 298 
Skipped atom 315 because residue number 32  < previous residue 298 
Skipped atom 316 because residue number 33  < previous residue 298 
Skipped atom 317 because residue number 33  < previous residue 298 
Skipped atom 318 because residue number 33  < previous residue 298 
Skipped atom 319 because residue number 33  < previous residue 298 
Skipped atom 320 because residue number 33  < previous residue 298 
Skipped atom 321 because residue number 33  < previous residue 298 
Skipped atom 322 because residue number 33  < previous residue 298 
Skipped atom 323 because residue number 33  < previous residue 298 
Skipped atom 324 because residue number 34  < previous residue 298 
Skipped atom 325 because residue number 34  < previous residue 298 
Skipped atom 326 because residue number 34  < previous residue 298 
Skipped atom 327 because residue number 34  < previous residue 298 
Skipped atom 328 because residue number 34  < previous residue 298 
Skipped atom 329 because residue number 34  < previous residue 298 
Skipped atom 330 because residue number 34  < previous residue 298 
Skipped atom 331 because residue number 34  < previous residue 298 
Skipped atom 332 because residue number 35  < previous residue 298 
Skipped atom 333 because residue number 35  < previous residue 298 
Skipped atom 334 because residue number 35  < previous residue 298 
Skipped atom 335 because residue number 35  < previous residue 298 
Skipped atom 336 because residue number 35  < previous residue 298 
Skipped atom 337 because residue number 35  < previous residue 298 
Skipped atom 338 because residue number 35  < previous residue 298 
Skipped atom 339 because residue number 35  < previous residue 298 
Skipped atom 340 because residue number 36  < previous residue 298 
Skipped atom 341 because residue number 36  < previous residue 298 
Skipped atom 342 because residue number 36  < previous residue 298 
Skipped atom 343 because residue number 36  < previous residue 298 
Skipped atom 344 because residue number 36  < previous residue 298 
Skipped atom 345 because residue number 36  < previous residue 298 
Skipped atom 346 because residue number 36  < previous residue 298 
Skipped atom 347 because residue number 36  < previous residue 298 
Skipped atom 348 because residue number 37  < previous residue 298 
Skipped atom 349 because residue number 37  < previous residue 298 
Skipped atom 350 because residue number 37  < previous residue 298 
Skipped atom 351 because residue number 37  < previous residue 298 
Skipped atom 352 because residue number 37  < previous residue 298 
Skipped atom 353 because residue number 37  < previous residue 298 
Skipped atom 354 because residue number 37  < previous residue 298 
Skipped atom 355 because residue number 37  < previous residue 298 
Skipped atom 356 because residue number 37  < previous residue 298 
Skipped atom 357 because residue number 38  < previous residue 298 
Skipped atom 358 because residue number 38  < previous residue 298 
Skipped atom 359 because residue number 38  < previous residue 298 
Skipped atom 360 because residue number 38  < previous residue 298 
Skipped atom 361 because residue number 38  < previous residue 298 
Skipped atom 362 because residue number 38  < previous residue 298 
Skipped atom 363 because residue number 38  < previous residue 298 
Skipped atom 364 because residue number 38  < previous residue 298 
Skipped atom 365 because residue number 38  < previous residue 298 
Skipped atom 366 because residue number 39  < previous residue 298 
Skipped atom 367 because residue number 39  < previous residue 298 
Skipped atom 368 because residue number 39  < previous residue 298 
Skipped atom 369 because residue number 39  < previous residue 298 
Skipped atom 370 because residue number 39  < previous residue 298 
Skipped atom 371 because residue number 39  < previous residue 298 
Skipped atom 372 because residue number 39  < previous residue 298 
Skipped atom 373 because residue number 39  < previous residue 298 
Skipped atom 374 because residue number 39  < previous residue 298 
Skipped atom 375 because residue number 40  < previous residue 298 
Skipped atom 376 because residue number 40  < previous residue 298 
Skipped atom 377 because residue number 40  < previous residue 298 
Skipped atom 378 because residue number 40  < previous residue 298 
Skipped atom 379 because residue number 40  < previous residue 298 
Skipped atom 380 because residue number 40  < previous residue 298 
Skipped atom 381 because residue number 40  < previous residue 298 
Skipped atom 382 because residue number 40  < previous residue 298 
Skipped atom 383 because residue number 40  < previous residue 298 
Skipped atom 384 because residue number 40  < previous residue 298 
Skipped atom 385 because residue number 40  < previous residue 298 
Skipped atom 386 because residue number 40  < previous residue 298 
Skipped atom 387 because residue number 41  < previous residue 298 
Skipped atom 388 because residue number 41  < previous residue 298 
Skipped atom 389 because residue number 41  < previous residue 298 
Skipped atom 390 because residue number 41  < previous residue 298 
Skipped atom 391 because residue number 41  < previous residue 298 
Skipped atom 392 because residue number 41  < previous residue 298 
Skipped atom 393 because residue number 41  < previous residue 298 
Skipped atom 394 because residue number 41  < previous residue 298 
Skipped atom 395 because residue number 42  < previous residue 298 
Skipped atom 396 because residue number 42  < previous residue 298 
Skipped atom 397 because residue number 42  < previous residue 298 
Skipped atom 398 because residue number 42  < previous residue 298 
Skipped atom 399 because residue number 42  < previous residue 298 
Skipped atom 400 because residue number 43  < previous residue 298 
Skipped atom 401 because residue number 43  < previous residue 298 
Skipped atom 402 because residue number 43  < previous residue 298 
Skipped atom 403 because residue number 43  < previous residue 298 
Skipped atom 404 because residue number 43  < previous residue 298 
Skipped atom 405 because residue number 43  < previous residue 298 
Skipped atom 406 because residue number 43  < previous residue 298 
Skipped atom 407 because residue number 43  < previous residue 298 
Skipped atom 408 because residue number 43  < previous residue 298 
Skipped atom 409 because residue number 43  < previous residue 298 
Skipped atom 410 because residue number 44  < previous residue 298 
Skipped atom 411 because residue number 44  < previous residue 298 
Skipped atom 412 because residue number 44  < previous residue 298 
Skipped atom 413 because residue number 44  < previous residue 298 
Skipped atom 414 because residue number 44  < previous residue 298 
Skipped atom 415 because residue number 44  < previous residue 298 
Skipped atom 416 because residue number 44  < previous residue 298 
Skipped atom 417 because residue number 44  < previous residue 298 
Skipped atom 418 because residue number 45  < previous residue 298 
Skipped atom 419 because residue number 45  < previous residue 298 
Skipped atom 420 because residue number 45  < previous residue 298 
Skipped atom 421 because residue number 45  < previous residue 298 
Skipped atom 422 because residue number 46  < previous residue 298 
Skipped atom 423 because residue number 46  < previous residue 298 
Skipped atom 424 because residue number 46  < previous residue 298 
Skipped atom 425 because residue number 46  < previous residue 298 
Skipped atom 426 because residue number 46  < previous residue 298 
Skipped atom 427 because residue number 46  < previous residue 298 
Skipped atom 428 because residue number 46  < previous residue 298 
Skipped atom 429 because residue number 47  < previous residue 298 
Skipped atom 430 because residue number 47  < previous residue 298 
Skipped atom 431 because residue number 47  < previous residue 298 
Skipped atom 432 because residue number 47  < previous residue 298 
Skipped atom 433 because residue number 47  < previous residue 298 
Skipped atom 434 because residue number 47  < previous residue 298 
Skipped atom 435 because residue number 47  < previous residue 298 
Skipped atom 436 because residue number 47  < previous residue 298 
Skipped atom 437 because residue number 47  < previous residue 298 
Skipped atom 438 because residue number 47  < previous residue 298 
Skipped atom 439 because residue number 47  < previous residue 298 
Skipped atom 440 because residue number 47  < previous residue 298 
Skipped atom 441 because residue number 48  < previous residue 298 
Skipped atom 442 because residue number 48  < previous residue 298 
Skipped atom 443 because residue number 48  < previous residue 298 
Skipped atom 444 because residue number 48  < previous residue 298 
Skipped atom 445 because residue number 48  < previous residue 298 
Skipped atom 446 because residue number 49  < previous residue 298 
Skipped atom 447 because residue number 49  < previous residue 298 
Skipped atom 448 because residue number 49  < previous residue 298 
Skipped atom 449 because residue number 49  < previous residue 298 
Skipped atom 450 because residue number 49  < previous residue 298 
Skipped atom 451 because residue number 49  < previous residue 298 
Skipped atom 452 because residue number 49  < previous residue 298 
Skipped atom 453 because residue number 49  < previous residue 298 
Skipped atom 454 because residue number 50  < previous residue 298 
Skipped atom 455 because residue number 50  < previous residue 298 
Skipped atom 456 because residue number 50  < previous residue 298 
Skipped atom 457 because residue number 50  < previous residue 298 
Skipped atom 458 because residue number 50  < previous residue 298 
Skipped atom 459 because residue number 50  < previous residue 298 
Skipped atom 460 because residue number 50  < previous residue 298 
Skipped atom 461 because residue number 50  < previous residue 298 
Skipped atom 462 because residue number 51  < previous residue 298 
Skipped atom 463 because residue number 51  < previous residue 298 
Skipped atom 464 because residue number 51  < previous residue 298 
Skipped atom 465 because residue number 51  < previous residue 298 
Skipped atom 466 because residue number 51  < previous residue 298 
Skipped atom 467 because residue number 51  < previous residue 298 
Skipped atom 468 because residue number 51  < previous residue 298 
Skipped atom 469 because residue number 52  < previous residue 298 
Skipped atom 470 because residue number 52  < previous residue 298 
Skipped atom 471 because residue number 52  < previous residue 298 
Skipped atom 472 because residue number 52  < previous residue 298 
Skipped atom 473 because residue number 52  < previous residue 298 
Skipped atom 474 because residue number 52  < previous residue 298 
Skipped atom 475 because residue number 52  < previous residue 298 
Skipped atom 476 because residue number 52  < previous residue 298 
Skipped atom 477 because residue number 52  < previous residue 298 
Skipped atom 478 because residue number 53  < previous residue 298 
Skipped atom 479 because residue number 53  < previous residue 298 
Skipped atom 480 because residue number 53  < previous residue 298 
Skipped atom 481 because residue number 53  < previous residue 298 
Skipped atom 482 because residue number 53  < previous residue 298 
Skipped atom 483 because residue number 53  < previous residue 298 
Skipped atom 484 because residue number 54  < previous residue 298 
Skipped atom 485 because residue number 54  < previous residue 298 
Skipped atom 486 because residue number 54  < previous residue 298 
Skipped atom 487 because residue number 54  < previous residue 298 
Skipped atom 488 because residue number 55  < previous residue 298 
Skipped atom 489 because residue number 55  < previous residue 298 
Skipped atom 490 because residue number 55  < previous residue 298 
Skipped atom 491 because residue number 55  < previous residue 298 
Skipped atom 492 because residue number 55  < previous residue 298 
Skipped atom 493 because residue number 55  < previous residue 298 
Skipped atom 494 because residue number 55  < previous residue 298 
Skipped atom 495 because residue number 55  < previous residue 298 
Skipped atom 496 because residue number 55  < previous residue 298 
Skipped atom 497 because residue number 56  < previous residue 298 
Skipped atom 498 because residue number 56  < previous residue 298 
Skipped atom 499 because residue number 56  < previous residue 298 
Skipped atom 500 because residue number 56  < previous residue 298 
Skipped atom 501 because residue number 56  < previous residue 298 
Skipped atom 502 because residue number 56  < previous residue 298 
Skipped atom 503 because residue number 56  < previous residue 298 
Skipped atom 504 because residue number 56  < previous residue 298 
Skipped atom 505 because residue number 56  < previous residue 298 
Skipped atom 506 because residue number 57  < previous residue 298 
Skipped atom 507 because residue number 57  < previous residue 298 
Skipped atom 508 because residue number 57  < previous residue 298 
Skipped atom 509 because residue number 57  < previous residue 298 
Skipped atom 510 because residue number 57  < previous residue 298 
Skipped atom 511 because residue number 57  < previous residue 298 
Skipped atom 512 because residue number 57  < previous residue 298 
Skipped atom 513 because residue number 59  < previous residue 298 
Skipped atom 514 because residue number 59  < previous residue 298 
Skipped atom 515 because residue number 59  < previous residue 298 
Skipped atom 516 because residue number 59  < previous residue 298 
Skipped atom 517 because residue number 59  < previous residue 298 
Skipped atom 518 because residue number 59  < previous residue 298 
Skipped atom 519 because residue number 59  < previous residue 298 
Skipped atom 520 because residue number 59  < previous residue 298 
Skipped atom 521 because residue number 59  < previous residue 298 
Skipped atom 522 because residue number 60  < previous residue 298 
Skipped atom 523 because residue number 60  < previous residue 298 
Skipped atom 524 because residue number 60  < previous residue 298 
Skipped atom 525 because residue number 60  < previous residue 298 
Skipped atom 526 because residue number 60  < previous residue 298 
Skipped atom 527 because residue number 60  < previous residue 298 
Skipped atom 528 because residue number 60  < previous residue 298 
Skipped atom 529 because residue number 60  < previous residue 298 
Skipped atom 530 because residue number 60  < previous residue 298 
Skipped atom 531 because residue number 60  < previous residue 298 
Skipped atom 532 because residue number 60  < previous residue 298 
Skipped atom 533 because residue number 61  < previous residue 298 
Skipped atom 534 because residue number 61  < previous residue 298 
Skipped atom 535 because residue number 61  < previous residue 298 
Skipped atom 536 because residue number 61  < previous residue 298 
Skipped atom 537 because residue number 61  < previous residue 298 
Skipped atom 538 because residue number 61  < previous residue 298 
Skipped atom 539 because residue number 61  < previous residue 298 
Skipped atom 540 because residue number 61  < previous residue 298 
Skipped atom 541 because residue number 62  < previous residue 298 
Skipped atom 542 because residue number 62  < previous residue 298 
Skipped atom 543 because residue number 62  < previous residue 298 
Skipped atom 544 because residue number 62  < previous residue 298 
Skipped atom 545 because residue number 62  < previous residue 298 
Skipped atom 546 because residue number 62  < previous residue 298 
Skipped atom 547 because residue number 63  < previous residue 298 
Skipped atom 548 because residue number 63  < previous residue 298 
Skipped atom 549 because residue number 63  < previous residue 298 
Skipped atom 550 because residue number 63  < previous residue 298 
Skipped atom 551 because residue number 63  < previous residue 298 
Skipped atom 552 because residue number 63  < previous residue 298 
Skipped atom 553 because residue number 63  < previous residue 298 
Skipped atom 554 because residue number 63  < previous residue 298 
Skipped atom 555 because residue number 64  < previous residue 298 
Skipped atom 556 because residue number 64  < previous residue 298 
Skipped atom 557 because residue number 64  < previous residue 298 
Skipped atom 558 because residue number 64  < previous residue 298 
Skipped atom 559 because residue number 64  < previous residue 298 
Skipped atom 560 because residue number 64  < previous residue 298 
Skipped atom 561 because residue number 64  < previous residue 298 
Skipped atom 562 because residue number 64  < previous residue 298 
Skipped atom 563 because residue number 64  < previous residue 298 
Skipped atom 564 because residue number 65  < previous residue 298 
Skipped atom 565 because residue number 65  < previous residue 298 
Skipped atom 566 because residue number 65  < previous residue 298 
Skipped atom 567 because residue number 65  < previous residue 298 
Skipped atom 568 because residue number 65  < previous residue 298 
Skipped atom 569 because residue number 65  < previous residue 298 
Skipped atom 570 because residue number 65  < previous residue 298 
Skipped atom 571 because residue number 65  < previous residue 298 
Skipped atom 572 because residue number 65  < previous residue 298 
Skipped atom 573 because residue number 65  < previous residue 298 
Skipped atom 574 because residue number 65  < previous residue 298 
Skipped atom 575 because residue number 66  < previous residue 298 
Skipped atom 576 because residue number 66  < previous residue 298 
Skipped atom 577 because residue number 66  < previous residue 298 
Skipped atom 578 because residue number 66  < previous residue 298 
Skipped atom 579 because residue number 66  < previous residue 298 
Skipped atom 580 because residue number 66  < previous residue 298 
Skipped atom 581 because residue number 66  < previous residue 298 
Skipped atom 582 because residue number 66  < previous residue 298 
Skipped atom 583 because residue number 66  < previous residue 298 
Skipped atom 584 because residue number 66  < previous residue 298 
Skipped atom 585 because residue number 66  < previous residue 298 
Skipped atom 586 because residue number 67  < previous residue 298 
Skipped atom 587 because residue number 67  < previous residue 298 
Skipped atom 588 because residue number 67  < previous residue 298 
Skipped atom 589 because residue number 67  < previous residue 298 
Skipped atom 590 because residue number 67  < previous residue 298 
Skipped atom 591 because residue number 68  < previous residue 298 
Skipped atom 592 because residue number 68  < previous residue 298 
Skipped atom 593 because residue number 68  < previous residue 298 
Skipped atom 594 because residue number 68  < previous residue 298 
Skipped atom 595 because residue number 68  < previous residue 298 
Skipped atom 596 because residue number 68  < previous residue 298 
Skipped atom 597 because residue number 68  < previous residue 298 
Skipped atom 598 because residue number 68  < previous residue 298 
Skipped atom 599 because residue number 68  < previous residue 298 
Skipped atom 600 because residue number 68  < previous residue 298 
Skipped atom 601 because residue number 68  < previous residue 298 
Skipped atom 602 because residue number 68  < previous residue 298 
Skipped atom 603 because residue number 69  < previous residue 298 
Skipped atom 604 because residue number 69  < previous residue 298 
Skipped atom 605 because residue number 69  < previous residue 298 
Skipped atom 606 because residue number 69  < previous residue 298 
Skipped atom 607 because residue number 69  < previous residue 298 
Skipped atom 608 because residue number 70  < previous residue 298 
Skipped atom 609 because residue number 70  < previous residue 298 
Skipped atom 610 because residue number 70  < previous residue 298 
Skipped atom 611 because residue number 70  < previous residue 298 
Skipped atom 612 because residue number 70  < previous residue 298 
Skipped atom 613 because residue number 70  < previous residue 298 
Skipped atom 614 because residue number 71  < previous residue 298 
Skipped atom 615 because residue number 71  < previous residue 298 
Skipped atom 616 because residue number 71  < previous residue 298 
Skipped atom 617 because residue number 71  < previous residue 298 
Skipped atom 618 because residue number 71  < previous residue 298 
Skipped atom 619 because residue number 71  < previous residue 298 
Skipped atom 620 because residue number 71  < previous residue 298 
Skipped atom 621 because residue number 72  < previous residue 298 
Skipped atom 622 because residue number 72  < previous residue 298 
Skipped atom 623 because residue number 72  < previous residue 298 
Skipped atom 624 because residue number 72  < previous residue 298 
Skipped atom 625 because residue number 72  < previous residue 298 
Skipped atom 626 because residue number 72  < previous residue 298 
Skipped atom 627 because residue number 73  < previous residue 298 
Skipped atom 628 because residue number 73  < previous residue 298 
Skipped atom 629 because residue number 73  < previous residue 298 
Skipped atom 630 because residue number 73  < previous residue 298 
Skipped atom 631 because residue number 73  < previous residue 298 
Skipped atom 632 because residue number 73  < previous residue 298 
Skipped atom 633 because residue number 73  < previous residue 298 
Skipped atom 634 because residue number 73  < previous residue 298 
Skipped atom 635 because residue number 73  < previous residue 298 
Skipped atom 636 because residue number 74  < previous residue 298 
Skipped atom 637 because residue number 74  < previous residue 298 
Skipped atom 638 because residue number 74  < previous residue 298 
Skipped atom 639 because residue number 74  < previous residue 298 
Skipped atom 640 because residue number 74  < previous residue 298 
Skipped atom 641 because residue number 75  < previous residue 298 
Skipped atom 642 because residue number 75  < previous residue 298 
Skipped atom 643 because residue number 75  < previous residue 298 
Skipped atom 644 because residue number 75  < previous residue 298 
Skipped atom 645 because residue number 75  < previous residue 298 
Skipped atom 646 because residue number 75  < previous residue 298 
Skipped atom 647 because residue number 75  < previous residue 298 
Skipped atom 648 because residue number 75  < previous residue 298 
Skipped atom 649 because residue number 76  < previous residue 298 
Skipped atom 650 because residue number 76  < previous residue 298 
Skipped atom 651 because residue number 76  < previous residue 298 
Skipped atom 652 because residue number 76  < previous residue 298 
Skipped atom 653 because residue number 76  < previous residue 298 
Skipped atom 654 because residue number 76  < previous residue 298 
Skipped atom 655 because residue number 76  < previous residue 298 
Skipped atom 656 because residue number 76  < previous residue 298 
Skipped atom 657 because residue number 77  < previous residue 298 
Skipped atom 658 because residue number 77  < previous residue 298 
Skipped atom 659 because residue number 77  < previous residue 298 
Skipped atom 660 because residue number 77  < previous residue 298 
Skipped atom 661 because residue number 77  < previous residue 298 
Skipped atom 662 because residue number 77  < previous residue 298 
Skipped atom 663 because residue number 78  < previous residue 298 
Skipped atom 664 because residue number 78  < previous residue 298 
Skipped atom 665 because residue number 78  < previous residue 298 
Skipped atom 666 because residue number 78  < previous residue 298 
Skipped atom 667 because residue number 78  < previous residue 298 
Skipped atom 668 because residue number 79  < previous residue 298 
Skipped atom 669 because residue number 79  < previous residue 298 
Skipped atom 670 because residue number 79  < previous residue 298 
Skipped atom 671 because residue number 79  < previous residue 298 
Skipped atom 672 because residue number 79  < previous residue 298 
Skipped atom 673 because residue number 79  < previous residue 298 
Skipped atom 674 because residue number 79  < previous residue 298 
Skipped atom 675 because residue number 79  < previous residue 298 
Skipped atom 676 because residue number 80  < previous residue 298 
Skipped atom 677 because residue number 80  < previous residue 298 
Skipped atom 678 because residue number 80  < previous residue 298 
Skipped atom 679 because residue number 80  < previous residue 298 
Skipped atom 680 because residue number 80  < previous residue 298 
Skipped atom 681 because residue number 80  < previous residue 298 
Skipped atom 682 because residue number 80  < previous residue 298 
Skipped atom 683 because residue number 80  < previous residue 298 
Skipped atom 684 because residue number 81  < previous residue 298 
Skipped atom 685 because residue number 81  < previous residue 298 
Skipped atom 686 because residue number 81  < previous residue 298 
Skipped atom 687 because residue number 81  < previous residue 298 
Skipped atom 688 because residue number 81  < previous residue 298 
Skipped atom 689 because residue number 81  < previous residue 298 
Skipped atom 690 because residue number 81  < previous residue 298 
Skipped atom 691 because residue number 81  < previous residue 298 
Skipped atom 692 because residue number 82  < previous residue 298 
Skipped atom 693 because residue number 82  < previous residue 298 
Skipped atom 694 because residue number 82  < previous residue 298 
Skipped atom 695 because residue number 82  < previous residue 298 
Skipped atom 696 because residue number 82  < previous residue 298 
Skipped atom 697 because residue number 82  < previous residue 298 
Skipped atom 698 because residue number 82  < previous residue 298 
Skipped atom 699 because residue number 82  < previous residue 298 
Skipped atom 700 because residue number 82  < previous residue 298 
Skipped atom 701 because residue number 83  < previous residue 298 
Skipped atom 702 because residue number 83  < previous residue 298 
Skipped atom 703 because residue number 83  < previous residue 298 
Skipped atom 704 because residue number 83  < previous residue 298 
Skipped atom 705 because residue number 83  < previous residue 298 
Skipped atom 706 because residue number 83  < previous residue 298 
Skipped atom 707 because residue number 83  < previous residue 298 
Skipped atom 708 because residue number 83  < previous residue 298 
Skipped atom 709 because residue number 83  < previous residue 298 
Skipped atom 710 because residue number 84  < previous residue 298 
Skipped atom 711 because residue number 84  < previous residue 298 
Skipped atom 712 because residue number 84  < previous residue 298 
Skipped atom 713 because residue number 84  < previous residue 298 
Skipped atom 714 because residue number 84  < previous residue 298 
Skipped atom 715 because residue number 84  < previous residue 298 
Skipped atom 716 because residue number 84  < previous residue 298 
Skipped atom 717 because residue number 87  < previous residue 298 
Skipped atom 718 because residue number 87  < previous residue 298 
Skipped atom 719 because residue number 87  < previous residue 298 
Skipped atom 720 because residue number 87  < previous residue 298 
Skipped atom 721 because residue number 87  < previous residue 298 
Skipped atom 722 because residue number 87  < previous residue 298 
Skipped atom 723 because residue number 87  < previous residue 298 
Skipped atom 724 because residue number 88  < previous residue 298 
Skipped atom 725 because residue number 88  < previous residue 298 
Skipped atom 726 because residue number 88  < previous residue 298 
Skipped atom 727 because residue number 88  < previous residue 298 
Skipped atom 728 because residue number 88  < previous residue 298 
Skipped atom 729 because residue number 88  < previous residue 298 
Skipped atom 730 because residue number 88  < previous residue 298 
Skipped atom 731 because residue number 88  < previous residue 298 
Skipped atom 732 because residue number 88  < previous residue 298 
Skipped atom 733 because residue number 88  < previous residue 298 
Skipped atom 734 because residue number 88  < previous residue 298 
Skipped atom 735 because residue number 88  < previous residue 298 
Skipped atom 736 because residue number 89  < previous residue 298 
Skipped atom 737 because residue number 89  < previous residue 298 
Skipped atom 738 because residue number 89  < previous residue 298 
Skipped atom 739 because residue number 89  < previous residue 298 
Skipped atom 740 because residue number 89  < previous residue 298 
Skipped atom 741 because residue number 89  < previous residue 298 
Skipped atom 742 because residue number 89  < previous residue 298 
Skipped atom 743 because residue number 89  < previous residue 298 
Skipped atom 744 because residue number 90  < previous residue 298 
Skipped atom 745 because residue number 90  < previous residue 298 
Skipped atom 746 because residue number 90  < previous residue 298 
Skipped atom 747 because residue number 90  < previous residue 298 
Skipped atom 748 because residue number 90  < previous residue 298 
Skipped atom 749 because residue number 90  < previous residue 298 
Skipped atom 750 because residue number 90  < previous residue 298 
Skipped atom 751 because residue number 90  < previous residue 298 
Skipped atom 752 because residue number 90  < previous residue 298 
Skipped atom 753 because residue number 91  < previous residue 298 
Skipped atom 754 because residue number 91  < previous residue 298 
Skipped atom 755 because residue number 91  < previous residue 298 
Skipped atom 756 because residue number 91  < previous residue 298 
Skipped atom 757 because residue number 91  < previous residue 298 
Skipped atom 758 because residue number 91  < previous residue 298 
Skipped atom 759 because residue number 91  < previous residue 298 
Skipped atom 760 because residue number 91  < previous residue 298 
Skipped atom 761 because residue number 92  < previous residue 298 
Skipped atom 762 because residue number 92  < previous residue 298 
Skipped atom 763 because residue number 92  < previous residue 298 
Skipped atom 764 because residue number 92  < previous residue 298 
Skipped atom 765 because residue number 92  < previous residue 298 
Skipped atom 766 because residue number 92  < previous residue 298 
Skipped atom 767 because residue number 92  < previous residue 298 
Skipped atom 768 because residue number 92  < previous residue 298 
Skipped atom 769 because residue number 93  < previous residue 298 
Skipped atom 770 because residue number 93  < previous residue 298 
Skipped atom 771 because residue number 93  < previous residue 298 
Skipped atom 772 because residue number 93  < previous residue 298 
Skipped atom 773 because residue number 93  < previous residue 298 
Skipped atom 774 because residue number 93  < previous residue 298 
Skipped atom 775 because residue number 93  < previous residue 298 
Skipped atom 776 because residue number 93  < previous residue 298 
Skipped atom 777 because residue number 93  < previous residue 298 
Skipped atom 778 because residue number 94  < previous residue 298 
Skipped atom 779 because residue number 94  < previous residue 298 
Skipped atom 780 because residue number 94  < previous residue 298 
Skipped atom 781 because residue number 94  < previous residue 298 
Skipped atom 782 because residue number 94  < previous residue 298 
Skipped atom 783 because residue number 94  < previous residue 298 
Skipped atom 784 because residue number 94  < previous residue 298 
Skipped atom 785 because residue number 94  < previous residue 298 
Skipped atom 786 because residue number 94  < previous residue 298 
Skipped atom 787 because residue number 95  < previous residue 298 
Skipped atom 788 because residue number 95  < previous residue 298 
Skipped atom 789 because residue number 95  < previous residue 298 
Skipped atom 790 because residue number 95  < previous residue 298 
Skipped atom 791 because residue number 95  < previous residue 298 
Skipped atom 792 because residue number 95  < previous residue 298 
Skipped atom 793 because residue number 95  < previous residue 298 
Skipped atom 794 because residue number 96  < previous residue 298 
Skipped atom 795 because residue number 96  < previous residue 298 
Skipped atom 796 because residue number 96  < previous residue 298 
Skipped atom 797 because residue number 96  < previous residue 298 
Skipped atom 798 because residue number 96  < previous residue 298 
Skipped atom 799 because residue number 96  < previous residue 298 
Skipped atom 800 because residue number 96  < previous residue 298 
Skipped atom 801 because residue number 96  < previous residue 298 
Skipped atom 802 because residue number 96  < previous residue 298 
Skipped atom 803 because residue number 96  < previous residue 298 
Skipped atom 804 because residue number 97  < previous residue 298 
Skipped atom 805 because residue number 97  < previous residue 298 
Skipped atom 806 because residue number 97  < previous residue 298 
Skipped atom 807 because residue number 97  < previous residue 298 
Skipped atom 808 because residue number 97  < previous residue 298 
Skipped atom 809 because residue number 97  < previous residue 298 
Skipped atom 810 because residue number 97  < previous residue 298 
Skipped atom 811 because residue number 97  < previous residue 298 
Skipped atom 812 because residue number 98  < previous residue 298 
Skipped atom 813 because residue number 98  < previous residue 298 
Skipped atom 814 because residue number 98  < previous residue 298 
Skipped atom 815 because residue number 98  < previous residue 298 
Skipped atom 816 because residue number 98  < previous residue 298 
Skipped atom 817 because residue number 98  < previous residue 298 
Skipped atom 818 because residue number 98  < previous residue 298 
Skipped atom 819 because residue number 98  < previous residue 298 
Skipped atom 820 because residue number 99  < previous residue 298 
Skipped atom 821 because residue number 99  < previous residue 298 
Skipped atom 822 because residue number 99  < previous residue 298 
Skipped atom 823 because residue number 99  < previous residue 298 
Skipped atom 824 because residue number 99  < previous residue 298 
Skipped atom 825 because residue number 99  < previous residue 298 
Skipped atom 826 because residue number 99  < previous residue 298 
Skipped atom 827 because residue number 99  < previous residue 298 
Skipped atom 828 because residue number 99  < previous residue 298 
Skipped atom 829 because residue number 100  < previous residue 298 
Skipped atom 830 because residue number 100  < previous residue 298 
Skipped atom 831 because residue number 100  < previous residue 298 
Skipped atom 832 because residue number 100  < previous residue 298 
Skipped atom 833 because residue number 100  < previous residue 298 
Skipped atom 834 because residue number 100  < previous residue 298 
Skipped atom 835 because residue number 100  < previous residue 298 
Skipped atom 836 because residue number 100  < previous residue 298 
Skipped atom 837 because residue number 101  < previous residue 298 
Skipped atom 838 because residue number 101  < previous residue 298 
Skipped atom 839 because residue number 101  < previous residue 298 
Skipped atom 840 because residue number 101  < previous residue 298 
Skipped atom 841 because residue number 101  < previous residue 298 
Skipped atom 842 because residue number 101  < previous residue 298 
Skipped atom 843 because residue number 101  < previous residue 298 
Skipped atom 844 because residue number 101  < previous residue 298 
Skipped atom 845 because residue number 102  < previous residue 298 
Skipped atom 846 because residue number 102  < previous residue 298 
Skipped atom 847 because residue number 102  < previous residue 298 
Skipped atom 848 because residue number 102  < previous residue 298 
Skipped atom 849 because residue number 102  < previous residue 298 
Skipped atom 850 because residue number 102  < previous residue 298 
Skipped atom 851 because residue number 102  < previous residue 298 
Skipped atom 852 because residue number 102  < previous residue 298 
Skipped atom 853 because residue number 103  < previous residue 298 
Skipped atom 854 because residue number 103  < previous residue 298 
Skipped atom 855 because residue number 103  < previous residue 298 
Skipped atom 856 because residue number 103  < previous residue 298 
Skipped atom 857 because residue number 103  < previous residue 298 
Skipped atom 858 because residue number 103  < previous residue 298 
Skipped atom 859 because residue number 103  < previous residue 298 
Skipped atom 860 because residue number 104  < previous residue 298 
Skipped atom 861 because residue number 104  < previous residue 298 
Skipped atom 862 because residue number 104  < previous residue 298 
Skipped atom 863 because residue number 104  < previous residue 298 
Skipped atom 864 because residue number 104  < previous residue 298 
Skipped atom 865 because residue number 105  < previous residue 298 
Skipped atom 866 because residue number 105  < previous residue 298 
Skipped atom 867 because residue number 105  < previous residue 298 
Skipped atom 868 because residue number 105  < previous residue 298 
Skipped atom 869 because residue number 105  < previous residue 298 
Skipped atom 870 because residue number 105  < previous residue 298 
Skipped atom 871 because residue number 105  < previous residue 298 
Skipped atom 872 because residue number 105  < previous residue 298 
Skipped atom 873 because residue number 105  < previous residue 298 
Skipped atom 874 because residue number 105  < previous residue 298 
Skipped atom 875 because residue number 105  < previous residue 298 
Skipped atom 876 because residue number 105  < previous residue 298 
Skipped atom 877 because residue number 106  < previous residue 298 
Skipped atom 878 because residue number 106  < previous residue 298 
Skipped atom 879 because residue number 106  < previous residue 298 
Skipped atom 880 because residue number 106  < previous residue 298 
Skipped atom 881 because residue number 106  < previous residue 298 
Skipped atom 882 because residue number 106  < previous residue 298 
Skipped atom 883 because residue number 107  < previous residue 298 
Skipped atom 884 because residue number 107  < previous residue 298 
Skipped atom 885 because residue number 107  < previous residue 298 
Skipped atom 886 because residue number 107  < previous residue 298 
Skipped atom 887 because residue number 107  < previous residue 298 
Skipped atom 888 because residue number 107  < previous residue 298 
Skipped atom 889 because residue number 107  < previous residue 298 
Skipped atom 890 because residue number 108  < previous residue 298 
Skipped atom 891 because residue number 108  < previous residue 298 
Skipped atom 892 because residue number 108  < previous residue 298 
Skipped atom 893 because residue number 108  < previous residue 298 
Skipped atom 894 because residue number 108  < previous residue 298 
Skipped atom 895 because residue number 108  < previous residue 298 
Skipped atom 896 because residue number 108  < previous residue 298 
Skipped atom 897 because residue number 108  < previous residue 298 
Skipped atom 898 because residue number 109  < previous residue 298 
Skipped atom 899 because residue number 109  < previous residue 298 
Skipped atom 900 because residue number 109  < previous residue 298 
Skipped atom 901 because residue number 109  < previous residue 298 
Skipped atom 902 because residue number 109  < previous residue 298 
Skipped atom 903 because residue number 109  < previous residue 298 
Skipped atom 904 because residue number 109  < previous residue 298 
Skipped atom 905 because residue number 109  < previous residue 298 
Skipped atom 906 because residue number 110  < previous residue 298 
Skipped atom 907 because residue number 110  < previous residue 298 
Skipped atom 908 because residue number 110  < previous residue 298 
Skipped atom 909 because residue number 110  < previous residue 298 
Skipped atom 910 because residue number 110  < previous residue 298 
Skipped atom 911 because residue number 110  < previous residue 298 
Skipped atom 912 because residue number 110  < previous residue 298 
Skipped atom 913 because residue number 110  < previous residue 298 
Skipped atom 914 because residue number 110  < previous residue 298 
Skipped atom 915 because residue number 111  < previous residue 298 
Skipped atom 916 because residue number 111  < previous residue 298 
Skipped atom 917 because residue number 111  < previous residue 298 
Skipped atom 918 because residue number 111  < previous residue 298 
Skipped atom 919 because residue number 111  < previous residue 298 
Skipped atom 920 because residue number 111  < previous residue 298 
Skipped atom 921 because residue number 111  < previous residue 298 
Skipped atom 922 because residue number 111  < previous residue 298 
Skipped atom 923 because residue number 111  < previous residue 298 
Skipped atom 924 because residue number 112  < previous residue 298 
Skipped atom 925 because residue number 112  < previous residue 298 
Skipped atom 926 because residue number 112  < previous residue 298 
Skipped atom 927 because residue number 112  < previous residue 298 
Skipped atom 928 because residue number 112  < previous residue 298 
Skipped atom 929 because residue number 112  < previous residue 298 
Skipped atom 930 because residue number 112  < previous residue 298 
Skipped atom 931 because residue number 112  < previous residue 298 
Skipped atom 932 because residue number 112  < previous residue 298 
Skipped atom 933 because residue number 112  < previous residue 298 
Skipped atom 934 because residue number 112  < previous residue 298 
Skipped atom 935 because residue number 112  < previous residue 298 
Skipped atom 936 because residue number 113  < previous residue 298 
Skipped atom 937 because residue number 113  < previous residue 298 
Skipped atom 938 because residue number 113  < previous residue 298 
Skipped atom 939 because residue number 113  < previous residue 298 
Skipped atom 940 because residue number 113  < previous residue 298 
Skipped atom 941 because residue number 113  < previous residue 298 
Skipped atom 942 because residue number 113  < previous residue 298 
Skipped atom 943 because residue number 114  < previous residue 298 
Skipped atom 944 because residue number 114  < previous residue 298 
Skipped atom 945 because residue number 114  < previous residue 298 
Skipped atom 946 because residue number 114  < previous residue 298 
Skipped atom 947 because residue number 115  < previous residue 298 
Skipped atom 948 because residue number 115  < previous residue 298 
Skipped atom 949 because residue number 115  < previous residue 298 
Skipped atom 950 because residue number 115  < previous residue 298 
Skipped atom 951 because residue number 115  < previous residue 298 
Skipped atom 952 because residue number 115  < previous residue 298 
Skipped atom 953 because residue number 115  < previous residue 298 
Skipped atom 954 because residue number 115  < previous residue 298 
Skipped atom 955 because residue number 115  < previous residue 298 
Skipped atom 956 because residue number 116  < previous residue 298 
Skipped atom 957 because residue number 116  < previous residue 298 
Skipped atom 958 because residue number 116  < previous residue 298 
Skipped atom 959 because residue number 116  < previous residue 298 
Skipped atom 960 because residue number 116  < previous residue 298 
Skipped atom 961 because residue number 116  < previous residue 298 
Skipped atom 962 because residue number 116  < previous residue 298 
Skipped atom 963 because residue number 116  < previous residue 298 
Skipped atom 964 because residue number 117  < previous residue 298 
Skipped atom 965 because residue number 117  < previous residue 298 
Skipped atom 966 because residue number 117  < previous residue 298 
Skipped atom 967 because residue number 117  < previous residue 298 
Skipped atom 968 because residue number 117  < previous residue 298 
Skipped atom 969 because residue number 117  < previous residue 298 
Skipped atom 970 because residue number 117  < previous residue 298 
Skipped atom 971 because residue number 117  < previous residue 298 
Skipped atom 972 because residue number 118  < previous residue 298 
Skipped atom 973 because residue number 118  < previous residue 298 
Skipped atom 974 because residue number 118  < previous residue 298 
Skipped atom 975 because residue number 118  < previous residue 298 
Skipped atom 976 because residue number 118  < previous residue 298 
Skipped atom 977 because residue number 118  < previous residue 298 
Skipped atom 978 because residue number 118  < previous residue 298 
Skipped atom 979 because residue number 119  < previous residue 298 
Skipped atom 980 because residue number 119  < previous residue 298 
Skipped atom 981 because residue number 119  < previous residue 298 
Skipped atom 982 because residue number 119  < previous residue 298 
Skipped atom 983 because residue number 119  < previous residue 298 
Skipped atom 984 because residue number 119  < previous residue 298 
Skipped atom 985 because residue number 119  < previous residue 298 
Skipped atom 986 because residue number 119  < previous residue 298 
Skipped atom 987 because residue number 120  < previous residue 298 
Skipped atom 988 because residue number 120  < previous residue 298 
Skipped atom 989 because residue number 120  < previous residue 298 
Skipped atom 990 because residue number 120  < previous residue 298 
Skipped atom 991 because residue number 120  < previous residue 298 
Skipped atom 992 because residue number 120  < previous residue 298 
Skipped atom 993 because residue number 120  < previous residue 298 
Skipped atom 994 because residue number 120  < previous residue 298 
Skipped atom 995 because residue number 120  < previous residue 298 
Skipped atom 996 because residue number 121  < previous residue 298 
Skipped atom 997 because residue number 121  < previous residue 298 
Skipped atom 998 because residue number 121  < previous residue 298 
Skipped atom 999 because residue number 121  < previous residue 298 
Skipped atom 1000 because residue number 121  < previous residue 298 
Skipped atom 1001 because residue number 122  < previous residue 298 
Skipped atom 1002 because residue number 122  < previous residue 298 
Skipped atom 1003 because residue number 122  < previous residue 298 
Skipped atom 1004 because residue number 122  < previous residue 298 
Skipped atom 1005 because residue number 122  < previous residue 298 
Skipped atom 1006 because residue number 122  < previous residue 298 
Skipped atom 1007 because residue number 122  < previous residue 298 
Skipped atom 1008 because residue number 122  < previous residue 298 
Skipped atom 1009 because residue number 123  < previous residue 298 
Skipped atom 1010 because residue number 123  < previous residue 298 
Skipped atom 1011 because residue number 123  < previous residue 298 
Skipped atom 1012 because residue number 123  < previous residue 298 
Skipped atom 1013 because residue number 123  < previous residue 298 
Skipped atom 1014 because residue number 123  < previous residue 298 
Skipped atom 1015 because residue number 123  < previous residue 298 
Skipped atom 1016 because residue number 123  < previous residue 298 
Skipped atom 1017 because residue number 124  < previous residue 298 
Skipped atom 1018 because residue number 124  < previous residue 298 
Skipped atom 1019 because residue number 124  < previous residue 298 
Skipped atom 1020 because residue number 124  < previous residue 298 
Skipped atom 1021 because residue number 124  < previous residue 298 
Skipped atom 1022 because residue number 124  < previous residue 298 
Skipped atom 1023 because residue number 124  < previous residue 298 
Skipped atom 1024 because residue number 124  < previous residue 298 
Skipped atom 1025 because residue number 124  < previous residue 298 
Skipped atom 1026 because residue number 125  < previous residue 298 
Skipped atom 1027 because residue number 125  < previous residue 298 
Skipped atom 1028 because residue number 125  < previous residue 298 
Skipped atom 1029 because residue number 125  < previous residue 298 
Skipped atom 1030 because residue number 125  < previous residue 298 
Skipped atom 1031 because residue number 126  < previous residue 298 
Skipped atom 1032 because residue number 126  < previous residue 298 
Skipped atom 1033 because residue number 126  < previous residue 298 
Skipped atom 1034 because residue number 126  < previous residue 298 
Skipped atom 1035 because residue number 126  < previous residue 298 
Skipped atom 1036 because residue number 126  < previous residue 298 
Skipped atom 1037 because residue number 127  < previous residue 298 
Skipped atom 1038 because residue number 127  < previous residue 298 
Skipped atom 1039 because residue number 127  < previous residue 298 
Skipped atom 1040 because residue number 127  < previous residue 298 
Skipped atom 1041 because residue number 127  < previous residue 298 
Skipped atom 1042 because residue number 127  < previous residue 298 
Skipped atom 1043 because residue number 127  < previous residue 298 
Skipped atom 1044 because residue number 127  < previous residue 298 
Skipped atom 1045 because residue number 128  < previous residue 298 
Skipped atom 1046 because residue number 128  < previous residue 298 
Skipped atom 1047 because residue number 128  < previous residue 298 
Skipped atom 1048 because residue number 128  < previous residue 298 
Skipped atom 1049 because residue number 128  < previous residue 298 
Skipped atom 1050 because residue number 128  < previous residue 298 
Skipped atom 1051 because residue number 128  < previous residue 298 
Skipped atom 1052 because residue number 129  < previous residue 298 
Skipped atom 1053 because residue number 129  < previous residue 298 
Skipped atom 1054 because residue number 129  < previous residue 298 
Skipped atom 1055 because residue number 129  < previous residue 298 
Skipped atom 1056 because residue number 129  < previous residue 298 
Skipped atom 1057 because residue number 129  < previous residue 298 
Skipped atom 1058 because residue number 129  < previous residue 298 
Skipped atom 1059 because residue number 129  < previous residue 298 
Skipped atom 1060 because residue number 129  < previous residue 298 
Skipped atom 1061 because residue number 129  < previous residue 298 
Skipped atom 1062 because residue number 129  < previous residue 298 
Skipped atom 1063 because residue number 129  < previous residue 298 
Skipped atom 1064 because residue number 130  < previous residue 298 
Skipped atom 1065 because residue number 130  < previous residue 298 
Skipped atom 1066 because residue number 130  < previous residue 298 
Skipped atom 1067 because residue number 130  < previous residue 298 
Skipped atom 1068 because residue number 130  < previous residue 298 
Skipped atom 1069 because residue number 130  < previous residue 298 
Skipped atom 1070 because residue number 131  < previous residue 298 
Skipped atom 1071 because residue number 131  < previous residue 298 
Skipped atom 1072 because residue number 131  < previous residue 298 
Skipped atom 1073 because residue number 131  < previous residue 298 
Skipped atom 1074 because residue number 131  < previous residue 298 
Skipped atom 1075 because residue number 131  < previous residue 298 
Skipped atom 1076 because residue number 131  < previous residue 298 
Skipped atom 1077 because residue number 131  < previous residue 298 
Skipped atom 1078 because residue number 132  < previous residue 298 
Skipped atom 1079 because residue number 132  < previous residue 298 
Skipped atom 1080 because residue number 132  < previous residue 298 
Skipped atom 1081 because residue number 132  < previous residue 298 
Skipped atom 1082 because residue number 132  < previous residue 298 
Skipped atom 1083 because residue number 132  < previous residue 298 
Skipped atom 1084 because residue number 132  < previous residue 298 
Skipped atom 1085 because residue number 132  < previous residue 298 
Skipped atom 1086 because residue number 133  < previous residue 298 
Skipped atom 1087 because residue number 133  < previous residue 298 
Skipped atom 1088 because residue number 133  < previous residue 298 
Skipped atom 1089 because residue number 133  < previous residue 298 
Skipped atom 1090 because residue number 133  < previous residue 298 
Skipped atom 1091 because residue number 133  < previous residue 298 
Skipped atom 1092 because residue number 133  < previous residue 298 
Skipped atom 1093 because residue number 134  < previous residue 298 
Skipped atom 1094 because residue number 134  < previous residue 298 
Skipped atom 1095 because residue number 134  < previous residue 298 
Skipped atom 1096 because residue number 134  < previous residue 298 
Skipped atom 1097 because residue number 134  < previous residue 298 
Skipped atom 1098 because residue number 135  < previous residue 298 
Skipped atom 1099 because residue number 135  < previous residue 298 
Skipped atom 1100 because residue number 135  < previous residue 298 
Skipped atom 1101 because residue number 135  < previous residue 298 
Skipped atom 1102 because residue number 135  < previous residue 298 
Skipped atom 1103 because residue number 135  < previous residue 298 
Skipped atom 1104 because residue number 135  < previous residue 298 
Skipped atom 1105 because residue number 135  < previous residue 298 
Skipped atom 1106 because residue number 136  < previous residue 298 
Skipped atom 1107 because residue number 136  < previous residue 298 
Skipped atom 1108 because residue number 136  < previous residue 298 
Skipped atom 1109 because residue number 136  < previous residue 298 
Skipped atom 1110 because residue number 136  < previous residue 298 
Skipped atom 1111 because residue number 136  < previous residue 298 
Skipped atom 1112 because residue number 136  < previous residue 298 
Skipped atom 1113 because residue number 136  < previous residue 298 
Skipped atom 1114 because residue number 137  < previous residue 298 
Skipped atom 1115 because residue number 137  < previous residue 298 
Skipped atom 1116 because residue number 137  < previous residue 298 
Skipped atom 1117 because residue number 137  < previous residue 298 
Skipped atom 1118 because residue number 137  < previous residue 298 
Skipped atom 1119 because residue number 137  < previous residue 298 
Skipped atom 1120 because residue number 137  < previous residue 298 
Skipped atom 1121 because residue number 137  < previous residue 298 
Skipped atom 1122 because residue number 137  < previous residue 298 
Skipped atom 1123 because residue number 138  < previous residue 298 
Skipped atom 1124 because residue number 138  < previous residue 298 
Skipped atom 1125 because residue number 138  < previous residue 298 
Skipped atom 1126 because residue number 138  < previous residue 298 
Skipped atom 1127 because residue number 138  < previous residue 298 
Skipped atom 1128 because residue number 138  < previous residue 298 
Skipped atom 1129 because residue number 138  < previous residue 298 
Skipped atom 1130 because residue number 138  < previous residue 298 
Skipped atom 1131 because residue number 139  < previous residue 298 
Skipped atom 1132 because residue number 139  < previous residue 298 
Skipped atom 1133 because residue number 139  < previous residue 298 
Skipped atom 1134 because residue number 139  < previous residue 298 
Skipped atom 1135 because residue number 139  < previous residue 298 
Skipped atom 1136 because residue number 139  < previous residue 298 
Skipped atom 1137 because residue number 139  < previous residue 298 
Skipped atom 1138 because residue number 139  < previous residue 298 
Skipped atom 1139 because residue number 140  < previous residue 298 
Skipped atom 1140 because residue number 140  < previous residue 298 
Skipped atom 1141 because residue number 140  < previous residue 298 
Skipped atom 1142 because residue number 140  < previous residue 298 
Skipped atom 1143 because residue number 140  < previous residue 298 
Skipped atom 1144 because residue number 140  < previous residue 298 
Skipped atom 1145 because residue number 140  < previous residue 298 
Skipped atom 1146 because residue number 140  < previous residue 298 
Skipped atom 1147 because residue number 140  < previous residue 298 
Skipped atom 1148 because residue number 141  < previous residue 298 
Skipped atom 1149 because residue number 141  < previous residue 298 
Skipped atom 1150 because residue number 141  < previous residue 298 
Skipped atom 1151 because residue number 141  < previous residue 298 
Skipped atom 1152 because residue number 141  < previous residue 298 
Skipped atom 1153 because residue number 141  < previous residue 298 
Skipped atom 1154 because residue number 141  < previous residue 298 
Skipped atom 1155 because residue number 141  < previous residue 298 
Skipped atom 1156 because residue number 141  < previous residue 298 
Skipped atom 1157 because residue number 142  < previous residue 298 
Skipped atom 1158 because residue number 142  < previous residue 298 
Skipped atom 1159 because residue number 142  < previous residue 298 
Skipped atom 1160 because residue number 142  < previous residue 298 
Skipped atom 1161 because residue number 142  < previous residue 298 
Skipped atom 1162 because residue number 142  < previous residue 298 
Skipped atom 1163 because residue number 142  < previous residue 298 
Skipped atom 1164 because residue number 142  < previous residue 298 
Skipped atom 1165 because residue number 143  < previous residue 298 
Skipped atom 1166 because residue number 143  < previous residue 298 
Skipped atom 1167 because residue number 143  < previous residue 298 
Skipped atom 1168 because residue number 143  < previous residue 298 
Skipped atom 1169 because residue number 144  < previous residue 298 
Skipped atom 1170 because residue number 144  < previous residue 298 
Skipped atom 1171 because residue number 144  < previous residue 298 
Skipped atom 1172 because residue number 144  < previous residue 298 
Skipped atom 1173 because residue number 145  < previous residue 298 
Skipped atom 1174 because residue number 145  < previous residue 298 
Skipped atom 1175 because residue number 145  < previous residue 298 
Skipped atom 1176 because residue number 145  < previous residue 298 
Skipped atom 1177 because residue number 145  < previous residue 298 
Skipped atom 1178 because residue number 145  < previous residue 298 
Skipped atom 1179 because residue number 145  < previous residue 298 
Skipped atom 1180 because residue number 145  < previous residue 298 
Skipped atom 1181 because residue number 146  < previous residue 298 
Skipped atom 1182 because residue number 146  < previous residue 298 
Skipped atom 1183 because residue number 146  < previous residue 298 
Skipped atom 1184 because residue number 146  < previous residue 298 
Skipped atom 1185 because residue number 146  < previous residue 298 
Skipped atom 1186 because residue number 146  < previous residue 298 
Skipped atom 1187 because residue number 146  < previous residue 298 
Skipped atom 1188 because residue number 146  < previous residue 298 
Skipped atom 1189 because residue number 146  < previous residue 298 
Skipped atom 1190 because residue number 147  < previous residue 298 
Skipped atom 1191 because residue number 147  < previous residue 298 
Skipped atom 1192 because residue number 147  < previous residue 298 
Skipped atom 1193 because residue number 147  < previous residue 298 
Skipped atom 1194 because residue number 147  < previous residue 298 
Skipped atom 1195 because residue number 147  < previous residue 298 
Skipped atom 1196 because residue number 147  < previous residue 298 
Skipped atom 1197 because residue number 147  < previous residue 298 
Skipped atom 1198 because residue number 147  < previous residue 298 
Skipped atom 1199 because residue number 148  < previous residue 298 
Skipped atom 1200 because residue number 148  < previous residue 298 
Skipped atom 1201 because residue number 148  < previous residue 298 
Skipped atom 1202 because residue number 148  < previous residue 298 
Skipped atom 1203 because residue number 148  < previous residue 298 
Skipped atom 1204 because residue number 148  < previous residue 298 
Skipped atom 1205 because residue number 148  < previous residue 298 
Skipped atom 1206 because residue number 149  < previous residue 298 
Skipped atom 1207 because residue number 149  < previous residue 298 
Skipped atom 1208 because residue number 149  < previous residue 298 
Skipped atom 1209 because residue number 149  < previous residue 298 
Skipped atom 1210 because residue number 149  < previous residue 298 
Skipped atom 1211 because residue number 149  < previous residue 298 
Skipped atom 1212 because residue number 149  < previous residue 298 
Skipped atom 1213 because residue number 149  < previous residue 298 
Skipped atom 1214 because residue number 149  < previous residue 298 
Skipped atom 1215 because residue number 150  < previous residue 298 
Skipped atom 1216 because residue number 150  < previous residue 298 
Skipped atom 1217 because residue number 150  < previous residue 298 
Skipped atom 1218 because residue number 150  < previous residue 298 
Skipped atom 1219 because residue number 150  < previous residue 298 
Skipped atom 1220 because residue number 150  < previous residue 298 
Skipped atom 1221 because residue number 150  < previous residue 298 
Skipped atom 1222 because residue number 150  < previous residue 298 
Skipped atom 1223 because residue number 150  < previous residue 298 
Skipped atom 1224 because residue number 151  < previous residue 298 
Skipped atom 1225 because residue number 151  < previous residue 298 
Skipped atom 1226 because residue number 151  < previous residue 298 
Skipped atom 1227 because residue number 151  < previous residue 298 
Skipped atom 1228 because residue number 151  < previous residue 298 
Skipped atom 1229 because residue number 151  < previous residue 298 
Skipped atom 1230 because residue number 151  < previous residue 298 
Skipped atom 1231 because residue number 151  < previous residue 298 
Skipped atom 1232 because residue number 151  < previous residue 298 
Skipped atom 1233 because residue number 151  < previous residue 298 
Skipped atom 1234 because residue number 151  < previous residue 298 
Skipped atom 1235 because residue number 152  < previous residue 298 
Skipped atom 1236 because residue number 152  < previous residue 298 
Skipped atom 1237 because residue number 152  < previous residue 298 
Skipped atom 1238 because residue number 152  < previous residue 298 
Skipped atom 1239 because residue number 152  < previous residue 298 
Skipped atom 1240 because residue number 152  < previous residue 298 
Skipped atom 1241 because residue number 152  < previous residue 298 
Skipped atom 1242 because residue number 152  < previous residue 298 
Skipped atom 1243 because residue number 153  < previous residue 298 
Skipped atom 1244 because residue number 153  < previous residue 298 
Skipped atom 1245 because residue number 153  < previous residue 298 
Skipped atom 1246 because residue number 153  < previous residue 298 
Skipped atom 1247 because residue number 153  < previous residue 298 
Skipped atom 1248 because residue number 153  < previous residue 298 
Skipped atom 1249 because residue number 153  < previous residue 298 
Skipped atom 1250 because residue number 153  < previous residue 298 
Skipped atom 1251 because residue number 153  < previous residue 298 
Skipped atom 1252 because residue number 154  < previous residue 298 
Skipped atom 1253 because residue number 154  < previous residue 298 
Skipped atom 1254 because residue number 154  < previous residue 298 
Skipped atom 1255 because residue number 154  < previous residue 298 
Skipped atom 1256 because residue number 154  < previous residue 298 
Skipped atom 1257 because residue number 154  < previous residue 298 
Skipped atom 1258 because residue number 154  < previous residue 298 
Skipped atom 1259 because residue number 154  < previous residue 298 
Skipped atom 1260 because residue number 154  < previous residue 298 
Skipped atom 1261 because residue number 155  < previous residue 298 
Skipped atom 1262 because residue number 155  < previous residue 298 
Skipped atom 1263 because residue number 155  < previous residue 298 
Skipped atom 1264 because residue number 155  < previous residue 298 
Skipped atom 1265 because residue number 155  < previous residue 298 
Skipped atom 1266 because residue number 155  < previous residue 298 
Skipped atom 1267 because residue number 155  < previous residue 298 
Skipped atom 1268 because residue number 155  < previous residue 298 
Skipped atom 1269 because residue number 156  < previous residue 298 
Skipped atom 1270 because residue number 156  < previous residue 298 
Skipped atom 1271 because residue number 156  < previous residue 298 
Skipped atom 1272 because residue number 156  < previous residue 298 
Skipped atom 1273 because residue number 157  < previous residue 298 
Skipped atom 1274 because residue number 157  < previous residue 298 
Skipped atom 1275 because residue number 157  < previous residue 298 
Skipped atom 1276 because residue number 157  < previous residue 298 
Skipped atom 1277 because residue number 157  < previous residue 298 
Skipped atom 1278 because residue number 157  < previous residue 298 
Skipped atom 1279 because residue number 157  < previous residue 298 
Skipped atom 1280 because residue number 157  < previous residue 298 
Skipped atom 1281 because residue number 158  < previous residue 298 
Skipped atom 1282 because residue number 158  < previous residue 298 
Skipped atom 1283 because residue number 158  < previous residue 298 
Skipped atom 1284 because residue number 158  < previous residue 298 
Skipped atom 1285 because residue number 158  < previous residue 298 
Skipped atom 1286 because residue number 158  < previous residue 298 
Skipped atom 1287 because residue number 158  < previous residue 298 
Skipped atom 1288 because residue number 158  < previous residue 298 
Skipped atom 1289 because residue number 158  < previous residue 298 
Skipped atom 1290 because residue number 159  < previous residue 298 
Skipped atom 1291 because residue number 159  < previous residue 298 
Skipped atom 1292 because residue number 159  < previous residue 298 
Skipped atom 1293 because residue number 159  < previous residue 298 
Skipped atom 1294 because residue number 159  < previous residue 298 
Skipped atom 1295 because residue number 159  < previous residue 298 
Skipped atom 1296 because residue number 159  < previous residue 298 
Skipped atom 1297 because residue number 160  < previous residue 298 
Skipped atom 1298 because residue number 160  < previous residue 298 
Skipped atom 1299 because residue number 160  < previous residue 298 
Skipped atom 1300 because residue number 160  < previous residue 298 
Skipped atom 1301 because residue number 160  < previous residue 298 
Skipped atom 1302 because residue number 160  < previous residue 298 
Skipped atom 1303 because residue number 160  < previous residue 298 
Skipped atom 1304 because residue number 161  < previous residue 298 
Skipped atom 1305 because residue number 161  < previous residue 298 
Skipped atom 1306 because residue number 161  < previous residue 298 
Skipped atom 1307 because residue number 161  < previous residue 298 
Skipped atom 1308 because residue number 161  < previous residue 298 
Skipped atom 1309 because residue number 161  < previous residue 298 
Skipped atom 1310 because residue number 161  < previous residue 298 
Skipped atom 1311 because residue number 161  < previous residue 298 
Skipped atom 1312 because residue number 162  < previous residue 298 
Skipped atom 1313 because residue number 162  < previous residue 298 
Skipped atom 1314 because residue number 162  < previous residue 298 
Skipped atom 1315 because residue number 162  < previous residue 298 
Skipped atom 1316 because residue number 162  < previous residue 298 
Skipped atom 1317 because residue number 162  < previous residue 298 
Skipped atom 1318 because residue number 162  < previous residue 298 
Skipped atom 1319 because residue number 163  < previous residue 298 
Skipped atom 1320 because residue number 163  < previous residue 298 
Skipped atom 1321 because residue number 163  < previous residue 298 
Skipped atom 1322 because residue number 163  < previous residue 298 
Skipped atom 1323 because residue number 163  < previous residue 298 
Skipped atom 1324 because residue number 163  < previous residue 298 
Skipped atom 1325 because residue number 163  < previous residue 298 
Skipped atom 1326 because residue number 164  < previous residue 298 
Skipped atom 1327 because residue number 164  < previous residue 298 
Skipped atom 1328 because residue number 164  < previous residue 298 
Skipped atom 1329 because residue number 164  < previous residue 298 
Skipped atom 1330 because residue number 164  < previous residue 298 
Skipped atom 1331 because residue number 164  < previous residue 298 
Skipped atom 1332 because residue number 164  < previous residue 298 
Skipped atom 1333 because residue number 164  < previous residue 298 
Skipped atom 1334 because residue number 164  < previous residue 298 
Skipped atom 1335 because residue number 164  < previous residue 298 
Skipped atom 1336 because residue number 164  < previous residue 298 
Skipped atom 1337 because residue number 165  < previous residue 298 
Skipped atom 1338 because residue number 165  < previous residue 298 
Skipped atom 1339 because residue number 165  < previous residue 298 
Skipped atom 1340 because residue number 165  < previous residue 298 
Skipped atom 1341 because residue number 165  < previous residue 298 
Skipped atom 1342 because residue number 165  < previous residue 298 
Skipped atom 1343 because residue number 165  < previous residue 298 
Skipped atom 1344 because residue number 165  < previous residue 298 
Skipped atom 1345 because residue number 165  < previous residue 298 
Skipped atom 1346 because residue number 165  < previous residue 298 
Skipped atom 1347 because residue number 165  < previous residue 298 
Skipped atom 1348 because residue number 165  < previous residue 298 
Skipped atom 1349 because residue number 166  < previous residue 298 
Skipped atom 1350 because residue number 166  < previous residue 298 
Skipped atom 1351 because residue number 166  < previous residue 298 
Skipped atom 1352 because residue number 166  < previous residue 298 
Skipped atom 1353 because residue number 166  < previous residue 298 
Skipped atom 1354 because residue number 166  < previous residue 298 
Skipped atom 1355 because residue number 166  < previous residue 298 
Skipped atom 1356 because residue number 166  < previous residue 298 
Skipped atom 1357 because residue number 166  < previous residue 298 
Skipped atom 1358 because residue number 167  < previous residue 298 
Skipped atom 1359 because residue number 167  < previous residue 298 
Skipped atom 1360 because residue number 167  < previous residue 298 
Skipped atom 1361 because residue number 167  < previous residue 298 
Skipped atom 1362 because residue number 167  < previous residue 298 
Skipped atom 1363 because residue number 167  < previous residue 298 
Skipped atom 1364 because residue number 167  < previous residue 298 
Skipped atom 1365 because residue number 167  < previous residue 298 
Skipped atom 1366 because residue number 168  < previous residue 298 
Skipped atom 1367 because residue number 168  < previous residue 298 
Skipped atom 1368 because residue number 168  < previous residue 298 
Skipped atom 1369 because residue number 168  < previous residue 298 
Skipped atom 1370 because residue number 168  < previous residue 298 
Skipped atom 1371 because residue number 168  < previous residue 298 
Skipped atom 1372 because residue number 168  < previous residue 298 
Skipped atom 1373 because residue number 168  < previous residue 298 
Skipped atom 1374 because residue number 168  < previous residue 298 
Skipped atom 1375 because residue number 169  < previous residue 298 
Skipped atom 1376 because residue number 169  < previous residue 298 
Skipped atom 1377 because residue number 169  < previous residue 298 
Skipped atom 1378 because residue number 169  < previous residue 298 
Skipped atom 1379 because residue number 169  < previous residue 298 
Skipped atom 1380 because residue number 169  < previous residue 298 
Skipped atom 1381 because residue number 169  < previous residue 298 
Skipped atom 1382 because residue number 169  < previous residue 298 
Skipped atom 1383 because residue number 170  < previous residue 298 
Skipped atom 1384 because residue number 170  < previous residue 298 
Skipped atom 1385 because residue number 170  < previous residue 298 
Skipped atom 1386 because residue number 170  < previous residue 298 
Skipped atom 1387 because residue number 170  < previous residue 298 
Skipped atom 1388 because residue number 170  < previous residue 298 
Skipped atom 1389 because residue number 170  < previous residue 298 
Skipped atom 1390 because residue number 170  < previous residue 298 
Skipped atom 1391 because residue number 171  < previous residue 298 
Skipped atom 1392 because residue number 171  < previous residue 298 
Skipped atom 1393 because residue number 171  < previous residue 298 
Skipped atom 1394 because residue number 171  < previous residue 298 
Skipped atom 1395 because residue number 171  < previous residue 298 
Skipped atom 1396 because residue number 171  < previous residue 298 
Skipped atom 1397 because residue number 171  < previous residue 298 
Skipped atom 1398 because residue number 171  < previous residue 298 
Skipped atom 1399 because residue number 171  < previous residue 298 
Skipped atom 1400 because residue number 171  < previous residue 298 
Skipped atom 1401 because residue number 171  < previous residue 298 
Skipped atom 1402 because residue number 171  < previous residue 298 
Skipped atom 1403 because residue number 172  < previous residue 298 
Skipped atom 1404 because residue number 172  < previous residue 298 
Skipped atom 1405 because residue number 172  < previous residue 298 
Skipped atom 1406 because residue number 172  < previous residue 298 
Skipped atom 1407 because residue number 172  < previous residue 298 
Skipped atom 1408 because residue number 172  < previous residue 298 
Skipped atom 1409 because residue number 172  < previous residue 298 
Skipped atom 1410 because residue number 172  < previous residue 298 
Skipped atom 1411 because residue number 172  < previous residue 298 
Skipped atom 1412 because residue number 172  < previous residue 298 
Skipped atom 1413 because residue number 172  < previous residue 298 
Skipped atom 1414 because residue number 172  < previous residue 298 
Skipped atom 1415 because residue number 173  < previous residue 298 
Skipped atom 1416 because residue number 173  < previous residue 298 
Skipped atom 1417 because residue number 173  < previous residue 298 
Skipped atom 1418 because residue number 173  < previous residue 298 
Skipped atom 1419 because residue number 173  < previous residue 298 
Skipped atom 1420 because residue number 173  < previous residue 298 
Skipped atom 1421 because residue number 174  < previous residue 298 
Skipped atom 1422 because residue number 174  < previous residue 298 
Skipped atom 1423 because residue number 174  < previous residue 298 
Skipped atom 1424 because residue number 174  < previous residue 298 
Skipped atom 1425 because residue number 174  < previous residue 298 
Skipped atom 1426 because residue number 174  < previous residue 298 
Skipped atom 1427 because residue number 174  < previous residue 298 
Skipped atom 1428 because residue number 175  < previous residue 298 
Skipped atom 1429 because residue number 175  < previous residue 298 
Skipped atom 1430 because residue number 175  < previous residue 298 
Skipped atom 1431 because residue number 175  < previous residue 298 
Skipped atom 1432 because residue number 175  < previous residue 298 
Skipped atom 1433 because residue number 175  < previous residue 298 
Skipped atom 1434 because residue number 175  < previous residue 298 
Skipped atom 1435 because residue number 175  < previous residue 298 
Skipped atom 1436 because residue number 175  < previous residue 298 
Skipped atom 1437 because residue number 176  < previous residue 298 
Skipped atom 1438 because residue number 176  < previous residue 298 
Skipped atom 1439 because residue number 176  < previous residue 298 
Skipped atom 1440 because residue number 176  < previous residue 298 
Skipped atom 1441 because residue number 176  < previous residue 298 
Skipped atom 1442 because residue number 176  < previous residue 298 
Skipped atom 1443 because residue number 177  < previous residue 298 
Skipped atom 1444 because residue number 177  < previous residue 298 
Skipped atom 1445 because residue number 177  < previous residue 298 
Skipped atom 1446 because residue number 177  < previous residue 298 
Skipped atom 1447 because residue number 177  < previous residue 298 
Skipped atom 1448 because residue number 177  < previous residue 298 
Skipped atom 1449 because residue number 177  < previous residue 298 
Skipped atom 1450 because residue number 177  < previous residue 298 
Skipped atom 1451 because residue number 177  < previous residue 298 
Skipped atom 1452 because residue number 178  < previous residue 298 
Skipped atom 1453 because residue number 178  < previous residue 298 
Skipped atom 1454 because residue number 178  < previous residue 298 
Skipped atom 1455 because residue number 178  < previous residue 298 
Skipped atom 1456 because residue number 178  < previous residue 298 
Skipped atom 1457 because residue number 178  < previous residue 298 
Skipped atom 1458 because residue number 178  < previous residue 298 
Skipped atom 1459 because residue number 178  < previous residue 298 
Skipped atom 1460 because residue number 178  < previous residue 298 
Skipped atom 1461 because residue number 179  < previous residue 298 
Skipped atom 1462 because residue number 179  < previous residue 298 
Skipped atom 1463 because residue number 179  < previous residue 298 
Skipped atom 1464 because residue number 179  < previous residue 298 
Skipped atom 1465 because residue number 179  < previous residue 298 
Skipped atom 1466 because residue number 179  < previous residue 298 
Skipped atom 1467 because residue number 179  < previous residue 298 
Skipped atom 1468 because residue number 179  < previous residue 298 
Skipped atom 1469 because residue number 180  < previous residue 298 
Skipped atom 1470 because residue number 180  < previous residue 298 
Skipped atom 1471 because residue number 180  < previous residue 298 
Skipped atom 1472 because residue number 180  < previous residue 298 
Skipped atom 1473 because residue number 180  < previous residue 298 
Skipped atom 1474 because residue number 180  < previous residue 298 
Skipped atom 1475 because residue number 180  < previous residue 298 
Skipped atom 1476 because residue number 181  < previous residue 298 
Skipped atom 1477 because residue number 181  < previous residue 298 
Skipped atom 1478 because residue number 181  < previous residue 298 
Skipped atom 1479 because residue number 181  < previous residue 298 
Skipped atom 1480 because residue number 181  < previous residue 298 
Skipped atom 1481 because residue number 181  < previous residue 298 
Skipped atom 1482 because residue number 182  < previous residue 298 
Skipped atom 1483 because residue number 182  < previous residue 298 
Skipped atom 1484 because residue number 182  < previous residue 298 
Skipped atom 1485 because residue number 182  < previous residue 298 
Skipped atom 1486 because residue number 182  < previous residue 298 
Skipped atom 1487 because residue number 182  < previous residue 298 
Skipped atom 1488 because residue number 182  < previous residue 298 
Skipped atom 1489 because residue number 183  < previous residue 298 
Skipped atom 1490 because residue number 183  < previous residue 298 
Skipped atom 1491 because residue number 183  < previous residue 298 
Skipped atom 1492 because residue number 183  < previous residue 298 
Skipped atom 1493 because residue number 183  < previous residue 298 
Skipped atom 1494 because residue number 183  < previous residue 298 
Skipped atom 1495 because residue number 183  < previous residue 298 
Skipped atom 1496 because residue number 184  < previous residue 298 
Skipped atom 1497 because residue number 184  < previous residue 298 
Skipped atom 1498 because residue number 184  < previous residue 298 
Skipped atom 1499 because residue number 184  < previous residue 298 
Skipped atom 1500 because residue number 184  < previous residue 298 
Skipped atom 1501 because residue number 185  < previous residue 298 
Skipped atom 1502 because residue number 185  < previous residue 298 
Skipped atom 1503 because residue number 185  < previous residue 298 
Skipped atom 1504 because residue number 185  < previous residue 298 
Skipped atom 1505 because residue number 185  < previous residue 298 
Skipped atom 1506 because residue number 186  < previous residue 298 
Skipped atom 1507 because residue number 186  < previous residue 298 
Skipped atom 1508 because residue number 186  < previous residue 298 
Skipped atom 1509 because residue number 186  < previous residue 298 
Skipped atom 1510 because residue number 186  < previous residue 298 
Skipped atom 1511 because residue number 186  < previous residue 298 
Skipped atom 1512 because residue number 186  < previous residue 298 
Skipped atom 1513 because residue number 186  < previous residue 298 
Skipped atom 1514 because residue number 186  < previous residue 298 
Skipped atom 1515 because residue number 186  < previous residue 298 
Skipped atom 1516 because residue number 186  < previous residue 298 
Skipped atom 1517 because residue number 187  < previous residue 298 
Skipped atom 1518 because residue number 187  < previous residue 298 
Skipped atom 1519 because residue number 187  < previous residue 298 
Skipped atom 1520 because residue number 187  < previous residue 298 
Skipped atom 1521 because residue number 188  < previous residue 298 
Skipped atom 1522 because residue number 188  < previous residue 298 
Skipped atom 1523 because residue number 188  < previous residue 298 
Skipped atom 1524 because residue number 188  < previous residue 298 
Skipped atom 1525 because residue number 188  < previous residue 298 
Skipped atom 1526 because residue number 188  < previous residue 298 
Skipped atom 1527 because residue number 188  < previous residue 298 
Skipped atom 1528 because residue number 188  < previous residue 298 
Skipped atom 1529 because residue number 188  < previous residue 298 
Skipped atom 1530 because residue number 189  < previous residue 298 
Skipped atom 1531 because residue number 189  < previous residue 298 
Skipped atom 1532 because residue number 189  < previous residue 298 
Skipped atom 1533 because residue number 189  < previous residue 298 
Skipped atom 1534 because residue number 189  < previous residue 298 
Skipped atom 1535 because residue number 189  < previous residue 298 
Skipped atom 1536 because residue number 189  < previous residue 298 
Skipped atom 1537 because residue number 190  < previous residue 298 
Skipped atom 1538 because residue number 190  < previous residue 298 
Skipped atom 1539 because residue number 190  < previous residue 298 
Skipped atom 1540 because residue number 190  < previous residue 298 
Skipped atom 1541 because residue number 190  < previous residue 298 
Skipped atom 1542 because residue number 190  < previous residue 298 
Skipped atom 1543 because residue number 190  < previous residue 298 
Skipped atom 1544 because residue number 190  < previous residue 298 
Skipped atom 1545 because residue number 191  < previous residue 298 
Skipped atom 1546 because residue number 191  < previous residue 298 
Skipped atom 1547 because residue number 191  < previous residue 298 
Skipped atom 1548 because residue number 191  < previous residue 298 
Skipped atom 1549 because residue number 191  < previous residue 298 
Skipped atom 1550 because residue number 191  < previous residue 298 
Skipped atom 1551 because residue number 191  < previous residue 298 
Skipped atom 1552 because residue number 191  < previous residue 298 
Skipped atom 1553 because residue number 192  < previous residue 298 
Skipped atom 1554 because residue number 192  < previous residue 298 
Skipped atom 1555 because residue number 192  < previous residue 298 
Skipped atom 1556 because residue number 192  < previous residue 298 
Skipped atom 1557 because residue number 192  < previous residue 298 
Skipped atom 1558 because residue number 192  < previous residue 298 
Skipped atom 1559 because residue number 192  < previous residue 298 
Skipped atom 1560 because residue number 192  < previous residue 298 
Skipped atom 1561 because residue number 192  < previous residue 298 
Skipped atom 1562 because residue number 193  < previous residue 298 
Skipped atom 1563 because residue number 193  < previous residue 298 
Skipped atom 1564 because residue number 193  < previous residue 298 
Skipped atom 1565 because residue number 193  < previous residue 298 
Skipped atom 1566 because residue number 193  < previous residue 298 
Skipped atom 1567 because residue number 193  < previous residue 298 
Skipped atom 1568 because residue number 193  < previous residue 298 
Skipped atom 1569 because residue number 193  < previous residue 298 
Skipped atom 1570 because residue number 194  < previous residue 298 
Skipped atom 1571 because residue number 194  < previous residue 298 
Skipped atom 1572 because residue number 194  < previous residue 298 
Skipped atom 1573 because residue number 194  < previous residue 298 
Skipped atom 1574 because residue number 194  < previous residue 298 
Skipped atom 1575 because residue number 194  < previous residue 298 
Skipped atom 1576 because residue number 194  < previous residue 298 
Skipped atom 1577 because residue number 194  < previous residue 298 
Skipped atom 1578 because residue number 195  < previous residue 298 
Skipped atom 1579 because residue number 195  < previous residue 298 
Skipped atom 1580 because residue number 195  < previous residue 298 
Skipped atom 1581 because residue number 195  < previous residue 298 
Skipped atom 1582 because residue number 195  < previous residue 298 
Skipped atom 1583 because residue number 196  < previous residue 298 
Skipped atom 1584 because residue number 196  < previous residue 298 
Skipped atom 1585 because residue number 196  < previous residue 298 
Skipped atom 1586 because residue number 196  < previous residue 298 
Skipped atom 1587 because residue number 196  < previous residue 298 
Skipped atom 1588 because residue number 196  < previous residue 298 
Skipped atom 1589 because residue number 196  < previous residue 298 
Skipped atom 1590 because residue number 196  < previous residue 298 
Skipped atom 1591 because residue number 197  < previous residue 298 
Skipped atom 1592 because residue number 197  < previous residue 298 
Skipped atom 1593 because residue number 197  < previous residue 298 
Skipped atom 1594 because residue number 197  < previous residue 298 
Skipped atom 1595 because residue number 198  < previous residue 298 
Skipped atom 1596 because residue number 198  < previous residue 298 
Skipped atom 1597 because residue number 198  < previous residue 298 
Skipped atom 1598 because residue number 198  < previous residue 298 
Skipped atom 1599 because residue number 198  < previous residue 298 
Skipped atom 1600 because residue number 198  < previous residue 298 
Skipped atom 1601 because residue number 198  < previous residue 298 
Skipped atom 1602 because residue number 198  < previous residue 298 
Skipped atom 1603 because residue number 198  < previous residue 298 
Skipped atom 1604 because residue number 199  < previous residue 298 
Skipped atom 1605 because residue number 199  < previous residue 298 
Skipped atom 1606 because residue number 199  < previous residue 298 
Skipped atom 1607 because residue number 199  < previous residue 298 
Skipped atom 1608 because residue number 199  < previous residue 298 
Skipped atom 1609 because residue number 199  < previous residue 298 
Skipped atom 1610 because residue number 199  < previous residue 298 
Skipped atom 1611 because residue number 199  < previous residue 298 
Skipped atom 1612 because residue number 200  < previous residue 298 
Skipped atom 1613 because residue number 200  < previous residue 298 
Skipped atom 1614 because residue number 200  < previous residue 298 
Skipped atom 1615 because residue number 200  < previous residue 298 
Skipped atom 1616 because residue number 200  < previous residue 298 
Skipped atom 1617 because residue number 200  < previous residue 298 
Skipped atom 1618 because residue number 201  < previous residue 298 
Skipped atom 1619 because residue number 201  < previous residue 298 
Skipped atom 1620 because residue number 201  < previous residue 298 
Skipped atom 1621 because residue number 201  < previous residue 298 
Skipped atom 1622 because residue number 201  < previous residue 298 
Skipped atom 1623 because residue number 201  < previous residue 298 
Skipped atom 1624 because residue number 201  < previous residue 298 
Skipped atom 1625 because residue number 201  < previous residue 298 
Skipped atom 1626 because residue number 201  < previous residue 298 
Skipped atom 1627 because residue number 202  < previous residue 298 
Skipped atom 1628 because residue number 202  < previous residue 298 
Skipped atom 1629 because residue number 202  < previous residue 298 
Skipped atom 1630 because residue number 202  < previous residue 298 
Skipped atom 1631 because residue number 202  < previous residue 298 
Skipped atom 1632 because residue number 202  < previous residue 298 
Skipped atom 1633 because residue number 202  < previous residue 298 
Skipped atom 1634 because residue number 202  < previous residue 298 
Skipped atom 1635 because residue number 202  < previous residue 298 
Skipped atom 1636 because residue number 203  < previous residue 298 
Skipped atom 1637 because residue number 203  < previous residue 298 
Skipped atom 1638 because residue number 203  < previous residue 298 
Skipped atom 1639 because residue number 203  < previous residue 298 
Skipped atom 1640 because residue number 203  < previous residue 298 
Skipped atom 1641 because residue number 203  < previous residue 298 
Skipped atom 1642 because residue number 203  < previous residue 298 
Skipped atom 1643 because residue number 203  < previous residue 298 
Skipped atom 1644 because residue number 204  < previous residue 298 
Skipped atom 1645 because residue number 204  < previous residue 298 
Skipped atom 1646 because residue number 204  < previous residue 298 
Skipped atom 1647 because residue number 204  < previous residue 298 
Skipped atom 1648 because residue number 204  < previous residue 298 
Skipped atom 1649 because residue number 204  < previous residue 298 
Skipped atom 1650 because residue number 204  < previous residue 298 
Skipped atom 1651 because residue number 204  < previous residue 298 
Skipped atom 1652 because residue number 204  < previous residue 298 
Skipped atom 1653 because residue number 205  < previous residue 298 
Skipped atom 1654 because residue number 205  < previous residue 298 
Skipped atom 1655 because residue number 205  < previous residue 298 
Skipped atom 1656 because residue number 205  < previous residue 298 
Skipped atom 1657 because residue number 205  < previous residue 298 
Skipped atom 1658 because residue number 205  < previous residue 298 
Skipped atom 1659 because residue number 205  < previous residue 298 
Skipped atom 1660 because residue number 205  < previous residue 298 
Skipped atom 1661 because residue number 205  < previous residue 298 
Skipped atom 1662 because residue number 206  < previous residue 298 
Skipped atom 1663 because residue number 206  < previous residue 298 
Skipped atom 1664 because residue number 206  < previous residue 298 
Skipped atom 1665 because residue number 206  < previous residue 298 
Skipped atom 1666 because residue number 206  < previous residue 298 
Skipped atom 1667 because residue number 206  < previous residue 298 
Skipped atom 1668 because residue number 206  < previous residue 298 
Skipped atom 1669 because residue number 206  < previous residue 298 
Skipped atom 1670 because residue number 206  < previous residue 298 
Skipped atom 1671 because residue number 206  < previous residue 298 
Skipped atom 1672 because residue number 206  < previous residue 298 
Skipped atom 1673 because residue number 207  < previous residue 298 
Skipped atom 1674 because residue number 207  < previous residue 298 
Skipped atom 1675 because residue number 207  < previous residue 298 
Skipped atom 1676 because residue number 207  < previous residue 298 
Skipped atom 1677 because residue number 207  < previous residue 298 
Skipped atom 1678 because residue number 207  < previous residue 298 
Skipped atom 1679 because residue number 207  < previous residue 298 
Skipped atom 1680 because residue number 207  < previous residue 298 
Skipped atom 1681 because residue number 208  < previous residue 298 
Skipped atom 1682 because residue number 208  < previous residue 298 
Skipped atom 1683 because residue number 208  < previous residue 298 
Skipped atom 1684 because residue number 208  < previous residue 298 
Skipped atom 1685 because residue number 208  < previous residue 298 
Skipped atom 1686 because residue number 208  < previous residue 298 
Skipped atom 1687 because residue number 208  < previous residue 298 
Skipped atom 1688 because residue number 208  < previous residue 298 
Skipped atom 1689 because residue number 209  < previous residue 298 
Skipped atom 1690 because residue number 209  < previous residue 298 
Skipped atom 1691 because residue number 209  < previous residue 298 
Skipped atom 1692 because residue number 209  < previous residue 298 
Skipped atom 1693 because residue number 209  < previous residue 298 
Skipped atom 1694 because residue number 209  < previous residue 298 
Skipped atom 1695 because residue number 209  < previous residue 298 
Skipped atom 1696 because residue number 209  < previous residue 298 
Skipped atom 1697 because residue number 210  < previous residue 298 
Skipped atom 1698 because residue number 210  < previous residue 298 
Skipped atom 1699 because residue number 210  < previous residue 298 
Skipped atom 1700 because residue number 210  < previous residue 298 
Skipped atom 1701 because residue number 210  < previous residue 298 
Skipped atom 1702 because residue number 210  < previous residue 298 
Skipped atom 1703 because residue number 210  < previous residue 298 
Skipped atom 1704 because residue number 210  < previous residue 298 
Skipped atom 1705 because residue number 211  < previous residue 298 
Skipped atom 1706 because residue number 211  < previous residue 298 
Skipped atom 1707 because residue number 211  < previous residue 298 
Skipped atom 1708 because residue number 211  < previous residue 298 
Skipped atom 1709 because residue number 211  < previous residue 298 
Skipped atom 1710 because residue number 211  < previous residue 298 
Skipped atom 1711 because residue number 211  < previous residue 298 
Skipped atom 1712 because residue number 211  < previous residue 298 
Skipped atom 1713 because residue number 212  < previous residue 298 
Skipped atom 1714 because residue number 212  < previous residue 298 
Skipped atom 1715 because residue number 212  < previous residue 298 
Skipped atom 1716 because residue number 212  < previous residue 298 
Skipped atom 1717 because residue number 212  < previous residue 298 
Skipped atom 1718 because residue number 212  < previous residue 298 
Skipped atom 1719 because residue number 212  < previous residue 298 
Skipped atom 1720 because residue number 212  < previous residue 298 
Skipped atom 1721 because residue number 213  < previous residue 298 
Skipped atom 1722 because residue number 213  < previous residue 298 
Skipped atom 1723 because residue number 213  < previous residue 298 
Skipped atom 1724 because residue number 213  < previous residue 298 
Skipped atom 1725 because residue number 213  < previous residue 298 
Skipped atom 1726 because residue number 213  < previous residue 298 
Skipped atom 1727 because residue number 213  < previous residue 298 
Skipped atom 1728 because residue number 213  < previous residue 298 
Skipped atom 1729 because residue number 214  < previous residue 298 
Skipped atom 1730 because residue number 214  < previous residue 298 
Skipped atom 1731 because residue number 214  < previous residue 298 
Skipped atom 1732 because residue number 214  < previous residue 298 
Skipped atom 1733 because residue number 214  < previous residue 298 
Skipped atom 1734 because residue number 214  < previous residue 298 
Skipped atom 1735 because residue number 214  < previous residue 298 
Skipped atom 1736 because residue number 214  < previous residue 298 
Skipped atom 1737 because residue number 215  < previous residue 298 
Skipped atom 1738 because residue number 215  < previous residue 298 
Skipped atom 1739 because residue number 215  < previous residue 298 
Skipped atom 1740 because residue number 215  < previous residue 298 
Skipped atom 1741 because residue number 215  < previous residue 298 
Skipped atom 1742 because residue number 215  < previous residue 298 
Skipped atom 1743 because residue number 215  < previous residue 298 
Skipped atom 1744 because residue number 215  < previous residue 298 
Skipped atom 1745 because residue number 215  < previous residue 298 
Skipped atom 1746 because residue number 216  < previous residue 298 
Skipped atom 1747 because residue number 216  < previous residue 298 
Skipped atom 1748 because residue number 216  < previous residue 298 
Skipped atom 1749 because residue number 216  < previous residue 298 
Skipped atom 1750 because residue number 216  < previous residue 298 
Skipped atom 1751 because residue number 216  < previous residue 298 
Skipped atom 1752 because residue number 217  < previous residue 298 
Skipped atom 1753 because residue number 217  < previous residue 298 
Skipped atom 1754 because residue number 217  < previous residue 298 
Skipped atom 1755 because residue number 217  < previous residue 298 
Skipped atom 1756 because residue number 218  < previous residue 298 
Skipped atom 1757 because residue number 218  < previous residue 298 
Skipped atom 1758 because residue number 218  < previous residue 298 
Skipped atom 1759 because residue number 218  < previous residue 298 
Skipped atom 1760 because residue number 218  < previous residue 298 
Skipped atom 1761 because residue number 218  < previous residue 298 
Skipped atom 1762 because residue number 218  < previous residue 298 
Skipped atom 1763 because residue number 218  < previous residue 298 
Skipped atom 1764 because residue number 219  < previous residue 298 
Skipped atom 1765 because residue number 219  < previous residue 298 
Skipped atom 1766 because residue number 219  < previous residue 298 
Skipped atom 1767 because residue number 219  < previous residue 298 
Skipped atom 1768 because residue number 219  < previous residue 298 
Skipped atom 1769 because residue number 219  < previous residue 298 
Skipped atom 1770 because residue number 219  < previous residue 298 
Skipped atom 1771 because residue number 220  < previous residue 298 
Skipped atom 1772 because residue number 220  < previous residue 298 
Skipped atom 1773 because residue number 220  < previous residue 298 
Skipped atom 1774 because residue number 220  < previous residue 298 
Skipped atom 1775 because residue number 220  < previous residue 298 
Skipped atom 1776 because residue number 220  < previous residue 298 
Skipped atom 1777 because residue number 220  < previous residue 298 
Skipped atom 1778 because residue number 220  < previous residue 298 
Skipped atom 1779 because residue number 221  < previous residue 298 
Skipped atom 1780 because residue number 221  < previous residue 298 
Skipped atom 1781 because residue number 221  < previous residue 298 
Skipped atom 1782 because residue number 221  < previous residue 298 
Skipped atom 1783 because residue number 221  < previous residue 298 
Skipped atom 1784 because residue number 221  < previous residue 298 
Skipped atom 1785 because residue number 221  < previous residue 298 
Skipped atom 1786 because residue number 221  < previous residue 298 
Skipped atom 1787 because residue number 222  < previous residue 298 
Skipped atom 1788 because residue number 222  < previous residue 298 
Skipped atom 1789 because residue number 222  < previous residue 298 
Skipped atom 1790 because residue number 222  < previous residue 298 
Skipped atom 1791 because residue number 222  < previous residue 298 
Skipped atom 1792 because residue number 222  < previous residue 298 
Skipped atom 1793 because residue number 222  < previous residue 298 
Skipped atom 1794 because residue number 222  < previous residue 298 
Skipped atom 1795 because residue number 222  < previous residue 298 
Skipped atom 1796 because residue number 223  < previous residue 298 
Skipped atom 1797 because residue number 223  < previous residue 298 
Skipped atom 1798 because residue number 223  < previous residue 298 
Skipped atom 1799 because residue number 223  < previous residue 298 
Skipped atom 1800 because residue number 223  < previous residue 298 
Skipped atom 1801 because residue number 223  < previous residue 298 
Skipped atom 1802 because residue number 223  < previous residue 298 
Skipped atom 1803 because residue number 223  < previous residue 298 
Skipped atom 1804 because residue number 224  < previous residue 298 
Skipped atom 1805 because residue number 224  < previous residue 298 
Skipped atom 1806 because residue number 224  < previous residue 298 
Skipped atom 1807 because residue number 224  < previous residue 298 
Skipped atom 1808 because residue number 225  < previous residue 298 
Skipped atom 1809 because residue number 225  < previous residue 298 
Skipped atom 1810 because residue number 225  < previous residue 298 
Skipped atom 1811 because residue number 225  < previous residue 298 
Skipped atom 1812 because residue number 225  < previous residue 298 
Skipped atom 1813 because residue number 225  < previous residue 298 
Skipped atom 1814 because residue number 225  < previous residue 298 
Skipped atom 1815 because residue number 226  < previous residue 298 
Skipped atom 1816 because residue number 226  < previous residue 298 
Skipped atom 1817 because residue number 226  < previous residue 298 
Skipped atom 1818 because residue number 226  < previous residue 298 
Skipped atom 1819 because residue number 226  < previous residue 298 
Skipped atom 1820 because residue number 226  < previous residue 298 
Skipped atom 1821 because residue number 226  < previous residue 298 
Skipped atom 1822 because residue number 227  < previous residue 298 
Skipped atom 1823 because residue number 227  < previous residue 298 
Skipped atom 1824 because residue number 227  < previous residue 298 
Skipped atom 1825 because residue number 227  < previous residue 298 
Skipped atom 1826 because residue number 227  < previous residue 298 
Skipped atom 1827 because residue number 227  < previous residue 298 
Skipped atom 1828 because residue number 228  < previous residue 298 
Skipped atom 1829 because residue number 228  < previous residue 298 
Skipped atom 1830 because residue number 228  < previous residue 298 
Skipped atom 1831 because residue number 228  < previous residue 298 
Skipped atom 1832 because residue number 228  < previous residue 298 
Skipped atom 1833 because residue number 228  < previous residue 298 
Skipped atom 1834 because residue number 228  < previous residue 298 
Skipped atom 1835 because residue number 228  < previous residue 298 
Skipped atom 1836 because residue number 229  < previous residue 298 
Skipped atom 1837 because residue number 229  < previous residue 298 
Skipped atom 1838 because residue number 229  < previous residue 298 
Skipped atom 1839 because residue number 229  < previous residue 298 
Skipped atom 1840 because residue number 229  < previous residue 298 
Skipped atom 1841 because residue number 229  < previous residue 298 
Skipped atom 1842 because residue number 229  < previous residue 298 
Skipped atom 1843 because residue number 229  < previous residue 298 
Skipped atom 1844 because residue number 229  < previous residue 298 
Skipped atom 1845 because residue number 229  < previous residue 298 
Skipped atom 1846 because residue number 229  < previous residue 298 
Skipped atom 1847 because residue number 229  < previous residue 298 
Skipped atom 1848 because residue number 230  < previous residue 298 
Skipped atom 1849 because residue number 230  < previous residue 298 
Skipped atom 1850 because residue number 230  < previous residue 298 
Skipped atom 1851 because residue number 230  < previous residue 298 
Skipped atom 1852 because residue number 230  < previous residue 298 
Skipped atom 1853 because residue number 230  < previous residue 298 
Skipped atom 1854 because residue number 230  < previous residue 298 
Skipped atom 1855 because residue number 230  < previous residue 298 
Skipped atom 1856 because residue number 230  < previous residue 298 
Skipped atom 1857 because residue number 231  < previous residue 298 
Skipped atom 1858 because residue number 231  < previous residue 298 
Skipped atom 1859 because residue number 231  < previous residue 298 
Skipped atom 1860 because residue number 231  < previous residue 298 
Skipped atom 1861 because residue number 231  < previous residue 298 
Skipped atom 1862 because residue number 231  < previous residue 298 
Skipped atom 1863 because residue number 231  < previous residue 298 
Skipped atom 1864 because residue number 232  < previous residue 298 
Skipped atom 1865 because residue number 232  < previous residue 298 
Skipped atom 1866 because residue number 232  < previous residue 298 
Skipped atom 1867 because residue number 232  < previous residue 298 
Skipped atom 1868 because residue number 232  < previous residue 298 
Skipped atom 1869 because residue number 233  < previous residue 298 
Skipped atom 1870 because residue number 233  < previous residue 298 
Skipped atom 1871 because residue number 233  < previous residue 298 
Skipped atom 1872 because residue number 233  < previous residue 298 
Skipped atom 1873 because residue number 233  < previous residue 298 
Skipped atom 1874 because residue number 233  < previous residue 298 
Skipped atom 1875 because residue number 233  < previous residue 298 
Skipped atom 1876 because residue number 233  < previous residue 298 
Skipped atom 1877 because residue number 234  < previous residue 298 
Skipped atom 1878 because residue number 234  < previous residue 298 
Skipped atom 1879 because residue number 234  < previous residue 298 
Skipped atom 1880 because residue number 234  < previous residue 298 
Skipped atom 1881 because residue number 234  < previous residue 298 
Skipped atom 1882 because residue number 234  < previous residue 298 
Skipped atom 1883 because residue number 234  < previous residue 298 
Skipped atom 1884 because residue number 234  < previous residue 298 
Skipped atom 1885 because residue number 234  < previous residue 298 
Skipped atom 1886 because residue number 235  < previous residue 298 
Skipped atom 1887 because residue number 235  < previous residue 298 
Skipped atom 1888 because residue number 235  < previous residue 298 
Skipped atom 1889 because residue number 235  < previous residue 298 
Skipped atom 1890 because residue number 235  < previous residue 298 
Skipped atom 1891 because residue number 235  < previous residue 298 
Skipped atom 1892 because residue number 236  < previous residue 298 
Skipped atom 1893 because residue number 236  < previous residue 298 
Skipped atom 1894 because residue number 236  < previous residue 298 
Skipped atom 1895 because residue number 236  < previous residue 298 
Skipped atom 1896 because residue number 237  < previous residue 298 
Skipped atom 1897 because residue number 237  < previous residue 298 
Skipped atom 1898 because residue number 237  < previous residue 298 
Skipped atom 1899 because residue number 237  < previous residue 298 
Skipped atom 1900 because residue number 237  < previous residue 298 
Skipped atom 1901 because residue number 237  < previous residue 298 
Skipped atom 1902 because residue number 237  < previous residue 298 
Skipped atom 1903 because residue number 237  < previous residue 298 
Skipped atom 1904 because residue number 237  < previous residue 298 
Skipped atom 1905 because residue number 238  < previous residue 298 
Skipped atom 1906 because residue number 238  < previous residue 298 
Skipped atom 1907 because residue number 238  < previous residue 298 
Skipped atom 1908 because residue number 238  < previous residue 298 
Skipped atom 1909 because residue number 238  < previous residue 298 
Skipped atom 1910 because residue number 239  < previous residue 298 
Skipped atom 1911 because residue number 239  < previous residue 298 
Skipped atom 1912 because residue number 239  < previous residue 298 
Skipped atom 1913 because residue number 239  < previous residue 298 
Skipped atom 1914 because residue number 239  < previous residue 298 
Skipped atom 1915 because residue number 239  < previous residue 298 
Skipped atom 1916 because residue number 239  < previous residue 298 
Skipped atom 1917 because residue number 239  < previous residue 298 
Skipped atom 1918 because residue number 240  < previous residue 298 
Skipped atom 1919 because residue number 240  < previous residue 298 
Skipped atom 1920 because residue number 240  < previous residue 298 
Skipped atom 1921 because residue number 240  < previous residue 298 
Skipped atom 1922 because residue number 240  < previous residue 298 
Skipped atom 1923 because residue number 240  < previous residue 298 
Skipped atom 1924 because residue number 240  < previous residue 298 
Skipped atom 1925 because residue number 241  < previous residue 298 
Skipped atom 1926 because residue number 241  < previous residue 298 
Skipped atom 1927 because residue number 241  < previous residue 298 
Skipped atom 1928 because residue number 241  < previous residue 298 
Skipped atom 1929 because residue number 241  < previous residue 298 
Skipped atom 1930 because residue number 241  < previous residue 298 
Skipped atom 1931 because residue number 241  < previous residue 298 
Skipped atom 1932 because residue number 241  < previous residue 298 
Skipped atom 1933 because residue number 241  < previous residue 298 
Skipped atom 1934 because residue number 241  < previous residue 298 
Skipped atom 1935 because residue number 241  < previous residue 298 
Skipped atom 1936 because residue number 241  < previous residue 298 
Skipped atom 1937 because residue number 242  < previous residue 298 
Skipped atom 1938 because residue number 242  < previous residue 298 
Skipped atom 1939 because residue number 242  < previous residue 298 
Skipped atom 1940 because residue number 242  < previous residue 298 
Skipped atom 1941 because residue number 242  < previous residue 298 
Skipped atom 1942 because residue number 243  < previous residue 298 
Skipped atom 1943 because residue number 243  < previous residue 298 
Skipped atom 1944 because residue number 243  < previous residue 298 
Skipped atom 1945 because residue number 243  < previous residue 298 
Skipped atom 1946 because residue number 243  < previous residue 298 
Skipped atom 1947 because residue number 243  < previous residue 298 
Skipped atom 1948 because residue number 244  < previous residue 298 
Skipped atom 1949 because residue number 244  < previous residue 298 
Skipped atom 1950 because residue number 244  < previous residue 298 
Skipped atom 1951 because residue number 244  < previous residue 298 
Skipped atom 1952 because residue number 244  < previous residue 298 
Skipped atom 1953 because residue number 244  < previous residue 298 
Skipped atom 1954 because residue number 244  < previous residue 298 
Skipped atom 1955 because residue number 244  < previous residue 298 
Skipped atom 1956 because residue number 244  < previous residue 298 
Skipped atom 1957 because residue number 244  < previous residue 298 
Skipped atom 1958 because residue number 244  < previous residue 298 
Skipped atom 1959 because residue number 245  < previous residue 298 
Skipped atom 1960 because residue number 245  < previous residue 298 
Skipped atom 1961 because residue number 245  < previous residue 298 
Skipped atom 1962 because residue number 245  < previous residue 298 
Skipped atom 1963 because residue number 245  < previous residue 298 
Skipped atom 1964 because residue number 245  < previous residue 298 
Skipped atom 1965 because residue number 245  < previous residue 298 
Skipped atom 1966 because residue number 245  < previous residue 298 
Skipped atom 1967 because residue number 246  < previous residue 298 
Skipped atom 1968 because residue number 246  < previous residue 298 
Skipped atom 1969 because residue number 246  < previous residue 298 
Skipped atom 1970 because residue number 246  < previous residue 298 
Skipped atom 1971 because residue number 246  < previous residue 298 
Skipped atom 1972 because residue number 246  < previous residue 298 
Skipped atom 1973 because residue number 246  < previous residue 298 
Skipped atom 1974 because residue number 246  < previous residue 298 
Skipped atom 1975 because residue number 247  < previous residue 298 
Skipped atom 1976 because residue number 247  < previous residue 298 
Skipped atom 1977 because residue number 247  < previous residue 298 
Skipped atom 1978 because residue number 247  < previous residue 298 
Skipped atom 1979 because residue number 247  < previous residue 298 
Skipped atom 1980 because residue number 247  < previous residue 298 
Skipped atom 1981 because residue number 247  < previous residue 298 
Skipped atom 1982 because residue number 248  < previous residue 298 
Skipped atom 1983 because residue number 248  < previous residue 298 
Skipped atom 1984 because residue number 248  < previous residue 298 
Skipped atom 1985 because residue number 248  < previous residue 298 
Skipped atom 1986 because residue number 248  < previous residue 298 
Skipped atom 1987 because residue number 249  < previous residue 298 
Skipped atom 1988 because residue number 249  < previous residue 298 
Skipped atom 1989 because residue number 249  < previous residue 298 
Skipped atom 1990 because residue number 249  < previous residue 298 
Skipped atom 1991 because residue number 249  < previous residue 298 
Skipped atom 1992 because residue number 249  < previous residue 298 
Skipped atom 1993 because residue number 249  < previous residue 298 
Skipped atom 1994 because residue number 249  < previous residue 298 
Skipped atom 1995 because residue number 249  < previous residue 298 
Skipped atom 1996 because residue number 249  < previous residue 298 
Skipped atom 1997 because residue number 249  < previous residue 298 
Skipped atom 1998 because residue number 250  < previous residue 298 
Skipped atom 1999 because residue number 250  < previous residue 298 
Skipped atom 2000 because residue number 250  < previous residue 298 
Skipped atom 2001 because residue number 250  < previous residue 298 
Skipped atom 2002 because residue number 250  < previous residue 298 
Skipped atom 2003 because residue number 250  < previous residue 298 
Skipped atom 2004 because residue number 250  < previous residue 298 
Skipped atom 2005 because residue number 251  < previous residue 298 
Skipped atom 2006 because residue number 251  < previous residue 298 
Skipped atom 2007 because residue number 251  < previous residue 298 
Skipped atom 2008 because residue number 251  < previous residue 298 
Skipped atom 2009 because residue number 251  < previous residue 298 
Skipped atom 2010 because residue number 251  < previous residue 298 
Skipped atom 2011 because residue number 251  < previous residue 298 
Skipped atom 2012 because residue number 251  < previous residue 298 
Skipped atom 2013 because residue number 251  < previous residue 298 
Skipped atom 2014 because residue number 251  < previous residue 298 
Skipped atom 2015 because residue number 251  < previous residue 298 
Skipped atom 2016 because residue number 251  < previous residue 298 
Skipped atom 2017 because residue number 252  < previous residue 298 
Skipped atom 2018 because residue number 252  < previous residue 298 
Skipped atom 2019 because residue number 252  < previous residue 298 
Skipped atom 2020 because residue number 252  < previous residue 298 
Skipped atom 2021 because residue number 252  < previous residue 298 
Skipped atom 2022 because residue number 252  < previous residue 298 
Skipped atom 2023 because residue number 252  < previous residue 298 
Skipped atom 2024 because residue number 253  < previous residue 298 
Skipped atom 2025 because residue number 253  < previous residue 298 
Skipped atom 2026 because residue number 253  < previous residue 298 
Skipped atom 2027 because residue number 253  < previous residue 298 
Skipped atom 2028 because residue number 253  < previous residue 298 
Skipped atom 2029 because residue number 253  < previous residue 298 
Skipped atom 2030 because residue number 253  < previous residue 298 
Skipped atom 2031 because residue number 253  < previous residue 298 
Skipped atom 2032 because residue number 253  < previous residue 298 
Skipped atom 2033 because residue number 253  < previous residue 298 
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1alq-orig.a2m
Writing a2m file: tmp/1alq-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29112


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29112/tmp -alignfile tmp/1alq-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1alq-orig.a2m (1 sequences, 266 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29112/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29112/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29112/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29112/tmp.a2m (1 sequences, 266 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29112/tmp.mod tmp/1alq-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29112 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1alq-align.mod
tmp/1alq-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29112/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1alq-orig.a2m tmp/1alq-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1alq-align.mod
Running w0.5 tmp/1alq-orig.a2m tmp/1alq-align.mod
Running align2model tmp/1alq-align -i tmp/1alq-align.mod -db tmp/1alq-orig.a2m -db tmp/1alq-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1alq.141.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1alq.142.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1alq.142.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1alq.142.3.a2m \
	-target T0124 -template 1alq \
	-out T0124-1alq.142.3 -outdir und
Skipped atom 298 because residue number 31  < previous residue 298 
Skipped atom 299 because residue number 31  < previous residue 298 
Skipped atom 300 because residue number 31  < previous residue 298 
Skipped atom 301 because residue number 31  < previous residue 298 
Skipped atom 302 because residue number 31  < previous residue 298 
Skipped atom 303 because residue number 31  < previous residue 298 
Skipped atom 304 because residue number 31  < previous residue 298 
Skipped atom 305 because residue number 31  < previous residue 298 
Skipped atom 306 because residue number 31  < previous residue 298 
Skipped atom 307 because residue number 32  < previous residue 298 
Skipped atom 308 because residue number 32  < previous residue 298 
Skipped atom 309 because residue number 32  < previous residue 298 
Skipped atom 310 because residue number 32  < previous residue 298 
Skipped atom 311 because residue number 32  < previous residue 298 
Skipped atom 312 because residue number 32  < previous residue 298 
Skipped atom 313 because residue number 32  < previous residue 298 
Skipped atom 314 because residue number 32  < previous residue 298 
Skipped atom 315 because residue number 32  < previous residue 298 
Skipped atom 316 because residue number 33  < previous residue 298 
Skipped atom 317 because residue number 33  < previous residue 298 
Skipped atom 318 because residue number 33  < previous residue 298 
Skipped atom 319 because residue number 33  < previous residue 298 
Skipped atom 320 because residue number 33  < previous residue 298 
Skipped atom 321 because residue number 33  < previous residue 298 
Skipped atom 322 because residue number 33  < previous residue 298 
Skipped atom 323 because residue number 33  < previous residue 298 
Skipped atom 324 because residue number 34  < previous residue 298 
Skipped atom 325 because residue number 34  < previous residue 298 
Skipped atom 326 because residue number 34  < previous residue 298 
Skipped atom 327 because residue number 34  < previous residue 298 
Skipped atom 328 because residue number 34  < previous residue 298 
Skipped atom 329 because residue number 34  < previous residue 298 
Skipped atom 330 because residue number 34  < previous residue 298 
Skipped atom 331 because residue number 34  < previous residue 298 
Skipped atom 332 because residue number 35  < previous residue 298 
Skipped atom 333 because residue number 35  < previous residue 298 
Skipped atom 334 because residue number 35  < previous residue 298 
Skipped atom 335 because residue number 35  < previous residue 298 
Skipped atom 336 because residue number 35  < previous residue 298 
Skipped atom 337 because residue number 35  < previous residue 298 
Skipped atom 338 because residue number 35  < previous residue 298 
Skipped atom 339 because residue number 35  < previous residue 298 
Skipped atom 340 because residue number 36  < previous residue 298 
Skipped atom 341 because residue number 36  < previous residue 298 
Skipped atom 342 because residue number 36  < previous residue 298 
Skipped atom 343 because residue number 36  < previous residue 298 
Skipped atom 344 because residue number 36  < previous residue 298 
Skipped atom 345 because residue number 36  < previous residue 298 
Skipped atom 346 because residue number 36  < previous residue 298 
Skipped atom 347 because residue number 36  < previous residue 298 
Skipped atom 348 because residue number 37  < previous residue 298 
Skipped atom 349 because residue number 37  < previous residue 298 
Skipped atom 350 because residue number 37  < previous residue 298 
Skipped atom 351 because residue number 37  < previous residue 298 
Skipped atom 352 because residue number 37  < previous residue 298 
Skipped atom 353 because residue number 37  < previous residue 298 
Skipped atom 354 because residue number 37  < previous residue 298 
Skipped atom 355 because residue number 37  < previous residue 298 
Skipped atom 356 because residue number 37  < previous residue 298 
Skipped atom 357 because residue number 38  < previous residue 298 
Skipped atom 358 because residue number 38  < previous residue 298 
Skipped atom 359 because residue number 38  < previous residue 298 
Skipped atom 360 because residue number 38  < previous residue 298 
Skipped atom 361 because residue number 38  < previous residue 298 
Skipped atom 362 because residue number 38  < previous residue 298 
Skipped atom 363 because residue number 38  < previous residue 298 
Skipped atom 364 because residue number 38  < previous residue 298 
Skipped atom 365 because residue number 38  < previous residue 298 
Skipped atom 366 because residue number 39  < previous residue 298 
Skipped atom 367 because residue number 39  < previous residue 298 
Skipped atom 368 because residue number 39  < previous residue 298 
Skipped atom 369 because residue number 39  < previous residue 298 
Skipped atom 370 because residue number 39  < previous residue 298 
Skipped atom 371 because residue number 39  < previous residue 298 
Skipped atom 372 because residue number 39  < previous residue 298 
Skipped atom 373 because residue number 39  < previous residue 298 
Skipped atom 374 because residue number 39  < previous residue 298 
Skipped atom 375 because residue number 40  < previous residue 298 
Skipped atom 376 because residue number 40  < previous residue 298 
Skipped atom 377 because residue number 40  < previous residue 298 
Skipped atom 378 because residue number 40  < previous residue 298 
Skipped atom 379 because residue number 40  < previous residue 298 
Skipped atom 380 because residue number 40  < previous residue 298 
Skipped atom 381 because residue number 40  < previous residue 298 
Skipped atom 382 because residue number 40  < previous residue 298 
Skipped atom 383 because residue number 40  < previous residue 298 
Skipped atom 384 because residue number 40  < previous residue 298 
Skipped atom 385 because residue number 40  < previous residue 298 
Skipped atom 386 because residue number 40  < previous residue 298 
Skipped atom 387 because residue number 41  < previous residue 298 
Skipped atom 388 because residue number 41  < previous residue 298 
Skipped atom 389 because residue number 41  < previous residue 298 
Skipped atom 390 because residue number 41  < previous residue 298 
Skipped atom 391 because residue number 41  < previous residue 298 
Skipped atom 392 because residue number 41  < previous residue 298 
Skipped atom 393 because residue number 41  < previous residue 298 
Skipped atom 394 because residue number 41  < previous residue 298 
Skipped atom 395 because residue number 42  < previous residue 298 
Skipped atom 396 because residue number 42  < previous residue 298 
Skipped atom 397 because residue number 42  < previous residue 298 
Skipped atom 398 because residue number 42  < previous residue 298 
Skipped atom 399 because residue number 42  < previous residue 298 
Skipped atom 400 because residue number 43  < previous residue 298 
Skipped atom 401 because residue number 43  < previous residue 298 
Skipped atom 402 because residue number 43  < previous residue 298 
Skipped atom 403 because residue number 43  < previous residue 298 
Skipped atom 404 because residue number 43  < previous residue 298 
Skipped atom 405 because residue number 43  < previous residue 298 
Skipped atom 406 because residue number 43  < previous residue 298 
Skipped atom 407 because residue number 43  < previous residue 298 
Skipped atom 408 because residue number 43  < previous residue 298 
Skipped atom 409 because residue number 43  < previous residue 298 
Skipped atom 410 because residue number 44  < previous residue 298 
Skipped atom 411 because residue number 44  < previous residue 298 
Skipped atom 412 because residue number 44  < previous residue 298 
Skipped atom 413 because residue number 44  < previous residue 298 
Skipped atom 414 because residue number 44  < previous residue 298 
Skipped atom 415 because residue number 44  < previous residue 298 
Skipped atom 416 because residue number 44  < previous residue 298 
Skipped atom 417 because residue number 44  < previous residue 298 
Skipped atom 418 because residue number 45  < previous residue 298 
Skipped atom 419 because residue number 45  < previous residue 298 
Skipped atom 420 because residue number 45  < previous residue 298 
Skipped atom 421 because residue number 45  < previous residue 298 
Skipped atom 422 because residue number 46  < previous residue 298 
Skipped atom 423 because residue number 46  < previous residue 298 
Skipped atom 424 because residue number 46  < previous residue 298 
Skipped atom 425 because residue number 46  < previous residue 298 
Skipped atom 426 because residue number 46  < previous residue 298 
Skipped atom 427 because residue number 46  < previous residue 298 
Skipped atom 428 because residue number 46  < previous residue 298 
Skipped atom 429 because residue number 47  < previous residue 298 
Skipped atom 430 because residue number 47  < previous residue 298 
Skipped atom 431 because residue number 47  < previous residue 298 
Skipped atom 432 because residue number 47  < previous residue 298 
Skipped atom 433 because residue number 47  < previous residue 298 
Skipped atom 434 because residue number 47  < previous residue 298 
Skipped atom 435 because residue number 47  < previous residue 298 
Skipped atom 436 because residue number 47  < previous residue 298 
Skipped atom 437 because residue number 47  < previous residue 298 
Skipped atom 438 because residue number 47  < previous residue 298 
Skipped atom 439 because residue number 47  < previous residue 298 
Skipped atom 440 because residue number 47  < previous residue 298 
Skipped atom 441 because residue number 48  < previous residue 298 
Skipped atom 442 because residue number 48  < previous residue 298 
Skipped atom 443 because residue number 48  < previous residue 298 
Skipped atom 444 because residue number 48  < previous residue 298 
Skipped atom 445 because residue number 48  < previous residue 298 
Skipped atom 446 because residue number 49  < previous residue 298 
Skipped atom 447 because residue number 49  < previous residue 298 
Skipped atom 448 because residue number 49  < previous residue 298 
Skipped atom 449 because residue number 49  < previous residue 298 
Skipped atom 450 because residue number 49  < previous residue 298 
Skipped atom 451 because residue number 49  < previous residue 298 
Skipped atom 452 because residue number 49  < previous residue 298 
Skipped atom 453 because residue number 49  < previous residue 298 
Skipped atom 454 because residue number 50  < previous residue 298 
Skipped atom 455 because residue number 50  < previous residue 298 
Skipped atom 456 because residue number 50  < previous residue 298 
Skipped atom 457 because residue number 50  < previous residue 298 
Skipped atom 458 because residue number 50  < previous residue 298 
Skipped atom 459 because residue number 50  < previous residue 298 
Skipped atom 460 because residue number 50  < previous residue 298 
Skipped atom 461 because residue number 50  < previous residue 298 
Skipped atom 462 because residue number 51  < previous residue 298 
Skipped atom 463 because residue number 51  < previous residue 298 
Skipped atom 464 because residue number 51  < previous residue 298 
Skipped atom 465 because residue number 51  < previous residue 298 
Skipped atom 466 because residue number 51  < previous residue 298 
Skipped atom 467 because residue number 51  < previous residue 298 
Skipped atom 468 because residue number 51  < previous residue 298 
Skipped atom 469 because residue number 52  < previous residue 298 
Skipped atom 470 because residue number 52  < previous residue 298 
Skipped atom 471 because residue number 52  < previous residue 298 
Skipped atom 472 because residue number 52  < previous residue 298 
Skipped atom 473 because residue number 52  < previous residue 298 
Skipped atom 474 because residue number 52  < previous residue 298 
Skipped atom 475 because residue number 52  < previous residue 298 
Skipped atom 476 because residue number 52  < previous residue 298 
Skipped atom 477 because residue number 52  < previous residue 298 
Skipped atom 478 because residue number 53  < previous residue 298 
Skipped atom 479 because residue number 53  < previous residue 298 
Skipped atom 480 because residue number 53  < previous residue 298 
Skipped atom 481 because residue number 53  < previous residue 298 
Skipped atom 482 because residue number 53  < previous residue 298 
Skipped atom 483 because residue number 53  < previous residue 298 
Skipped atom 484 because residue number 54  < previous residue 298 
Skipped atom 485 because residue number 54  < previous residue 298 
Skipped atom 486 because residue number 54  < previous residue 298 
Skipped atom 487 because residue number 54  < previous residue 298 
Skipped atom 488 because residue number 55  < previous residue 298 
Skipped atom 489 because residue number 55  < previous residue 298 
Skipped atom 490 because residue number 55  < previous residue 298 
Skipped atom 491 because residue number 55  < previous residue 298 
Skipped atom 492 because residue number 55  < previous residue 298 
Skipped atom 493 because residue number 55  < previous residue 298 
Skipped atom 494 because residue number 55  < previous residue 298 
Skipped atom 495 because residue number 55  < previous residue 298 
Skipped atom 496 because residue number 55  < previous residue 298 
Skipped atom 497 because residue number 56  < previous residue 298 
Skipped atom 498 because residue number 56  < previous residue 298 
Skipped atom 499 because residue number 56  < previous residue 298 
Skipped atom 500 because residue number 56  < previous residue 298 
Skipped atom 501 because residue number 56  < previous residue 298 
Skipped atom 502 because residue number 56  < previous residue 298 
Skipped atom 503 because residue number 56  < previous residue 298 
Skipped atom 504 because residue number 56  < previous residue 298 
Skipped atom 505 because residue number 56  < previous residue 298 
Skipped atom 506 because residue number 57  < previous residue 298 
Skipped atom 507 because residue number 57  < previous residue 298 
Skipped atom 508 because residue number 57  < previous residue 298 
Skipped atom 509 because residue number 57  < previous residue 298 
Skipped atom 510 because residue number 57  < previous residue 298 
Skipped atom 511 because residue number 57  < previous residue 298 
Skipped atom 512 because residue number 57  < previous residue 298 
Skipped atom 513 because residue number 59  < previous residue 298 
Skipped atom 514 because residue number 59  < previous residue 298 
Skipped atom 515 because residue number 59  < previous residue 298 
Skipped atom 516 because residue number 59  < previous residue 298 
Skipped atom 517 because residue number 59  < previous residue 298 
Skipped atom 518 because residue number 59  < previous residue 298 
Skipped atom 519 because residue number 59  < previous residue 298 
Skipped atom 520 because residue number 59  < previous residue 298 
Skipped atom 521 because residue number 59  < previous residue 298 
Skipped atom 522 because residue number 60  < previous residue 298 
Skipped atom 523 because residue number 60  < previous residue 298 
Skipped atom 524 because residue number 60  < previous residue 298 
Skipped atom 525 because residue number 60  < previous residue 298 
Skipped atom 526 because residue number 60  < previous residue 298 
Skipped atom 527 because residue number 60  < previous residue 298 
Skipped atom 528 because residue number 60  < previous residue 298 
Skipped atom 529 because residue number 60  < previous residue 298 
Skipped atom 530 because residue number 60  < previous residue 298 
Skipped atom 531 because residue number 60  < previous residue 298 
Skipped atom 532 because residue number 60  < previous residue 298 
Skipped atom 533 because residue number 61  < previous residue 298 
Skipped atom 534 because residue number 61  < previous residue 298 
Skipped atom 535 because residue number 61  < previous residue 298 
Skipped atom 536 because residue number 61  < previous residue 298 
Skipped atom 537 because residue number 61  < previous residue 298 
Skipped atom 538 because residue number 61  < previous residue 298 
Skipped atom 539 because residue number 61  < previous residue 298 
Skipped atom 540 because residue number 61  < previous residue 298 
Skipped atom 541 because residue number 62  < previous residue 298 
Skipped atom 542 because residue number 62  < previous residue 298 
Skipped atom 543 because residue number 62  < previous residue 298 
Skipped atom 544 because residue number 62  < previous residue 298 
Skipped atom 545 because residue number 62  < previous residue 298 
Skipped atom 546 because residue number 62  < previous residue 298 
Skipped atom 547 because residue number 63  < previous residue 298 
Skipped atom 548 because residue number 63  < previous residue 298 
Skipped atom 549 because residue number 63  < previous residue 298 
Skipped atom 550 because residue number 63  < previous residue 298 
Skipped atom 551 because residue number 63  < previous residue 298 
Skipped atom 552 because residue number 63  < previous residue 298 
Skipped atom 553 because residue number 63  < previous residue 298 
Skipped atom 554 because residue number 63  < previous residue 298 
Skipped atom 555 because residue number 64  < previous residue 298 
Skipped atom 556 because residue number 64  < previous residue 298 
Skipped atom 557 because residue number 64  < previous residue 298 
Skipped atom 558 because residue number 64  < previous residue 298 
Skipped atom 559 because residue number 64  < previous residue 298 
Skipped atom 560 because residue number 64  < previous residue 298 
Skipped atom 561 because residue number 64  < previous residue 298 
Skipped atom 562 because residue number 64  < previous residue 298 
Skipped atom 563 because residue number 64  < previous residue 298 
Skipped atom 564 because residue number 65  < previous residue 298 
Skipped atom 565 because residue number 65  < previous residue 298 
Skipped atom 566 because residue number 65  < previous residue 298 
Skipped atom 567 because residue number 65  < previous residue 298 
Skipped atom 568 because residue number 65  < previous residue 298 
Skipped atom 569 because residue number 65  < previous residue 298 
Skipped atom 570 because residue number 65  < previous residue 298 
Skipped atom 571 because residue number 65  < previous residue 298 
Skipped atom 572 because residue number 65  < previous residue 298 
Skipped atom 573 because residue number 65  < previous residue 298 
Skipped atom 574 because residue number 65  < previous residue 298 
Skipped atom 575 because residue number 66  < previous residue 298 
Skipped atom 576 because residue number 66  < previous residue 298 
Skipped atom 577 because residue number 66  < previous residue 298 
Skipped atom 578 because residue number 66  < previous residue 298 
Skipped atom 579 because residue number 66  < previous residue 298 
Skipped atom 580 because residue number 66  < previous residue 298 
Skipped atom 581 because residue number 66  < previous residue 298 
Skipped atom 582 because residue number 66  < previous residue 298 
Skipped atom 583 because residue number 66  < previous residue 298 
Skipped atom 584 because residue number 66  < previous residue 298 
Skipped atom 585 because residue number 66  < previous residue 298 
Skipped atom 586 because residue number 67  < previous residue 298 
Skipped atom 587 because residue number 67  < previous residue 298 
Skipped atom 588 because residue number 67  < previous residue 298 
Skipped atom 589 because residue number 67  < previous residue 298 
Skipped atom 590 because residue number 67  < previous residue 298 
Skipped atom 591 because residue number 68  < previous residue 298 
Skipped atom 592 because residue number 68  < previous residue 298 
Skipped atom 593 because residue number 68  < previous residue 298 
Skipped atom 594 because residue number 68  < previous residue 298 
Skipped atom 595 because residue number 68  < previous residue 298 
Skipped atom 596 because residue number 68  < previous residue 298 
Skipped atom 597 because residue number 68  < previous residue 298 
Skipped atom 598 because residue number 68  < previous residue 298 
Skipped atom 599 because residue number 68  < previous residue 298 
Skipped atom 600 because residue number 68  < previous residue 298 
Skipped atom 601 because residue number 68  < previous residue 298 
Skipped atom 602 because residue number 68  < previous residue 298 
Skipped atom 603 because residue number 69  < previous residue 298 
Skipped atom 604 because residue number 69  < previous residue 298 
Skipped atom 605 because residue number 69  < previous residue 298 
Skipped atom 606 because residue number 69  < previous residue 298 
Skipped atom 607 because residue number 69  < previous residue 298 
Skipped atom 608 because residue number 70  < previous residue 298 
Skipped atom 609 because residue number 70  < previous residue 298 
Skipped atom 610 because residue number 70  < previous residue 298 
Skipped atom 611 because residue number 70  < previous residue 298 
Skipped atom 612 because residue number 70  < previous residue 298 
Skipped atom 613 because residue number 70  < previous residue 298 
Skipped atom 614 because residue number 71  < previous residue 298 
Skipped atom 615 because residue number 71  < previous residue 298 
Skipped atom 616 because residue number 71  < previous residue 298 
Skipped atom 617 because residue number 71  < previous residue 298 
Skipped atom 618 because residue number 71  < previous residue 298 
Skipped atom 619 because residue number 71  < previous residue 298 
Skipped atom 620 because residue number 71  < previous residue 298 
Skipped atom 621 because residue number 72  < previous residue 298 
Skipped atom 622 because residue number 72  < previous residue 298 
Skipped atom 623 because residue number 72  < previous residue 298 
Skipped atom 624 because residue number 72  < previous residue 298 
Skipped atom 625 because residue number 72  < previous residue 298 
Skipped atom 626 because residue number 72  < previous residue 298 
Skipped atom 627 because residue number 73  < previous residue 298 
Skipped atom 628 because residue number 73  < previous residue 298 
Skipped atom 629 because residue number 73  < previous residue 298 
Skipped atom 630 because residue number 73  < previous residue 298 
Skipped atom 631 because residue number 73  < previous residue 298 
Skipped atom 632 because residue number 73  < previous residue 298 
Skipped atom 633 because residue number 73  < previous residue 298 
Skipped atom 634 because residue number 73  < previous residue 298 
Skipped atom 635 because residue number 73  < previous residue 298 
Skipped atom 636 because residue number 74  < previous residue 298 
Skipped atom 637 because residue number 74  < previous residue 298 
Skipped atom 638 because residue number 74  < previous residue 298 
Skipped atom 639 because residue number 74  < previous residue 298 
Skipped atom 640 because residue number 74  < previous residue 298 
Skipped atom 641 because residue number 75  < previous residue 298 
Skipped atom 642 because residue number 75  < previous residue 298 
Skipped atom 643 because residue number 75  < previous residue 298 
Skipped atom 644 because residue number 75  < previous residue 298 
Skipped atom 645 because residue number 75  < previous residue 298 
Skipped atom 646 because residue number 75  < previous residue 298 
Skipped atom 647 because residue number 75  < previous residue 298 
Skipped atom 648 because residue number 75  < previous residue 298 
Skipped atom 649 because residue number 76  < previous residue 298 
Skipped atom 650 because residue number 76  < previous residue 298 
Skipped atom 651 because residue number 76  < previous residue 298 
Skipped atom 652 because residue number 76  < previous residue 298 
Skipped atom 653 because residue number 76  < previous residue 298 
Skipped atom 654 because residue number 76  < previous residue 298 
Skipped atom 655 because residue number 76  < previous residue 298 
Skipped atom 656 because residue number 76  < previous residue 298 
Skipped atom 657 because residue number 77  < previous residue 298 
Skipped atom 658 because residue number 77  < previous residue 298 
Skipped atom 659 because residue number 77  < previous residue 298 
Skipped atom 660 because residue number 77  < previous residue 298 
Skipped atom 661 because residue number 77  < previous residue 298 
Skipped atom 662 because residue number 77  < previous residue 298 
Skipped atom 663 because residue number 78  < previous residue 298 
Skipped atom 664 because residue number 78  < previous residue 298 
Skipped atom 665 because residue number 78  < previous residue 298 
Skipped atom 666 because residue number 78  < previous residue 298 
Skipped atom 667 because residue number 78  < previous residue 298 
Skipped atom 668 because residue number 79  < previous residue 298 
Skipped atom 669 because residue number 79  < previous residue 298 
Skipped atom 670 because residue number 79  < previous residue 298 
Skipped atom 671 because residue number 79  < previous residue 298 
Skipped atom 672 because residue number 79  < previous residue 298 
Skipped atom 673 because residue number 79  < previous residue 298 
Skipped atom 674 because residue number 79  < previous residue 298 
Skipped atom 675 because residue number 79  < previous residue 298 
Skipped atom 676 because residue number 80  < previous residue 298 
Skipped atom 677 because residue number 80  < previous residue 298 
Skipped atom 678 because residue number 80  < previous residue 298 
Skipped atom 679 because residue number 80  < previous residue 298 
Skipped atom 680 because residue number 80  < previous residue 298 
Skipped atom 681 because residue number 80  < previous residue 298 
Skipped atom 682 because residue number 80  < previous residue 298 
Skipped atom 683 because residue number 80  < previous residue 298 
Skipped atom 684 because residue number 81  < previous residue 298 
Skipped atom 685 because residue number 81  < previous residue 298 
Skipped atom 686 because residue number 81  < previous residue 298 
Skipped atom 687 because residue number 81  < previous residue 298 
Skipped atom 688 because residue number 81  < previous residue 298 
Skipped atom 689 because residue number 81  < previous residue 298 
Skipped atom 690 because residue number 81  < previous residue 298 
Skipped atom 691 because residue number 81  < previous residue 298 
Skipped atom 692 because residue number 82  < previous residue 298 
Skipped atom 693 because residue number 82  < previous residue 298 
Skipped atom 694 because residue number 82  < previous residue 298 
Skipped atom 695 because residue number 82  < previous residue 298 
Skipped atom 696 because residue number 82  < previous residue 298 
Skipped atom 697 because residue number 82  < previous residue 298 
Skipped atom 698 because residue number 82  < previous residue 298 
Skipped atom 699 because residue number 82  < previous residue 298 
Skipped atom 700 because residue number 82  < previous residue 298 
Skipped atom 701 because residue number 83  < previous residue 298 
Skipped atom 702 because residue number 83  < previous residue 298 
Skipped atom 703 because residue number 83  < previous residue 298 
Skipped atom 704 because residue number 83  < previous residue 298 
Skipped atom 705 because residue number 83  < previous residue 298 
Skipped atom 706 because residue number 83  < previous residue 298 
Skipped atom 707 because residue number 83  < previous residue 298 
Skipped atom 708 because residue number 83  < previous residue 298 
Skipped atom 709 because residue number 83  < previous residue 298 
Skipped atom 710 because residue number 84  < previous residue 298 
Skipped atom 711 because residue number 84  < previous residue 298 
Skipped atom 712 because residue number 84  < previous residue 298 
Skipped atom 713 because residue number 84  < previous residue 298 
Skipped atom 714 because residue number 84  < previous residue 298 
Skipped atom 715 because residue number 84  < previous residue 298 
Skipped atom 716 because residue number 84  < previous residue 298 
Skipped atom 717 because residue number 87  < previous residue 298 
Skipped atom 718 because residue number 87  < previous residue 298 
Skipped atom 719 because residue number 87  < previous residue 298 
Skipped atom 720 because residue number 87  < previous residue 298 
Skipped atom 721 because residue number 87  < previous residue 298 
Skipped atom 722 because residue number 87  < previous residue 298 
Skipped atom 723 because residue number 87  < previous residue 298 
Skipped atom 724 because residue number 88  < previous residue 298 
Skipped atom 725 because residue number 88  < previous residue 298 
Skipped atom 726 because residue number 88  < previous residue 298 
Skipped atom 727 because residue number 88  < previous residue 298 
Skipped atom 728 because residue number 88  < previous residue 298 
Skipped atom 729 because residue number 88  < previous residue 298 
Skipped atom 730 because residue number 88  < previous residue 298 
Skipped atom 731 because residue number 88  < previous residue 298 
Skipped atom 732 because residue number 88  < previous residue 298 
Skipped atom 733 because residue number 88  < previous residue 298 
Skipped atom 734 because residue number 88  < previous residue 298 
Skipped atom 735 because residue number 88  < previous residue 298 
Skipped atom 736 because residue number 89  < previous residue 298 
Skipped atom 737 because residue number 89  < previous residue 298 
Skipped atom 738 because residue number 89  < previous residue 298 
Skipped atom 739 because residue number 89  < previous residue 298 
Skipped atom 740 because residue number 89  < previous residue 298 
Skipped atom 741 because residue number 89  < previous residue 298 
Skipped atom 742 because residue number 89  < previous residue 298 
Skipped atom 743 because residue number 89  < previous residue 298 
Skipped atom 744 because residue number 90  < previous residue 298 
Skipped atom 745 because residue number 90  < previous residue 298 
Skipped atom 746 because residue number 90  < previous residue 298 
Skipped atom 747 because residue number 90  < previous residue 298 
Skipped atom 748 because residue number 90  < previous residue 298 
Skipped atom 749 because residue number 90  < previous residue 298 
Skipped atom 750 because residue number 90  < previous residue 298 
Skipped atom 751 because residue number 90  < previous residue 298 
Skipped atom 752 because residue number 90  < previous residue 298 
Skipped atom 753 because residue number 91  < previous residue 298 
Skipped atom 754 because residue number 91  < previous residue 298 
Skipped atom 755 because residue number 91  < previous residue 298 
Skipped atom 756 because residue number 91  < previous residue 298 
Skipped atom 757 because residue number 91  < previous residue 298 
Skipped atom 758 because residue number 91  < previous residue 298 
Skipped atom 759 because residue number 91  < previous residue 298 
Skipped atom 760 because residue number 91  < previous residue 298 
Skipped atom 761 because residue number 92  < previous residue 298 
Skipped atom 762 because residue number 92  < previous residue 298 
Skipped atom 763 because residue number 92  < previous residue 298 
Skipped atom 764 because residue number 92  < previous residue 298 
Skipped atom 765 because residue number 92  < previous residue 298 
Skipped atom 766 because residue number 92  < previous residue 298 
Skipped atom 767 because residue number 92  < previous residue 298 
Skipped atom 768 because residue number 92  < previous residue 298 
Skipped atom 769 because residue number 93  < previous residue 298 
Skipped atom 770 because residue number 93  < previous residue 298 
Skipped atom 771 because residue number 93  < previous residue 298 
Skipped atom 772 because residue number 93  < previous residue 298 
Skipped atom 773 because residue number 93  < previous residue 298 
Skipped atom 774 because residue number 93  < previous residue 298 
Skipped atom 775 because residue number 93  < previous residue 298 
Skipped atom 776 because residue number 93  < previous residue 298 
Skipped atom 777 because residue number 93  < previous residue 298 
Skipped atom 778 because residue number 94  < previous residue 298 
Skipped atom 779 because residue number 94  < previous residue 298 
Skipped atom 780 because residue number 94  < previous residue 298 
Skipped atom 781 because residue number 94  < previous residue 298 
Skipped atom 782 because residue number 94  < previous residue 298 
Skipped atom 783 because residue number 94  < previous residue 298 
Skipped atom 784 because residue number 94  < previous residue 298 
Skipped atom 785 because residue number 94  < previous residue 298 
Skipped atom 786 because residue number 94  < previous residue 298 
Skipped atom 787 because residue number 95  < previous residue 298 
Skipped atom 788 because residue number 95  < previous residue 298 
Skipped atom 789 because residue number 95  < previous residue 298 
Skipped atom 790 because residue number 95  < previous residue 298 
Skipped atom 791 because residue number 95  < previous residue 298 
Skipped atom 792 because residue number 95  < previous residue 298 
Skipped atom 793 because residue number 95  < previous residue 298 
Skipped atom 794 because residue number 96  < previous residue 298 
Skipped atom 795 because residue number 96  < previous residue 298 
Skipped atom 796 because residue number 96  < previous residue 298 
Skipped atom 797 because residue number 96  < previous residue 298 
Skipped atom 798 because residue number 96  < previous residue 298 
Skipped atom 799 because residue number 96  < previous residue 298 
Skipped atom 800 because residue number 96  < previous residue 298 
Skipped atom 801 because residue number 96  < previous residue 298 
Skipped atom 802 because residue number 96  < previous residue 298 
Skipped atom 803 because residue number 96  < previous residue 298 
Skipped atom 804 because residue number 97  < previous residue 298 
Skipped atom 805 because residue number 97  < previous residue 298 
Skipped atom 806 because residue number 97  < previous residue 298 
Skipped atom 807 because residue number 97  < previous residue 298 
Skipped atom 808 because residue number 97  < previous residue 298 
Skipped atom 809 because residue number 97  < previous residue 298 
Skipped atom 810 because residue number 97  < previous residue 298 
Skipped atom 811 because residue number 97  < previous residue 298 
Skipped atom 812 because residue number 98  < previous residue 298 
Skipped atom 813 because residue number 98  < previous residue 298 
Skipped atom 814 because residue number 98  < previous residue 298 
Skipped atom 815 because residue number 98  < previous residue 298 
Skipped atom 816 because residue number 98  < previous residue 298 
Skipped atom 817 because residue number 98  < previous residue 298 
Skipped atom 818 because residue number 98  < previous residue 298 
Skipped atom 819 because residue number 98  < previous residue 298 
Skipped atom 820 because residue number 99  < previous residue 298 
Skipped atom 821 because residue number 99  < previous residue 298 
Skipped atom 822 because residue number 99  < previous residue 298 
Skipped atom 823 because residue number 99  < previous residue 298 
Skipped atom 824 because residue number 99  < previous residue 298 
Skipped atom 825 because residue number 99  < previous residue 298 
Skipped atom 826 because residue number 99  < previous residue 298 
Skipped atom 827 because residue number 99  < previous residue 298 
Skipped atom 828 because residue number 99  < previous residue 298 
Skipped atom 829 because residue number 100  < previous residue 298 
Skipped atom 830 because residue number 100  < previous residue 298 
Skipped atom 831 because residue number 100  < previous residue 298 
Skipped atom 832 because residue number 100  < previous residue 298 
Skipped atom 833 because residue number 100  < previous residue 298 
Skipped atom 834 because residue number 100  < previous residue 298 
Skipped atom 835 because residue number 100  < previous residue 298 
Skipped atom 836 because residue number 100  < previous residue 298 
Skipped atom 837 because residue number 101  < previous residue 298 
Skipped atom 838 because residue number 101  < previous residue 298 
Skipped atom 839 because residue number 101  < previous residue 298 
Skipped atom 840 because residue number 101  < previous residue 298 
Skipped atom 841 because residue number 101  < previous residue 298 
Skipped atom 842 because residue number 101  < previous residue 298 
Skipped atom 843 because residue number 101  < previous residue 298 
Skipped atom 844 because residue number 101  < previous residue 298 
Skipped atom 845 because residue number 102  < previous residue 298 
Skipped atom 846 because residue number 102  < previous residue 298 
Skipped atom 847 because residue number 102  < previous residue 298 
Skipped atom 848 because residue number 102  < previous residue 298 
Skipped atom 849 because residue number 102  < previous residue 298 
Skipped atom 850 because residue number 102  < previous residue 298 
Skipped atom 851 because residue number 102  < previous residue 298 
Skipped atom 852 because residue number 102  < previous residue 298 
Skipped atom 853 because residue number 103  < previous residue 298 
Skipped atom 854 because residue number 103  < previous residue 298 
Skipped atom 855 because residue number 103  < previous residue 298 
Skipped atom 856 because residue number 103  < previous residue 298 
Skipped atom 857 because residue number 103  < previous residue 298 
Skipped atom 858 because residue number 103  < previous residue 298 
Skipped atom 859 because residue number 103  < previous residue 298 
Skipped atom 860 because residue number 104  < previous residue 298 
Skipped atom 861 because residue number 104  < previous residue 298 
Skipped atom 862 because residue number 104  < previous residue 298 
Skipped atom 863 because residue number 104  < previous residue 298 
Skipped atom 864 because residue number 104  < previous residue 298 
Skipped atom 865 because residue number 105  < previous residue 298 
Skipped atom 866 because residue number 105  < previous residue 298 
Skipped atom 867 because residue number 105  < previous residue 298 
Skipped atom 868 because residue number 105  < previous residue 298 
Skipped atom 869 because residue number 105  < previous residue 298 
Skipped atom 870 because residue number 105  < previous residue 298 
Skipped atom 871 because residue number 105  < previous residue 298 
Skipped atom 872 because residue number 105  < previous residue 298 
Skipped atom 873 because residue number 105  < previous residue 298 
Skipped atom 874 because residue number 105  < previous residue 298 
Skipped atom 875 because residue number 105  < previous residue 298 
Skipped atom 876 because residue number 105  < previous residue 298 
Skipped atom 877 because residue number 106  < previous residue 298 
Skipped atom 878 because residue number 106  < previous residue 298 
Skipped atom 879 because residue number 106  < previous residue 298 
Skipped atom 880 because residue number 106  < previous residue 298 
Skipped atom 881 because residue number 106  < previous residue 298 
Skipped atom 882 because residue number 106  < previous residue 298 
Skipped atom 883 because residue number 107  < previous residue 298 
Skipped atom 884 because residue number 107  < previous residue 298 
Skipped atom 885 because residue number 107  < previous residue 298 
Skipped atom 886 because residue number 107  < previous residue 298 
Skipped atom 887 because residue number 107  < previous residue 298 
Skipped atom 888 because residue number 107  < previous residue 298 
Skipped atom 889 because residue number 107  < previous residue 298 
Skipped atom 890 because residue number 108  < previous residue 298 
Skipped atom 891 because residue number 108  < previous residue 298 
Skipped atom 892 because residue number 108  < previous residue 298 
Skipped atom 893 because residue number 108  < previous residue 298 
Skipped atom 894 because residue number 108  < previous residue 298 
Skipped atom 895 because residue number 108  < previous residue 298 
Skipped atom 896 because residue number 108  < previous residue 298 
Skipped atom 897 because residue number 108  < previous residue 298 
Skipped atom 898 because residue number 109  < previous residue 298 
Skipped atom 899 because residue number 109  < previous residue 298 
Skipped atom 900 because residue number 109  < previous residue 298 
Skipped atom 901 because residue number 109  < previous residue 298 
Skipped atom 902 because residue number 109  < previous residue 298 
Skipped atom 903 because residue number 109  < previous residue 298 
Skipped atom 904 because residue number 109  < previous residue 298 
Skipped atom 905 because residue number 109  < previous residue 298 
Skipped atom 906 because residue number 110  < previous residue 298 
Skipped atom 907 because residue number 110  < previous residue 298 
Skipped atom 908 because residue number 110  < previous residue 298 
Skipped atom 909 because residue number 110  < previous residue 298 
Skipped atom 910 because residue number 110  < previous residue 298 
Skipped atom 911 because residue number 110  < previous residue 298 
Skipped atom 912 because residue number 110  < previous residue 298 
Skipped atom 913 because residue number 110  < previous residue 298 
Skipped atom 914 because residue number 110  < previous residue 298 
Skipped atom 915 because residue number 111  < previous residue 298 
Skipped atom 916 because residue number 111  < previous residue 298 
Skipped atom 917 because residue number 111  < previous residue 298 
Skipped atom 918 because residue number 111  < previous residue 298 
Skipped atom 919 because residue number 111  < previous residue 298 
Skipped atom 920 because residue number 111  < previous residue 298 
Skipped atom 921 because residue number 111  < previous residue 298 
Skipped atom 922 because residue number 111  < previous residue 298 
Skipped atom 923 because residue number 111  < previous residue 298 
Skipped atom 924 because residue number 112  < previous residue 298 
Skipped atom 925 because residue number 112  < previous residue 298 
Skipped atom 926 because residue number 112  < previous residue 298 
Skipped atom 927 because residue number 112  < previous residue 298 
Skipped atom 928 because residue number 112  < previous residue 298 
Skipped atom 929 because residue number 112  < previous residue 298 
Skipped atom 930 because residue number 112  < previous residue 298 
Skipped atom 931 because residue number 112  < previous residue 298 
Skipped atom 932 because residue number 112  < previous residue 298 
Skipped atom 933 because residue number 112  < previous residue 298 
Skipped atom 934 because residue number 112  < previous residue 298 
Skipped atom 935 because residue number 112  < previous residue 298 
Skipped atom 936 because residue number 113  < previous residue 298 
Skipped atom 937 because residue number 113  < previous residue 298 
Skipped atom 938 because residue number 113  < previous residue 298 
Skipped atom 939 because residue number 113  < previous residue 298 
Skipped atom 940 because residue number 113  < previous residue 298 
Skipped atom 941 because residue number 113  < previous residue 298 
Skipped atom 942 because residue number 113  < previous residue 298 
Skipped atom 943 because residue number 114  < previous residue 298 
Skipped atom 944 because residue number 114  < previous residue 298 
Skipped atom 945 because residue number 114  < previous residue 298 
Skipped atom 946 because residue number 114  < previous residue 298 
Skipped atom 947 because residue number 115  < previous residue 298 
Skipped atom 948 because residue number 115  < previous residue 298 
Skipped atom 949 because residue number 115  < previous residue 298 
Skipped atom 950 because residue number 115  < previous residue 298 
Skipped atom 951 because residue number 115  < previous residue 298 
Skipped atom 952 because residue number 115  < previous residue 298 
Skipped atom 953 because residue number 115  < previous residue 298 
Skipped atom 954 because residue number 115  < previous residue 298 
Skipped atom 955 because residue number 115  < previous residue 298 
Skipped atom 956 because residue number 116  < previous residue 298 
Skipped atom 957 because residue number 116  < previous residue 298 
Skipped atom 958 because residue number 116  < previous residue 298 
Skipped atom 959 because residue number 116  < previous residue 298 
Skipped atom 960 because residue number 116  < previous residue 298 
Skipped atom 961 because residue number 116  < previous residue 298 
Skipped atom 962 because residue number 116  < previous residue 298 
Skipped atom 963 because residue number 116  < previous residue 298 
Skipped atom 964 because residue number 117  < previous residue 298 
Skipped atom 965 because residue number 117  < previous residue 298 
Skipped atom 966 because residue number 117  < previous residue 298 
Skipped atom 967 because residue number 117  < previous residue 298 
Skipped atom 968 because residue number 117  < previous residue 298 
Skipped atom 969 because residue number 117  < previous residue 298 
Skipped atom 970 because residue number 117  < previous residue 298 
Skipped atom 971 because residue number 117  < previous residue 298 
Skipped atom 972 because residue number 118  < previous residue 298 
Skipped atom 973 because residue number 118  < previous residue 298 
Skipped atom 974 because residue number 118  < previous residue 298 
Skipped atom 975 because residue number 118  < previous residue 298 
Skipped atom 976 because residue number 118  < previous residue 298 
Skipped atom 977 because residue number 118  < previous residue 298 
Skipped atom 978 because residue number 118  < previous residue 298 
Skipped atom 979 because residue number 119  < previous residue 298 
Skipped atom 980 because residue number 119  < previous residue 298 
Skipped atom 981 because residue number 119  < previous residue 298 
Skipped atom 982 because residue number 119  < previous residue 298 
Skipped atom 983 because residue number 119  < previous residue 298 
Skipped atom 984 because residue number 119  < previous residue 298 
Skipped atom 985 because residue number 119  < previous residue 298 
Skipped atom 986 because residue number 119  < previous residue 298 
Skipped atom 987 because residue number 120  < previous residue 298 
Skipped atom 988 because residue number 120  < previous residue 298 
Skipped atom 989 because residue number 120  < previous residue 298 
Skipped atom 990 because residue number 120  < previous residue 298 
Skipped atom 991 because residue number 120  < previous residue 298 
Skipped atom 992 because residue number 120  < previous residue 298 
Skipped atom 993 because residue number 120  < previous residue 298 
Skipped atom 994 because residue number 120  < previous residue 298 
Skipped atom 995 because residue number 120  < previous residue 298 
Skipped atom 996 because residue number 121  < previous residue 298 
Skipped atom 997 because residue number 121  < previous residue 298 
Skipped atom 998 because residue number 121  < previous residue 298 
Skipped atom 999 because residue number 121  < previous residue 298 
Skipped atom 1000 because residue number 121  < previous residue 298 
Skipped atom 1001 because residue number 122  < previous residue 298 
Skipped atom 1002 because residue number 122  < previous residue 298 
Skipped atom 1003 because residue number 122  < previous residue 298 
Skipped atom 1004 because residue number 122  < previous residue 298 
Skipped atom 1005 because residue number 122  < previous residue 298 
Skipped atom 1006 because residue number 122  < previous residue 298 
Skipped atom 1007 because residue number 122  < previous residue 298 
Skipped atom 1008 because residue number 122  < previous residue 298 
Skipped atom 1009 because residue number 123  < previous residue 298 
Skipped atom 1010 because residue number 123  < previous residue 298 
Skipped atom 1011 because residue number 123  < previous residue 298 
Skipped atom 1012 because residue number 123  < previous residue 298 
Skipped atom 1013 because residue number 123  < previous residue 298 
Skipped atom 1014 because residue number 123  < previous residue 298 
Skipped atom 1015 because residue number 123  < previous residue 298 
Skipped atom 1016 because residue number 123  < previous residue 298 
Skipped atom 1017 because residue number 124  < previous residue 298 
Skipped atom 1018 because residue number 124  < previous residue 298 
Skipped atom 1019 because residue number 124  < previous residue 298 
Skipped atom 1020 because residue number 124  < previous residue 298 
Skipped atom 1021 because residue number 124  < previous residue 298 
Skipped atom 1022 because residue number 124  < previous residue 298 
Skipped atom 1023 because residue number 124  < previous residue 298 
Skipped atom 1024 because residue number 124  < previous residue 298 
Skipped atom 1025 because residue number 124  < previous residue 298 
Skipped atom 1026 because residue number 125  < previous residue 298 
Skipped atom 1027 because residue number 125  < previous residue 298 
Skipped atom 1028 because residue number 125  < previous residue 298 
Skipped atom 1029 because residue number 125  < previous residue 298 
Skipped atom 1030 because residue number 125  < previous residue 298 
Skipped atom 1031 because residue number 126  < previous residue 298 
Skipped atom 1032 because residue number 126  < previous residue 298 
Skipped atom 1033 because residue number 126  < previous residue 298 
Skipped atom 1034 because residue number 126  < previous residue 298 
Skipped atom 1035 because residue number 126  < previous residue 298 
Skipped atom 1036 because residue number 126  < previous residue 298 
Skipped atom 1037 because residue number 127  < previous residue 298 
Skipped atom 1038 because residue number 127  < previous residue 298 
Skipped atom 1039 because residue number 127  < previous residue 298 
Skipped atom 1040 because residue number 127  < previous residue 298 
Skipped atom 1041 because residue number 127  < previous residue 298 
Skipped atom 1042 because residue number 127  < previous residue 298 
Skipped atom 1043 because residue number 127  < previous residue 298 
Skipped atom 1044 because residue number 127  < previous residue 298 
Skipped atom 1045 because residue number 128  < previous residue 298 
Skipped atom 1046 because residue number 128  < previous residue 298 
Skipped atom 1047 because residue number 128  < previous residue 298 
Skipped atom 1048 because residue number 128  < previous residue 298 
Skipped atom 1049 because residue number 128  < previous residue 298 
Skipped atom 1050 because residue number 128  < previous residue 298 
Skipped atom 1051 because residue number 128  < previous residue 298 
Skipped atom 1052 because residue number 129  < previous residue 298 
Skipped atom 1053 because residue number 129  < previous residue 298 
Skipped atom 1054 because residue number 129  < previous residue 298 
Skipped atom 1055 because residue number 129  < previous residue 298 
Skipped atom 1056 because residue number 129  < previous residue 298 
Skipped atom 1057 because residue number 129  < previous residue 298 
Skipped atom 1058 because residue number 129  < previous residue 298 
Skipped atom 1059 because residue number 129  < previous residue 298 
Skipped atom 1060 because residue number 129  < previous residue 298 
Skipped atom 1061 because residue number 129  < previous residue 298 
Skipped atom 1062 because residue number 129  < previous residue 298 
Skipped atom 1063 because residue number 129  < previous residue 298 
Skipped atom 1064 because residue number 130  < previous residue 298 
Skipped atom 1065 because residue number 130  < previous residue 298 
Skipped atom 1066 because residue number 130  < previous residue 298 
Skipped atom 1067 because residue number 130  < previous residue 298 
Skipped atom 1068 because residue number 130  < previous residue 298 
Skipped atom 1069 because residue number 130  < previous residue 298 
Skipped atom 1070 because residue number 131  < previous residue 298 
Skipped atom 1071 because residue number 131  < previous residue 298 
Skipped atom 1072 because residue number 131  < previous residue 298 
Skipped atom 1073 because residue number 131  < previous residue 298 
Skipped atom 1074 because residue number 131  < previous residue 298 
Skipped atom 1075 because residue number 131  < previous residue 298 
Skipped atom 1076 because residue number 131  < previous residue 298 
Skipped atom 1077 because residue number 131  < previous residue 298 
Skipped atom 1078 because residue number 132  < previous residue 298 
Skipped atom 1079 because residue number 132  < previous residue 298 
Skipped atom 1080 because residue number 132  < previous residue 298 
Skipped atom 1081 because residue number 132  < previous residue 298 
Skipped atom 1082 because residue number 132  < previous residue 298 
Skipped atom 1083 because residue number 132  < previous residue 298 
Skipped atom 1084 because residue number 132  < previous residue 298 
Skipped atom 1085 because residue number 132  < previous residue 298 
Skipped atom 1086 because residue number 133  < previous residue 298 
Skipped atom 1087 because residue number 133  < previous residue 298 
Skipped atom 1088 because residue number 133  < previous residue 298 
Skipped atom 1089 because residue number 133  < previous residue 298 
Skipped atom 1090 because residue number 133  < previous residue 298 
Skipped atom 1091 because residue number 133  < previous residue 298 
Skipped atom 1092 because residue number 133  < previous residue 298 
Skipped atom 1093 because residue number 134  < previous residue 298 
Skipped atom 1094 because residue number 134  < previous residue 298 
Skipped atom 1095 because residue number 134  < previous residue 298 
Skipped atom 1096 because residue number 134  < previous residue 298 
Skipped atom 1097 because residue number 134  < previous residue 298 
Skipped atom 1098 because residue number 135  < previous residue 298 
Skipped atom 1099 because residue number 135  < previous residue 298 
Skipped atom 1100 because residue number 135  < previous residue 298 
Skipped atom 1101 because residue number 135  < previous residue 298 
Skipped atom 1102 because residue number 135  < previous residue 298 
Skipped atom 1103 because residue number 135  < previous residue 298 
Skipped atom 1104 because residue number 135  < previous residue 298 
Skipped atom 1105 because residue number 135  < previous residue 298 
Skipped atom 1106 because residue number 136  < previous residue 298 
Skipped atom 1107 because residue number 136  < previous residue 298 
Skipped atom 1108 because residue number 136  < previous residue 298 
Skipped atom 1109 because residue number 136  < previous residue 298 
Skipped atom 1110 because residue number 136  < previous residue 298 
Skipped atom 1111 because residue number 136  < previous residue 298 
Skipped atom 1112 because residue number 136  < previous residue 298 
Skipped atom 1113 because residue number 136  < previous residue 298 
Skipped atom 1114 because residue number 137  < previous residue 298 
Skipped atom 1115 because residue number 137  < previous residue 298 
Skipped atom 1116 because residue number 137  < previous residue 298 
Skipped atom 1117 because residue number 137  < previous residue 298 
Skipped atom 1118 because residue number 137  < previous residue 298 
Skipped atom 1119 because residue number 137  < previous residue 298 
Skipped atom 1120 because residue number 137  < previous residue 298 
Skipped atom 1121 because residue number 137  < previous residue 298 
Skipped atom 1122 because residue number 137  < previous residue 298 
Skipped atom 1123 because residue number 138  < previous residue 298 
Skipped atom 1124 because residue number 138  < previous residue 298 
Skipped atom 1125 because residue number 138  < previous residue 298 
Skipped atom 1126 because residue number 138  < previous residue 298 
Skipped atom 1127 because residue number 138  < previous residue 298 
Skipped atom 1128 because residue number 138  < previous residue 298 
Skipped atom 1129 because residue number 138  < previous residue 298 
Skipped atom 1130 because residue number 138  < previous residue 298 
Skipped atom 1131 because residue number 139  < previous residue 298 
Skipped atom 1132 because residue number 139  < previous residue 298 
Skipped atom 1133 because residue number 139  < previous residue 298 
Skipped atom 1134 because residue number 139  < previous residue 298 
Skipped atom 1135 because residue number 139  < previous residue 298 
Skipped atom 1136 because residue number 139  < previous residue 298 
Skipped atom 1137 because residue number 139  < previous residue 298 
Skipped atom 1138 because residue number 139  < previous residue 298 
Skipped atom 1139 because residue number 140  < previous residue 298 
Skipped atom 1140 because residue number 140  < previous residue 298 
Skipped atom 1141 because residue number 140  < previous residue 298 
Skipped atom 1142 because residue number 140  < previous residue 298 
Skipped atom 1143 because residue number 140  < previous residue 298 
Skipped atom 1144 because residue number 140  < previous residue 298 
Skipped atom 1145 because residue number 140  < previous residue 298 
Skipped atom 1146 because residue number 140  < previous residue 298 
Skipped atom 1147 because residue number 140  < previous residue 298 
Skipped atom 1148 because residue number 141  < previous residue 298 
Skipped atom 1149 because residue number 141  < previous residue 298 
Skipped atom 1150 because residue number 141  < previous residue 298 
Skipped atom 1151 because residue number 141  < previous residue 298 
Skipped atom 1152 because residue number 141  < previous residue 298 
Skipped atom 1153 because residue number 141  < previous residue 298 
Skipped atom 1154 because residue number 141  < previous residue 298 
Skipped atom 1155 because residue number 141  < previous residue 298 
Skipped atom 1156 because residue number 141  < previous residue 298 
Skipped atom 1157 because residue number 142  < previous residue 298 
Skipped atom 1158 because residue number 142  < previous residue 298 
Skipped atom 1159 because residue number 142  < previous residue 298 
Skipped atom 1160 because residue number 142  < previous residue 298 
Skipped atom 1161 because residue number 142  < previous residue 298 
Skipped atom 1162 because residue number 142  < previous residue 298 
Skipped atom 1163 because residue number 142  < previous residue 298 
Skipped atom 1164 because residue number 142  < previous residue 298 
Skipped atom 1165 because residue number 143  < previous residue 298 
Skipped atom 1166 because residue number 143  < previous residue 298 
Skipped atom 1167 because residue number 143  < previous residue 298 
Skipped atom 1168 because residue number 143  < previous residue 298 
Skipped atom 1169 because residue number 144  < previous residue 298 
Skipped atom 1170 because residue number 144  < previous residue 298 
Skipped atom 1171 because residue number 144  < previous residue 298 
Skipped atom 1172 because residue number 144  < previous residue 298 
Skipped atom 1173 because residue number 145  < previous residue 298 
Skipped atom 1174 because residue number 145  < previous residue 298 
Skipped atom 1175 because residue number 145  < previous residue 298 
Skipped atom 1176 because residue number 145  < previous residue 298 
Skipped atom 1177 because residue number 145  < previous residue 298 
Skipped atom 1178 because residue number 145  < previous residue 298 
Skipped atom 1179 because residue number 145  < previous residue 298 
Skipped atom 1180 because residue number 145  < previous residue 298 
Skipped atom 1181 because residue number 146  < previous residue 298 
Skipped atom 1182 because residue number 146  < previous residue 298 
Skipped atom 1183 because residue number 146  < previous residue 298 
Skipped atom 1184 because residue number 146  < previous residue 298 
Skipped atom 1185 because residue number 146  < previous residue 298 
Skipped atom 1186 because residue number 146  < previous residue 298 
Skipped atom 1187 because residue number 146  < previous residue 298 
Skipped atom 1188 because residue number 146  < previous residue 298 
Skipped atom 1189 because residue number 146  < previous residue 298 
Skipped atom 1190 because residue number 147  < previous residue 298 
Skipped atom 1191 because residue number 147  < previous residue 298 
Skipped atom 1192 because residue number 147  < previous residue 298 
Skipped atom 1193 because residue number 147  < previous residue 298 
Skipped atom 1194 because residue number 147  < previous residue 298 
Skipped atom 1195 because residue number 147  < previous residue 298 
Skipped atom 1196 because residue number 147  < previous residue 298 
Skipped atom 1197 because residue number 147  < previous residue 298 
Skipped atom 1198 because residue number 147  < previous residue 298 
Skipped atom 1199 because residue number 148  < previous residue 298 
Skipped atom 1200 because residue number 148  < previous residue 298 
Skipped atom 1201 because residue number 148  < previous residue 298 
Skipped atom 1202 because residue number 148  < previous residue 298 
Skipped atom 1203 because residue number 148  < previous residue 298 
Skipped atom 1204 because residue number 148  < previous residue 298 
Skipped atom 1205 because residue number 148  < previous residue 298 
Skipped atom 1206 because residue number 149  < previous residue 298 
Skipped atom 1207 because residue number 149  < previous residue 298 
Skipped atom 1208 because residue number 149  < previous residue 298 
Skipped atom 1209 because residue number 149  < previous residue 298 
Skipped atom 1210 because residue number 149  < previous residue 298 
Skipped atom 1211 because residue number 149  < previous residue 298 
Skipped atom 1212 because residue number 149  < previous residue 298 
Skipped atom 1213 because residue number 149  < previous residue 298 
Skipped atom 1214 because residue number 149  < previous residue 298 
Skipped atom 1215 because residue number 150  < previous residue 298 
Skipped atom 1216 because residue number 150  < previous residue 298 
Skipped atom 1217 because residue number 150  < previous residue 298 
Skipped atom 1218 because residue number 150  < previous residue 298 
Skipped atom 1219 because residue number 150  < previous residue 298 
Skipped atom 1220 because residue number 150  < previous residue 298 
Skipped atom 1221 because residue number 150  < previous residue 298 
Skipped atom 1222 because residue number 150  < previous residue 298 
Skipped atom 1223 because residue number 150  < previous residue 298 
Skipped atom 1224 because residue number 151  < previous residue 298 
Skipped atom 1225 because residue number 151  < previous residue 298 
Skipped atom 1226 because residue number 151  < previous residue 298 
Skipped atom 1227 because residue number 151  < previous residue 298 
Skipped atom 1228 because residue number 151  < previous residue 298 
Skipped atom 1229 because residue number 151  < previous residue 298 
Skipped atom 1230 because residue number 151  < previous residue 298 
Skipped atom 1231 because residue number 151  < previous residue 298 
Skipped atom 1232 because residue number 151  < previous residue 298 
Skipped atom 1233 because residue number 151  < previous residue 298 
Skipped atom 1234 because residue number 151  < previous residue 298 
Skipped atom 1235 because residue number 152  < previous residue 298 
Skipped atom 1236 because residue number 152  < previous residue 298 
Skipped atom 1237 because residue number 152  < previous residue 298 
Skipped atom 1238 because residue number 152  < previous residue 298 
Skipped atom 1239 because residue number 152  < previous residue 298 
Skipped atom 1240 because residue number 152  < previous residue 298 
Skipped atom 1241 because residue number 152  < previous residue 298 
Skipped atom 1242 because residue number 152  < previous residue 298 
Skipped atom 1243 because residue number 153  < previous residue 298 
Skipped atom 1244 because residue number 153  < previous residue 298 
Skipped atom 1245 because residue number 153  < previous residue 298 
Skipped atom 1246 because residue number 153  < previous residue 298 
Skipped atom 1247 because residue number 153  < previous residue 298 
Skipped atom 1248 because residue number 153  < previous residue 298 
Skipped atom 1249 because residue number 153  < previous residue 298 
Skipped atom 1250 because residue number 153  < previous residue 298 
Skipped atom 1251 because residue number 153  < previous residue 298 
Skipped atom 1252 because residue number 154  < previous residue 298 
Skipped atom 1253 because residue number 154  < previous residue 298 
Skipped atom 1254 because residue number 154  < previous residue 298 
Skipped atom 1255 because residue number 154  < previous residue 298 
Skipped atom 1256 because residue number 154  < previous residue 298 
Skipped atom 1257 because residue number 154  < previous residue 298 
Skipped atom 1258 because residue number 154  < previous residue 298 
Skipped atom 1259 because residue number 154  < previous residue 298 
Skipped atom 1260 because residue number 154  < previous residue 298 
Skipped atom 1261 because residue number 155  < previous residue 298 
Skipped atom 1262 because residue number 155  < previous residue 298 
Skipped atom 1263 because residue number 155  < previous residue 298 
Skipped atom 1264 because residue number 155  < previous residue 298 
Skipped atom 1265 because residue number 155  < previous residue 298 
Skipped atom 1266 because residue number 155  < previous residue 298 
Skipped atom 1267 because residue number 155  < previous residue 298 
Skipped atom 1268 because residue number 155  < previous residue 298 
Skipped atom 1269 because residue number 156  < previous residue 298 
Skipped atom 1270 because residue number 156  < previous residue 298 
Skipped atom 1271 because residue number 156  < previous residue 298 
Skipped atom 1272 because residue number 156  < previous residue 298 
Skipped atom 1273 because residue number 157  < previous residue 298 
Skipped atom 1274 because residue number 157  < previous residue 298 
Skipped atom 1275 because residue number 157  < previous residue 298 
Skipped atom 1276 because residue number 157  < previous residue 298 
Skipped atom 1277 because residue number 157  < previous residue 298 
Skipped atom 1278 because residue number 157  < previous residue 298 
Skipped atom 1279 because residue number 157  < previous residue 298 
Skipped atom 1280 because residue number 157  < previous residue 298 
Skipped atom 1281 because residue number 158  < previous residue 298 
Skipped atom 1282 because residue number 158  < previous residue 298 
Skipped atom 1283 because residue number 158  < previous residue 298 
Skipped atom 1284 because residue number 158  < previous residue 298 
Skipped atom 1285 because residue number 158  < previous residue 298 
Skipped atom 1286 because residue number 158  < previous residue 298 
Skipped atom 1287 because residue number 158  < previous residue 298 
Skipped atom 1288 because residue number 158  < previous residue 298 
Skipped atom 1289 because residue number 158  < previous residue 298 
Skipped atom 1290 because residue number 159  < previous residue 298 
Skipped atom 1291 because residue number 159  < previous residue 298 
Skipped atom 1292 because residue number 159  < previous residue 298 
Skipped atom 1293 because residue number 159  < previous residue 298 
Skipped atom 1294 because residue number 159  < previous residue 298 
Skipped atom 1295 because residue number 159  < previous residue 298 
Skipped atom 1296 because residue number 159  < previous residue 298 
Skipped atom 1297 because residue number 160  < previous residue 298 
Skipped atom 1298 because residue number 160  < previous residue 298 
Skipped atom 1299 because residue number 160  < previous residue 298 
Skipped atom 1300 because residue number 160  < previous residue 298 
Skipped atom 1301 because residue number 160  < previous residue 298 
Skipped atom 1302 because residue number 160  < previous residue 298 
Skipped atom 1303 because residue number 160  < previous residue 298 
Skipped atom 1304 because residue number 161  < previous residue 298 
Skipped atom 1305 because residue number 161  < previous residue 298 
Skipped atom 1306 because residue number 161  < previous residue 298 
Skipped atom 1307 because residue number 161  < previous residue 298 
Skipped atom 1308 because residue number 161  < previous residue 298 
Skipped atom 1309 because residue number 161  < previous residue 298 
Skipped atom 1310 because residue number 161  < previous residue 298 
Skipped atom 1311 because residue number 161  < previous residue 298 
Skipped atom 1312 because residue number 162  < previous residue 298 
Skipped atom 1313 because residue number 162  < previous residue 298 
Skipped atom 1314 because residue number 162  < previous residue 298 
Skipped atom 1315 because residue number 162  < previous residue 298 
Skipped atom 1316 because residue number 162  < previous residue 298 
Skipped atom 1317 because residue number 162  < previous residue 298 
Skipped atom 1318 because residue number 162  < previous residue 298 
Skipped atom 1319 because residue number 163  < previous residue 298 
Skipped atom 1320 because residue number 163  < previous residue 298 
Skipped atom 1321 because residue number 163  < previous residue 298 
Skipped atom 1322 because residue number 163  < previous residue 298 
Skipped atom 1323 because residue number 163  < previous residue 298 
Skipped atom 1324 because residue number 163  < previous residue 298 
Skipped atom 1325 because residue number 163  < previous residue 298 
Skipped atom 1326 because residue number 164  < previous residue 298 
Skipped atom 1327 because residue number 164  < previous residue 298 
Skipped atom 1328 because residue number 164  < previous residue 298 
Skipped atom 1329 because residue number 164  < previous residue 298 
Skipped atom 1330 because residue number 164  < previous residue 298 
Skipped atom 1331 because residue number 164  < previous residue 298 
Skipped atom 1332 because residue number 164  < previous residue 298 
Skipped atom 1333 because residue number 164  < previous residue 298 
Skipped atom 1334 because residue number 164  < previous residue 298 
Skipped atom 1335 because residue number 164  < previous residue 298 
Skipped atom 1336 because residue number 164  < previous residue 298 
Skipped atom 1337 because residue number 165  < previous residue 298 
Skipped atom 1338 because residue number 165  < previous residue 298 
Skipped atom 1339 because residue number 165  < previous residue 298 
Skipped atom 1340 because residue number 165  < previous residue 298 
Skipped atom 1341 because residue number 165  < previous residue 298 
Skipped atom 1342 because residue number 165  < previous residue 298 
Skipped atom 1343 because residue number 165  < previous residue 298 
Skipped atom 1344 because residue number 165  < previous residue 298 
Skipped atom 1345 because residue number 165  < previous residue 298 
Skipped atom 1346 because residue number 165  < previous residue 298 
Skipped atom 1347 because residue number 165  < previous residue 298 
Skipped atom 1348 because residue number 165  < previous residue 298 
Skipped atom 1349 because residue number 166  < previous residue 298 
Skipped atom 1350 because residue number 166  < previous residue 298 
Skipped atom 1351 because residue number 166  < previous residue 298 
Skipped atom 1352 because residue number 166  < previous residue 298 
Skipped atom 1353 because residue number 166  < previous residue 298 
Skipped atom 1354 because residue number 166  < previous residue 298 
Skipped atom 1355 because residue number 166  < previous residue 298 
Skipped atom 1356 because residue number 166  < previous residue 298 
Skipped atom 1357 because residue number 166  < previous residue 298 
Skipped atom 1358 because residue number 167  < previous residue 298 
Skipped atom 1359 because residue number 167  < previous residue 298 
Skipped atom 1360 because residue number 167  < previous residue 298 
Skipped atom 1361 because residue number 167  < previous residue 298 
Skipped atom 1362 because residue number 167  < previous residue 298 
Skipped atom 1363 because residue number 167  < previous residue 298 
Skipped atom 1364 because residue number 167  < previous residue 298 
Skipped atom 1365 because residue number 167  < previous residue 298 
Skipped atom 1366 because residue number 168  < previous residue 298 
Skipped atom 1367 because residue number 168  < previous residue 298 
Skipped atom 1368 because residue number 168  < previous residue 298 
Skipped atom 1369 because residue number 168  < previous residue 298 
Skipped atom 1370 because residue number 168  < previous residue 298 
Skipped atom 1371 because residue number 168  < previous residue 298 
Skipped atom 1372 because residue number 168  < previous residue 298 
Skipped atom 1373 because residue number 168  < previous residue 298 
Skipped atom 1374 because residue number 168  < previous residue 298 
Skipped atom 1375 because residue number 169  < previous residue 298 
Skipped atom 1376 because residue number 169  < previous residue 298 
Skipped atom 1377 because residue number 169  < previous residue 298 
Skipped atom 1378 because residue number 169  < previous residue 298 
Skipped atom 1379 because residue number 169  < previous residue 298 
Skipped atom 1380 because residue number 169  < previous residue 298 
Skipped atom 1381 because residue number 169  < previous residue 298 
Skipped atom 1382 because residue number 169  < previous residue 298 
Skipped atom 1383 because residue number 170  < previous residue 298 
Skipped atom 1384 because residue number 170  < previous residue 298 
Skipped atom 1385 because residue number 170  < previous residue 298 
Skipped atom 1386 because residue number 170  < previous residue 298 
Skipped atom 1387 because residue number 170  < previous residue 298 
Skipped atom 1388 because residue number 170  < previous residue 298 
Skipped atom 1389 because residue number 170  < previous residue 298 
Skipped atom 1390 because residue number 170  < previous residue 298 
Skipped atom 1391 because residue number 171  < previous residue 298 
Skipped atom 1392 because residue number 171  < previous residue 298 
Skipped atom 1393 because residue number 171  < previous residue 298 
Skipped atom 1394 because residue number 171  < previous residue 298 
Skipped atom 1395 because residue number 171  < previous residue 298 
Skipped atom 1396 because residue number 171  < previous residue 298 
Skipped atom 1397 because residue number 171  < previous residue 298 
Skipped atom 1398 because residue number 171  < previous residue 298 
Skipped atom 1399 because residue number 171  < previous residue 298 
Skipped atom 1400 because residue number 171  < previous residue 298 
Skipped atom 1401 because residue number 171  < previous residue 298 
Skipped atom 1402 because residue number 171  < previous residue 298 
Skipped atom 1403 because residue number 172  < previous residue 298 
Skipped atom 1404 because residue number 172  < previous residue 298 
Skipped atom 1405 because residue number 172  < previous residue 298 
Skipped atom 1406 because residue number 172  < previous residue 298 
Skipped atom 1407 because residue number 172  < previous residue 298 
Skipped atom 1408 because residue number 172  < previous residue 298 
Skipped atom 1409 because residue number 172  < previous residue 298 
Skipped atom 1410 because residue number 172  < previous residue 298 
Skipped atom 1411 because residue number 172  < previous residue 298 
Skipped atom 1412 because residue number 172  < previous residue 298 
Skipped atom 1413 because residue number 172  < previous residue 298 
Skipped atom 1414 because residue number 172  < previous residue 298 
Skipped atom 1415 because residue number 173  < previous residue 298 
Skipped atom 1416 because residue number 173  < previous residue 298 
Skipped atom 1417 because residue number 173  < previous residue 298 
Skipped atom 1418 because residue number 173  < previous residue 298 
Skipped atom 1419 because residue number 173  < previous residue 298 
Skipped atom 1420 because residue number 173  < previous residue 298 
Skipped atom 1421 because residue number 174  < previous residue 298 
Skipped atom 1422 because residue number 174  < previous residue 298 
Skipped atom 1423 because residue number 174  < previous residue 298 
Skipped atom 1424 because residue number 174  < previous residue 298 
Skipped atom 1425 because residue number 174  < previous residue 298 
Skipped atom 1426 because residue number 174  < previous residue 298 
Skipped atom 1427 because residue number 174  < previous residue 298 
Skipped atom 1428 because residue number 175  < previous residue 298 
Skipped atom 1429 because residue number 175  < previous residue 298 
Skipped atom 1430 because residue number 175  < previous residue 298 
Skipped atom 1431 because residue number 175  < previous residue 298 
Skipped atom 1432 because residue number 175  < previous residue 298 
Skipped atom 1433 because residue number 175  < previous residue 298 
Skipped atom 1434 because residue number 175  < previous residue 298 
Skipped atom 1435 because residue number 175  < previous residue 298 
Skipped atom 1436 because residue number 175  < previous residue 298 
Skipped atom 1437 because residue number 176  < previous residue 298 
Skipped atom 1438 because residue number 176  < previous residue 298 
Skipped atom 1439 because residue number 176  < previous residue 298 
Skipped atom 1440 because residue number 176  < previous residue 298 
Skipped atom 1441 because residue number 176  < previous residue 298 
Skipped atom 1442 because residue number 176  < previous residue 298 
Skipped atom 1443 because residue number 177  < previous residue 298 
Skipped atom 1444 because residue number 177  < previous residue 298 
Skipped atom 1445 because residue number 177  < previous residue 298 
Skipped atom 1446 because residue number 177  < previous residue 298 
Skipped atom 1447 because residue number 177  < previous residue 298 
Skipped atom 1448 because residue number 177  < previous residue 298 
Skipped atom 1449 because residue number 177  < previous residue 298 
Skipped atom 1450 because residue number 177  < previous residue 298 
Skipped atom 1451 because residue number 177  < previous residue 298 
Skipped atom 1452 because residue number 178  < previous residue 298 
Skipped atom 1453 because residue number 178  < previous residue 298 
Skipped atom 1454 because residue number 178  < previous residue 298 
Skipped atom 1455 because residue number 178  < previous residue 298 
Skipped atom 1456 because residue number 178  < previous residue 298 
Skipped atom 1457 because residue number 178  < previous residue 298 
Skipped atom 1458 because residue number 178  < previous residue 298 
Skipped atom 1459 because residue number 178  < previous residue 298 
Skipped atom 1460 because residue number 178  < previous residue 298 
Skipped atom 1461 because residue number 179  < previous residue 298 
Skipped atom 1462 because residue number 179  < previous residue 298 
Skipped atom 1463 because residue number 179  < previous residue 298 
Skipped atom 1464 because residue number 179  < previous residue 298 
Skipped atom 1465 because residue number 179  < previous residue 298 
Skipped atom 1466 because residue number 179  < previous residue 298 
Skipped atom 1467 because residue number 179  < previous residue 298 
Skipped atom 1468 because residue number 179  < previous residue 298 
Skipped atom 1469 because residue number 180  < previous residue 298 
Skipped atom 1470 because residue number 180  < previous residue 298 
Skipped atom 1471 because residue number 180  < previous residue 298 
Skipped atom 1472 because residue number 180  < previous residue 298 
Skipped atom 1473 because residue number 180  < previous residue 298 
Skipped atom 1474 because residue number 180  < previous residue 298 
Skipped atom 1475 because residue number 180  < previous residue 298 
Skipped atom 1476 because residue number 181  < previous residue 298 
Skipped atom 1477 because residue number 181  < previous residue 298 
Skipped atom 1478 because residue number 181  < previous residue 298 
Skipped atom 1479 because residue number 181  < previous residue 298 
Skipped atom 1480 because residue number 181  < previous residue 298 
Skipped atom 1481 because residue number 181  < previous residue 298 
Skipped atom 1482 because residue number 182  < previous residue 298 
Skipped atom 1483 because residue number 182  < previous residue 298 
Skipped atom 1484 because residue number 182  < previous residue 298 
Skipped atom 1485 because residue number 182  < previous residue 298 
Skipped atom 1486 because residue number 182  < previous residue 298 
Skipped atom 1487 because residue number 182  < previous residue 298 
Skipped atom 1488 because residue number 182  < previous residue 298 
Skipped atom 1489 because residue number 183  < previous residue 298 
Skipped atom 1490 because residue number 183  < previous residue 298 
Skipped atom 1491 because residue number 183  < previous residue 298 
Skipped atom 1492 because residue number 183  < previous residue 298 
Skipped atom 1493 because residue number 183  < previous residue 298 
Skipped atom 1494 because residue number 183  < previous residue 298 
Skipped atom 1495 because residue number 183  < previous residue 298 
Skipped atom 1496 because residue number 184  < previous residue 298 
Skipped atom 1497 because residue number 184  < previous residue 298 
Skipped atom 1498 because residue number 184  < previous residue 298 
Skipped atom 1499 because residue number 184  < previous residue 298 
Skipped atom 1500 because residue number 184  < previous residue 298 
Skipped atom 1501 because residue number 185  < previous residue 298 
Skipped atom 1502 because residue number 185  < previous residue 298 
Skipped atom 1503 because residue number 185  < previous residue 298 
Skipped atom 1504 because residue number 185  < previous residue 298 
Skipped atom 1505 because residue number 185  < previous residue 298 
Skipped atom 1506 because residue number 186  < previous residue 298 
Skipped atom 1507 because residue number 186  < previous residue 298 
Skipped atom 1508 because residue number 186  < previous residue 298 
Skipped atom 1509 because residue number 186  < previous residue 298 
Skipped atom 1510 because residue number 186  < previous residue 298 
Skipped atom 1511 because residue number 186  < previous residue 298 
Skipped atom 1512 because residue number 186  < previous residue 298 
Skipped atom 1513 because residue number 186  < previous residue 298 
Skipped atom 1514 because residue number 186  < previous residue 298 
Skipped atom 1515 because residue number 186  < previous residue 298 
Skipped atom 1516 because residue number 186  < previous residue 298 
Skipped atom 1517 because residue number 187  < previous residue 298 
Skipped atom 1518 because residue number 187  < previous residue 298 
Skipped atom 1519 because residue number 187  < previous residue 298 
Skipped atom 1520 because residue number 187  < previous residue 298 
Skipped atom 1521 because residue number 188  < previous residue 298 
Skipped atom 1522 because residue number 188  < previous residue 298 
Skipped atom 1523 because residue number 188  < previous residue 298 
Skipped atom 1524 because residue number 188  < previous residue 298 
Skipped atom 1525 because residue number 188  < previous residue 298 
Skipped atom 1526 because residue number 188  < previous residue 298 
Skipped atom 1527 because residue number 188  < previous residue 298 
Skipped atom 1528 because residue number 188  < previous residue 298 
Skipped atom 1529 because residue number 188  < previous residue 298 
Skipped atom 1530 because residue number 189  < previous residue 298 
Skipped atom 1531 because residue number 189  < previous residue 298 
Skipped atom 1532 because residue number 189  < previous residue 298 
Skipped atom 1533 because residue number 189  < previous residue 298 
Skipped atom 1534 because residue number 189  < previous residue 298 
Skipped atom 1535 because residue number 189  < previous residue 298 
Skipped atom 1536 because residue number 189  < previous residue 298 
Skipped atom 1537 because residue number 190  < previous residue 298 
Skipped atom 1538 because residue number 190  < previous residue 298 
Skipped atom 1539 because residue number 190  < previous residue 298 
Skipped atom 1540 because residue number 190  < previous residue 298 
Skipped atom 1541 because residue number 190  < previous residue 298 
Skipped atom 1542 because residue number 190  < previous residue 298 
Skipped atom 1543 because residue number 190  < previous residue 298 
Skipped atom 1544 because residue number 190  < previous residue 298 
Skipped atom 1545 because residue number 191  < previous residue 298 
Skipped atom 1546 because residue number 191  < previous residue 298 
Skipped atom 1547 because residue number 191  < previous residue 298 
Skipped atom 1548 because residue number 191  < previous residue 298 
Skipped atom 1549 because residue number 191  < previous residue 298 
Skipped atom 1550 because residue number 191  < previous residue 298 
Skipped atom 1551 because residue number 191  < previous residue 298 
Skipped atom 1552 because residue number 191  < previous residue 298 
Skipped atom 1553 because residue number 192  < previous residue 298 
Skipped atom 1554 because residue number 192  < previous residue 298 
Skipped atom 1555 because residue number 192  < previous residue 298 
Skipped atom 1556 because residue number 192  < previous residue 298 
Skipped atom 1557 because residue number 192  < previous residue 298 
Skipped atom 1558 because residue number 192  < previous residue 298 
Skipped atom 1559 because residue number 192  < previous residue 298 
Skipped atom 1560 because residue number 192  < previous residue 298 
Skipped atom 1561 because residue number 192  < previous residue 298 
Skipped atom 1562 because residue number 193  < previous residue 298 
Skipped atom 1563 because residue number 193  < previous residue 298 
Skipped atom 1564 because residue number 193  < previous residue 298 
Skipped atom 1565 because residue number 193  < previous residue 298 
Skipped atom 1566 because residue number 193  < previous residue 298 
Skipped atom 1567 because residue number 193  < previous residue 298 
Skipped atom 1568 because residue number 193  < previous residue 298 
Skipped atom 1569 because residue number 193  < previous residue 298 
Skipped atom 1570 because residue number 194  < previous residue 298 
Skipped atom 1571 because residue number 194  < previous residue 298 
Skipped atom 1572 because residue number 194  < previous residue 298 
Skipped atom 1573 because residue number 194  < previous residue 298 
Skipped atom 1574 because residue number 194  < previous residue 298 
Skipped atom 1575 because residue number 194  < previous residue 298 
Skipped atom 1576 because residue number 194  < previous residue 298 
Skipped atom 1577 because residue number 194  < previous residue 298 
Skipped atom 1578 because residue number 195  < previous residue 298 
Skipped atom 1579 because residue number 195  < previous residue 298 
Skipped atom 1580 because residue number 195  < previous residue 298 
Skipped atom 1581 because residue number 195  < previous residue 298 
Skipped atom 1582 because residue number 195  < previous residue 298 
Skipped atom 1583 because residue number 196  < previous residue 298 
Skipped atom 1584 because residue number 196  < previous residue 298 
Skipped atom 1585 because residue number 196  < previous residue 298 
Skipped atom 1586 because residue number 196  < previous residue 298 
Skipped atom 1587 because residue number 196  < previous residue 298 
Skipped atom 1588 because residue number 196  < previous residue 298 
Skipped atom 1589 because residue number 196  < previous residue 298 
Skipped atom 1590 because residue number 196  < previous residue 298 
Skipped atom 1591 because residue number 197  < previous residue 298 
Skipped atom 1592 because residue number 197  < previous residue 298 
Skipped atom 1593 because residue number 197  < previous residue 298 
Skipped atom 1594 because residue number 197  < previous residue 298 
Skipped atom 1595 because residue number 198  < previous residue 298 
Skipped atom 1596 because residue number 198  < previous residue 298 
Skipped atom 1597 because residue number 198  < previous residue 298 
Skipped atom 1598 because residue number 198  < previous residue 298 
Skipped atom 1599 because residue number 198  < previous residue 298 
Skipped atom 1600 because residue number 198  < previous residue 298 
Skipped atom 1601 because residue number 198  < previous residue 298 
Skipped atom 1602 because residue number 198  < previous residue 298 
Skipped atom 1603 because residue number 198  < previous residue 298 
Skipped atom 1604 because residue number 199  < previous residue 298 
Skipped atom 1605 because residue number 199  < previous residue 298 
Skipped atom 1606 because residue number 199  < previous residue 298 
Skipped atom 1607 because residue number 199  < previous residue 298 
Skipped atom 1608 because residue number 199  < previous residue 298 
Skipped atom 1609 because residue number 199  < previous residue 298 
Skipped atom 1610 because residue number 199  < previous residue 298 
Skipped atom 1611 because residue number 199  < previous residue 298 
Skipped atom 1612 because residue number 200  < previous residue 298 
Skipped atom 1613 because residue number 200  < previous residue 298 
Skipped atom 1614 because residue number 200  < previous residue 298 
Skipped atom 1615 because residue number 200  < previous residue 298 
Skipped atom 1616 because residue number 200  < previous residue 298 
Skipped atom 1617 because residue number 200  < previous residue 298 
Skipped atom 1618 because residue number 201  < previous residue 298 
Skipped atom 1619 because residue number 201  < previous residue 298 
Skipped atom 1620 because residue number 201  < previous residue 298 
Skipped atom 1621 because residue number 201  < previous residue 298 
Skipped atom 1622 because residue number 201  < previous residue 298 
Skipped atom 1623 because residue number 201  < previous residue 298 
Skipped atom 1624 because residue number 201  < previous residue 298 
Skipped atom 1625 because residue number 201  < previous residue 298 
Skipped atom 1626 because residue number 201  < previous residue 298 
Skipped atom 1627 because residue number 202  < previous residue 298 
Skipped atom 1628 because residue number 202  < previous residue 298 
Skipped atom 1629 because residue number 202  < previous residue 298 
Skipped atom 1630 because residue number 202  < previous residue 298 
Skipped atom 1631 because residue number 202  < previous residue 298 
Skipped atom 1632 because residue number 202  < previous residue 298 
Skipped atom 1633 because residue number 202  < previous residue 298 
Skipped atom 1634 because residue number 202  < previous residue 298 
Skipped atom 1635 because residue number 202  < previous residue 298 
Skipped atom 1636 because residue number 203  < previous residue 298 
Skipped atom 1637 because residue number 203  < previous residue 298 
Skipped atom 1638 because residue number 203  < previous residue 298 
Skipped atom 1639 because residue number 203  < previous residue 298 
Skipped atom 1640 because residue number 203  < previous residue 298 
Skipped atom 1641 because residue number 203  < previous residue 298 
Skipped atom 1642 because residue number 203  < previous residue 298 
Skipped atom 1643 because residue number 203  < previous residue 298 
Skipped atom 1644 because residue number 204  < previous residue 298 
Skipped atom 1645 because residue number 204  < previous residue 298 
Skipped atom 1646 because residue number 204  < previous residue 298 
Skipped atom 1647 because residue number 204  < previous residue 298 
Skipped atom 1648 because residue number 204  < previous residue 298 
Skipped atom 1649 because residue number 204  < previous residue 298 
Skipped atom 1650 because residue number 204  < previous residue 298 
Skipped atom 1651 because residue number 204  < previous residue 298 
Skipped atom 1652 because residue number 204  < previous residue 298 
Skipped atom 1653 because residue number 205  < previous residue 298 
Skipped atom 1654 because residue number 205  < previous residue 298 
Skipped atom 1655 because residue number 205  < previous residue 298 
Skipped atom 1656 because residue number 205  < previous residue 298 
Skipped atom 1657 because residue number 205  < previous residue 298 
Skipped atom 1658 because residue number 205  < previous residue 298 
Skipped atom 1659 because residue number 205  < previous residue 298 
Skipped atom 1660 because residue number 205  < previous residue 298 
Skipped atom 1661 because residue number 205  < previous residue 298 
Skipped atom 1662 because residue number 206  < previous residue 298 
Skipped atom 1663 because residue number 206  < previous residue 298 
Skipped atom 1664 because residue number 206  < previous residue 298 
Skipped atom 1665 because residue number 206  < previous residue 298 
Skipped atom 1666 because residue number 206  < previous residue 298 
Skipped atom 1667 because residue number 206  < previous residue 298 
Skipped atom 1668 because residue number 206  < previous residue 298 
Skipped atom 1669 because residue number 206  < previous residue 298 
Skipped atom 1670 because residue number 206  < previous residue 298 
Skipped atom 1671 because residue number 206  < previous residue 298 
Skipped atom 1672 because residue number 206  < previous residue 298 
Skipped atom 1673 because residue number 207  < previous residue 298 
Skipped atom 1674 because residue number 207  < previous residue 298 
Skipped atom 1675 because residue number 207  < previous residue 298 
Skipped atom 1676 because residue number 207  < previous residue 298 
Skipped atom 1677 because residue number 207  < previous residue 298 
Skipped atom 1678 because residue number 207  < previous residue 298 
Skipped atom 1679 because residue number 207  < previous residue 298 
Skipped atom 1680 because residue number 207  < previous residue 298 
Skipped atom 1681 because residue number 208  < previous residue 298 
Skipped atom 1682 because residue number 208  < previous residue 298 
Skipped atom 1683 because residue number 208  < previous residue 298 
Skipped atom 1684 because residue number 208  < previous residue 298 
Skipped atom 1685 because residue number 208  < previous residue 298 
Skipped atom 1686 because residue number 208  < previous residue 298 
Skipped atom 1687 because residue number 208  < previous residue 298 
Skipped atom 1688 because residue number 208  < previous residue 298 
Skipped atom 1689 because residue number 209  < previous residue 298 
Skipped atom 1690 because residue number 209  < previous residue 298 
Skipped atom 1691 because residue number 209  < previous residue 298 
Skipped atom 1692 because residue number 209  < previous residue 298 
Skipped atom 1693 because residue number 209  < previous residue 298 
Skipped atom 1694 because residue number 209  < previous residue 298 
Skipped atom 1695 because residue number 209  < previous residue 298 
Skipped atom 1696 because residue number 209  < previous residue 298 
Skipped atom 1697 because residue number 210  < previous residue 298 
Skipped atom 1698 because residue number 210  < previous residue 298 
Skipped atom 1699 because residue number 210  < previous residue 298 
Skipped atom 1700 because residue number 210  < previous residue 298 
Skipped atom 1701 because residue number 210  < previous residue 298 
Skipped atom 1702 because residue number 210  < previous residue 298 
Skipped atom 1703 because residue number 210  < previous residue 298 
Skipped atom 1704 because residue number 210  < previous residue 298 
Skipped atom 1705 because residue number 211  < previous residue 298 
Skipped atom 1706 because residue number 211  < previous residue 298 
Skipped atom 1707 because residue number 211  < previous residue 298 
Skipped atom 1708 because residue number 211  < previous residue 298 
Skipped atom 1709 because residue number 211  < previous residue 298 
Skipped atom 1710 because residue number 211  < previous residue 298 
Skipped atom 1711 because residue number 211  < previous residue 298 
Skipped atom 1712 because residue number 211  < previous residue 298 
Skipped atom 1713 because residue number 212  < previous residue 298 
Skipped atom 1714 because residue number 212  < previous residue 298 
Skipped atom 1715 because residue number 212  < previous residue 298 
Skipped atom 1716 because residue number 212  < previous residue 298 
Skipped atom 1717 because residue number 212  < previous residue 298 
Skipped atom 1718 because residue number 212  < previous residue 298 
Skipped atom 1719 because residue number 212  < previous residue 298 
Skipped atom 1720 because residue number 212  < previous residue 298 
Skipped atom 1721 because residue number 213  < previous residue 298 
Skipped atom 1722 because residue number 213  < previous residue 298 
Skipped atom 1723 because residue number 213  < previous residue 298 
Skipped atom 1724 because residue number 213  < previous residue 298 
Skipped atom 1725 because residue number 213  < previous residue 298 
Skipped atom 1726 because residue number 213  < previous residue 298 
Skipped atom 1727 because residue number 213  < previous residue 298 
Skipped atom 1728 because residue number 213  < previous residue 298 
Skipped atom 1729 because residue number 214  < previous residue 298 
Skipped atom 1730 because residue number 214  < previous residue 298 
Skipped atom 1731 because residue number 214  < previous residue 298 
Skipped atom 1732 because residue number 214  < previous residue 298 
Skipped atom 1733 because residue number 214  < previous residue 298 
Skipped atom 1734 because residue number 214  < previous residue 298 
Skipped atom 1735 because residue number 214  < previous residue 298 
Skipped atom 1736 because residue number 214  < previous residue 298 
Skipped atom 1737 because residue number 215  < previous residue 298 
Skipped atom 1738 because residue number 215  < previous residue 298 
Skipped atom 1739 because residue number 215  < previous residue 298 
Skipped atom 1740 because residue number 215  < previous residue 298 
Skipped atom 1741 because residue number 215  < previous residue 298 
Skipped atom 1742 because residue number 215  < previous residue 298 
Skipped atom 1743 because residue number 215  < previous residue 298 
Skipped atom 1744 because residue number 215  < previous residue 298 
Skipped atom 1745 because residue number 215  < previous residue 298 
Skipped atom 1746 because residue number 216  < previous residue 298 
Skipped atom 1747 because residue number 216  < previous residue 298 
Skipped atom 1748 because residue number 216  < previous residue 298 
Skipped atom 1749 because residue number 216  < previous residue 298 
Skipped atom 1750 because residue number 216  < previous residue 298 
Skipped atom 1751 because residue number 216  < previous residue 298 
Skipped atom 1752 because residue number 217  < previous residue 298 
Skipped atom 1753 because residue number 217  < previous residue 298 
Skipped atom 1754 because residue number 217  < previous residue 298 
Skipped atom 1755 because residue number 217  < previous residue 298 
Skipped atom 1756 because residue number 218  < previous residue 298 
Skipped atom 1757 because residue number 218  < previous residue 298 
Skipped atom 1758 because residue number 218  < previous residue 298 
Skipped atom 1759 because residue number 218  < previous residue 298 
Skipped atom 1760 because residue number 218  < previous residue 298 
Skipped atom 1761 because residue number 218  < previous residue 298 
Skipped atom 1762 because residue number 218  < previous residue 298 
Skipped atom 1763 because residue number 218  < previous residue 298 
Skipped atom 1764 because residue number 219  < previous residue 298 
Skipped atom 1765 because residue number 219  < previous residue 298 
Skipped atom 1766 because residue number 219  < previous residue 298 
Skipped atom 1767 because residue number 219  < previous residue 298 
Skipped atom 1768 because residue number 219  < previous residue 298 
Skipped atom 1769 because residue number 219  < previous residue 298 
Skipped atom 1770 because residue number 219  < previous residue 298 
Skipped atom 1771 because residue number 220  < previous residue 298 
Skipped atom 1772 because residue number 220  < previous residue 298 
Skipped atom 1773 because residue number 220  < previous residue 298 
Skipped atom 1774 because residue number 220  < previous residue 298 
Skipped atom 1775 because residue number 220  < previous residue 298 
Skipped atom 1776 because residue number 220  < previous residue 298 
Skipped atom 1777 because residue number 220  < previous residue 298 
Skipped atom 1778 because residue number 220  < previous residue 298 
Skipped atom 1779 because residue number 221  < previous residue 298 
Skipped atom 1780 because residue number 221  < previous residue 298 
Skipped atom 1781 because residue number 221  < previous residue 298 
Skipped atom 1782 because residue number 221  < previous residue 298 
Skipped atom 1783 because residue number 221  < previous residue 298 
Skipped atom 1784 because residue number 221  < previous residue 298 
Skipped atom 1785 because residue number 221  < previous residue 298 
Skipped atom 1786 because residue number 221  < previous residue 298 
Skipped atom 1787 because residue number 222  < previous residue 298 
Skipped atom 1788 because residue number 222  < previous residue 298 
Skipped atom 1789 because residue number 222  < previous residue 298 
Skipped atom 1790 because residue number 222  < previous residue 298 
Skipped atom 1791 because residue number 222  < previous residue 298 
Skipped atom 1792 because residue number 222  < previous residue 298 
Skipped atom 1793 because residue number 222  < previous residue 298 
Skipped atom 1794 because residue number 222  < previous residue 298 
Skipped atom 1795 because residue number 222  < previous residue 298 
Skipped atom 1796 because residue number 223  < previous residue 298 
Skipped atom 1797 because residue number 223  < previous residue 298 
Skipped atom 1798 because residue number 223  < previous residue 298 
Skipped atom 1799 because residue number 223  < previous residue 298 
Skipped atom 1800 because residue number 223  < previous residue 298 
Skipped atom 1801 because residue number 223  < previous residue 298 
Skipped atom 1802 because residue number 223  < previous residue 298 
Skipped atom 1803 because residue number 223  < previous residue 298 
Skipped atom 1804 because residue number 224  < previous residue 298 
Skipped atom 1805 because residue number 224  < previous residue 298 
Skipped atom 1806 because residue number 224  < previous residue 298 
Skipped atom 1807 because residue number 224  < previous residue 298 
Skipped atom 1808 because residue number 225  < previous residue 298 
Skipped atom 1809 because residue number 225  < previous residue 298 
Skipped atom 1810 because residue number 225  < previous residue 298 
Skipped atom 1811 because residue number 225  < previous residue 298 
Skipped atom 1812 because residue number 225  < previous residue 298 
Skipped atom 1813 because residue number 225  < previous residue 298 
Skipped atom 1814 because residue number 225  < previous residue 298 
Skipped atom 1815 because residue number 226  < previous residue 298 
Skipped atom 1816 because residue number 226  < previous residue 298 
Skipped atom 1817 because residue number 226  < previous residue 298 
Skipped atom 1818 because residue number 226  < previous residue 298 
Skipped atom 1819 because residue number 226  < previous residue 298 
Skipped atom 1820 because residue number 226  < previous residue 298 
Skipped atom 1821 because residue number 226  < previous residue 298 
Skipped atom 1822 because residue number 227  < previous residue 298 
Skipped atom 1823 because residue number 227  < previous residue 298 
Skipped atom 1824 because residue number 227  < previous residue 298 
Skipped atom 1825 because residue number 227  < previous residue 298 
Skipped atom 1826 because residue number 227  < previous residue 298 
Skipped atom 1827 because residue number 227  < previous residue 298 
Skipped atom 1828 because residue number 228  < previous residue 298 
Skipped atom 1829 because residue number 228  < previous residue 298 
Skipped atom 1830 because residue number 228  < previous residue 298 
Skipped atom 1831 because residue number 228  < previous residue 298 
Skipped atom 1832 because residue number 228  < previous residue 298 
Skipped atom 1833 because residue number 228  < previous residue 298 
Skipped atom 1834 because residue number 228  < previous residue 298 
Skipped atom 1835 because residue number 228  < previous residue 298 
Skipped atom 1836 because residue number 229  < previous residue 298 
Skipped atom 1837 because residue number 229  < previous residue 298 
Skipped atom 1838 because residue number 229  < previous residue 298 
Skipped atom 1839 because residue number 229  < previous residue 298 
Skipped atom 1840 because residue number 229  < previous residue 298 
Skipped atom 1841 because residue number 229  < previous residue 298 
Skipped atom 1842 because residue number 229  < previous residue 298 
Skipped atom 1843 because residue number 229  < previous residue 298 
Skipped atom 1844 because residue number 229  < previous residue 298 
Skipped atom 1845 because residue number 229  < previous residue 298 
Skipped atom 1846 because residue number 229  < previous residue 298 
Skipped atom 1847 because residue number 229  < previous residue 298 
Skipped atom 1848 because residue number 230  < previous residue 298 
Skipped atom 1849 because residue number 230  < previous residue 298 
Skipped atom 1850 because residue number 230  < previous residue 298 
Skipped atom 1851 because residue number 230  < previous residue 298 
Skipped atom 1852 because residue number 230  < previous residue 298 
Skipped atom 1853 because residue number 230  < previous residue 298 
Skipped atom 1854 because residue number 230  < previous residue 298 
Skipped atom 1855 because residue number 230  < previous residue 298 
Skipped atom 1856 because residue number 230  < previous residue 298 
Skipped atom 1857 because residue number 231  < previous residue 298 
Skipped atom 1858 because residue number 231  < previous residue 298 
Skipped atom 1859 because residue number 231  < previous residue 298 
Skipped atom 1860 because residue number 231  < previous residue 298 
Skipped atom 1861 because residue number 231  < previous residue 298 
Skipped atom 1862 because residue number 231  < previous residue 298 
Skipped atom 1863 because residue number 231  < previous residue 298 
Skipped atom 1864 because residue number 232  < previous residue 298 
Skipped atom 1865 because residue number 232  < previous residue 298 
Skipped atom 1866 because residue number 232  < previous residue 298 
Skipped atom 1867 because residue number 232  < previous residue 298 
Skipped atom 1868 because residue number 232  < previous residue 298 
Skipped atom 1869 because residue number 233  < previous residue 298 
Skipped atom 1870 because residue number 233  < previous residue 298 
Skipped atom 1871 because residue number 233  < previous residue 298 
Skipped atom 1872 because residue number 233  < previous residue 298 
Skipped atom 1873 because residue number 233  < previous residue 298 
Skipped atom 1874 because residue number 233  < previous residue 298 
Skipped atom 1875 because residue number 233  < previous residue 298 
Skipped atom 1876 because residue number 233  < previous residue 298 
Skipped atom 1877 because residue number 234  < previous residue 298 
Skipped atom 1878 because residue number 234  < previous residue 298 
Skipped atom 1879 because residue number 234  < previous residue 298 
Skipped atom 1880 because residue number 234  < previous residue 298 
Skipped atom 1881 because residue number 234  < previous residue 298 
Skipped atom 1882 because residue number 234  < previous residue 298 
Skipped atom 1883 because residue number 234  < previous residue 298 
Skipped atom 1884 because residue number 234  < previous residue 298 
Skipped atom 1885 because residue number 234  < previous residue 298 
Skipped atom 1886 because residue number 235  < previous residue 298 
Skipped atom 1887 because residue number 235  < previous residue 298 
Skipped atom 1888 because residue number 235  < previous residue 298 
Skipped atom 1889 because residue number 235  < previous residue 298 
Skipped atom 1890 because residue number 235  < previous residue 298 
Skipped atom 1891 because residue number 235  < previous residue 298 
Skipped atom 1892 because residue number 236  < previous residue 298 
Skipped atom 1893 because residue number 236  < previous residue 298 
Skipped atom 1894 because residue number 236  < previous residue 298 
Skipped atom 1895 because residue number 236  < previous residue 298 
Skipped atom 1896 because residue number 237  < previous residue 298 
Skipped atom 1897 because residue number 237  < previous residue 298 
Skipped atom 1898 because residue number 237  < previous residue 298 
Skipped atom 1899 because residue number 237  < previous residue 298 
Skipped atom 1900 because residue number 237  < previous residue 298 
Skipped atom 1901 because residue number 237  < previous residue 298 
Skipped atom 1902 because residue number 237  < previous residue 298 
Skipped atom 1903 because residue number 237  < previous residue 298 
Skipped atom 1904 because residue number 237  < previous residue 298 
Skipped atom 1905 because residue number 238  < previous residue 298 
Skipped atom 1906 because residue number 238  < previous residue 298 
Skipped atom 1907 because residue number 238  < previous residue 298 
Skipped atom 1908 because residue number 238  < previous residue 298 
Skipped atom 1909 because residue number 238  < previous residue 298 
Skipped atom 1910 because residue number 239  < previous residue 298 
Skipped atom 1911 because residue number 239  < previous residue 298 
Skipped atom 1912 because residue number 239  < previous residue 298 
Skipped atom 1913 because residue number 239  < previous residue 298 
Skipped atom 1914 because residue number 239  < previous residue 298 
Skipped atom 1915 because residue number 239  < previous residue 298 
Skipped atom 1916 because residue number 239  < previous residue 298 
Skipped atom 1917 because residue number 239  < previous residue 298 
Skipped atom 1918 because residue number 240  < previous residue 298 
Skipped atom 1919 because residue number 240  < previous residue 298 
Skipped atom 1920 because residue number 240  < previous residue 298 
Skipped atom 1921 because residue number 240  < previous residue 298 
Skipped atom 1922 because residue number 240  < previous residue 298 
Skipped atom 1923 because residue number 240  < previous residue 298 
Skipped atom 1924 because residue number 240  < previous residue 298 
Skipped atom 1925 because residue number 241  < previous residue 298 
Skipped atom 1926 because residue number 241  < previous residue 298 
Skipped atom 1927 because residue number 241  < previous residue 298 
Skipped atom 1928 because residue number 241  < previous residue 298 
Skipped atom 1929 because residue number 241  < previous residue 298 
Skipped atom 1930 because residue number 241  < previous residue 298 
Skipped atom 1931 because residue number 241  < previous residue 298 
Skipped atom 1932 because residue number 241  < previous residue 298 
Skipped atom 1933 because residue number 241  < previous residue 298 
Skipped atom 1934 because residue number 241  < previous residue 298 
Skipped atom 1935 because residue number 241  < previous residue 298 
Skipped atom 1936 because residue number 241  < previous residue 298 
Skipped atom 1937 because residue number 242  < previous residue 298 
Skipped atom 1938 because residue number 242  < previous residue 298 
Skipped atom 1939 because residue number 242  < previous residue 298 
Skipped atom 1940 because residue number 242  < previous residue 298 
Skipped atom 1941 because residue number 242  < previous residue 298 
Skipped atom 1942 because residue number 243  < previous residue 298 
Skipped atom 1943 because residue number 243  < previous residue 298 
Skipped atom 1944 because residue number 243  < previous residue 298 
Skipped atom 1945 because residue number 243  < previous residue 298 
Skipped atom 1946 because residue number 243  < previous residue 298 
Skipped atom 1947 because residue number 243  < previous residue 298 
Skipped atom 1948 because residue number 244  < previous residue 298 
Skipped atom 1949 because residue number 244  < previous residue 298 
Skipped atom 1950 because residue number 244  < previous residue 298 
Skipped atom 1951 because residue number 244  < previous residue 298 
Skipped atom 1952 because residue number 244  < previous residue 298 
Skipped atom 1953 because residue number 244  < previous residue 298 
Skipped atom 1954 because residue number 244  < previous residue 298 
Skipped atom 1955 because residue number 244  < previous residue 298 
Skipped atom 1956 because residue number 244  < previous residue 298 
Skipped atom 1957 because residue number 244  < previous residue 298 
Skipped atom 1958 because residue number 244  < previous residue 298 
Skipped atom 1959 because residue number 245  < previous residue 298 
Skipped atom 1960 because residue number 245  < previous residue 298 
Skipped atom 1961 because residue number 245  < previous residue 298 
Skipped atom 1962 because residue number 245  < previous residue 298 
Skipped atom 1963 because residue number 245  < previous residue 298 
Skipped atom 1964 because residue number 245  < previous residue 298 
Skipped atom 1965 because residue number 245  < previous residue 298 
Skipped atom 1966 because residue number 245  < previous residue 298 
Skipped atom 1967 because residue number 246  < previous residue 298 
Skipped atom 1968 because residue number 246  < previous residue 298 
Skipped atom 1969 because residue number 246  < previous residue 298 
Skipped atom 1970 because residue number 246  < previous residue 298 
Skipped atom 1971 because residue number 246  < previous residue 298 
Skipped atom 1972 because residue number 246  < previous residue 298 
Skipped atom 1973 because residue number 246  < previous residue 298 
Skipped atom 1974 because residue number 246  < previous residue 298 
Skipped atom 1975 because residue number 247  < previous residue 298 
Skipped atom 1976 because residue number 247  < previous residue 298 
Skipped atom 1977 because residue number 247  < previous residue 298 
Skipped atom 1978 because residue number 247  < previous residue 298 
Skipped atom 1979 because residue number 247  < previous residue 298 
Skipped atom 1980 because residue number 247  < previous residue 298 
Skipped atom 1981 because residue number 247  < previous residue 298 
Skipped atom 1982 because residue number 248  < previous residue 298 
Skipped atom 1983 because residue number 248  < previous residue 298 
Skipped atom 1984 because residue number 248  < previous residue 298 
Skipped atom 1985 because residue number 248  < previous residue 298 
Skipped atom 1986 because residue number 248  < previous residue 298 
Skipped atom 1987 because residue number 249  < previous residue 298 
Skipped atom 1988 because residue number 249  < previous residue 298 
Skipped atom 1989 because residue number 249  < previous residue 298 
Skipped atom 1990 because residue number 249  < previous residue 298 
Skipped atom 1991 because residue number 249  < previous residue 298 
Skipped atom 1992 because residue number 249  < previous residue 298 
Skipped atom 1993 because residue number 249  < previous residue 298 
Skipped atom 1994 because residue number 249  < previous residue 298 
Skipped atom 1995 because residue number 249  < previous residue 298 
Skipped atom 1996 because residue number 249  < previous residue 298 
Skipped atom 1997 because residue number 249  < previous residue 298 
Skipped atom 1998 because residue number 250  < previous residue 298 
Skipped atom 1999 because residue number 250  < previous residue 298 
Skipped atom 2000 because residue number 250  < previous residue 298 
Skipped atom 2001 because residue number 250  < previous residue 298 
Skipped atom 2002 because residue number 250  < previous residue 298 
Skipped atom 2003 because residue number 250  < previous residue 298 
Skipped atom 2004 because residue number 250  < previous residue 298 
Skipped atom 2005 because residue number 251  < previous residue 298 
Skipped atom 2006 because residue number 251  < previous residue 298 
Skipped atom 2007 because residue number 251  < previous residue 298 
Skipped atom 2008 because residue number 251  < previous residue 298 
Skipped atom 2009 because residue number 251  < previous residue 298 
Skipped atom 2010 because residue number 251  < previous residue 298 
Skipped atom 2011 because residue number 251  < previous residue 298 
Skipped atom 2012 because residue number 251  < previous residue 298 
Skipped atom 2013 because residue number 251  < previous residue 298 
Skipped atom 2014 because residue number 251  < previous residue 298 
Skipped atom 2015 because residue number 251  < previous residue 298 
Skipped atom 2016 because residue number 251  < previous residue 298 
Skipped atom 2017 because residue number 252  < previous residue 298 
Skipped atom 2018 because residue number 252  < previous residue 298 
Skipped atom 2019 because residue number 252  < previous residue 298 
Skipped atom 2020 because residue number 252  < previous residue 298 
Skipped atom 2021 because residue number 252  < previous residue 298 
Skipped atom 2022 because residue number 252  < previous residue 298 
Skipped atom 2023 because residue number 252  < previous residue 298 
Skipped atom 2024 because residue number 253  < previous residue 298 
Skipped atom 2025 because residue number 253  < previous residue 298 
Skipped atom 2026 because residue number 253  < previous residue 298 
Skipped atom 2027 because residue number 253  < previous residue 298 
Skipped atom 2028 because residue number 253  < previous residue 298 
Skipped atom 2029 because residue number 253  < previous residue 298 
Skipped atom 2030 because residue number 253  < previous residue 298 
Skipped atom 2031 because residue number 253  < previous residue 298 
Skipped atom 2032 because residue number 253  < previous residue 298 
Skipped atom 2033 because residue number 253  < previous residue 298 
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1alq-orig.a2m
Writing a2m file: tmp/1alq-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25201


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25201/tmp -alignfile tmp/1alq-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1alq-orig.a2m (1 sequences, 266 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25201/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25201/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25201/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25201/tmp.a2m (1 sequences, 266 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25201/tmp.mod tmp/1alq-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25201 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1alq-align.mod
tmp/1alq-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25201/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1alq-orig.a2m tmp/1alq-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1alq-align.mod
Running w0.5 tmp/1alq-orig.a2m tmp/1alq-align.mod
Running align2model tmp/1alq-align -i tmp/1alq-align.mod -db tmp/1alq-orig.a2m -db tmp/1alq-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1alq.142.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1alq.143.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1alq.143.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1alq.143.3.a2m \
	-target T0124 -template 1alq \
	-out T0124-1alq.143.3 -outdir und
Skipped atom 298 because residue number 31  < previous residue 298 
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Skipped atom 621 because residue number 72  < previous residue 298 
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Skipped atom 729 because residue number 88  < previous residue 298 
Skipped atom 730 because residue number 88  < previous residue 298 
Skipped atom 731 because residue number 88  < previous residue 298 
Skipped atom 732 because residue number 88  < previous residue 298 
Skipped atom 733 because residue number 88  < previous residue 298 
Skipped atom 734 because residue number 88  < previous residue 298 
Skipped atom 735 because residue number 88  < previous residue 298 
Skipped atom 736 because residue number 89  < previous residue 298 
Skipped atom 737 because residue number 89  < previous residue 298 
Skipped atom 738 because residue number 89  < previous residue 298 
Skipped atom 739 because residue number 89  < previous residue 298 
Skipped atom 740 because residue number 89  < previous residue 298 
Skipped atom 741 because residue number 89  < previous residue 298 
Skipped atom 742 because residue number 89  < previous residue 298 
Skipped atom 743 because residue number 89  < previous residue 298 
Skipped atom 744 because residue number 90  < previous residue 298 
Skipped atom 745 because residue number 90  < previous residue 298 
Skipped atom 746 because residue number 90  < previous residue 298 
Skipped atom 747 because residue number 90  < previous residue 298 
Skipped atom 748 because residue number 90  < previous residue 298 
Skipped atom 749 because residue number 90  < previous residue 298 
Skipped atom 750 because residue number 90  < previous residue 298 
Skipped atom 751 because residue number 90  < previous residue 298 
Skipped atom 752 because residue number 90  < previous residue 298 
Skipped atom 753 because residue number 91  < previous residue 298 
Skipped atom 754 because residue number 91  < previous residue 298 
Skipped atom 755 because residue number 91  < previous residue 298 
Skipped atom 756 because residue number 91  < previous residue 298 
Skipped atom 757 because residue number 91  < previous residue 298 
Skipped atom 758 because residue number 91  < previous residue 298 
Skipped atom 759 because residue number 91  < previous residue 298 
Skipped atom 760 because residue number 91  < previous residue 298 
Skipped atom 761 because residue number 92  < previous residue 298 
Skipped atom 762 because residue number 92  < previous residue 298 
Skipped atom 763 because residue number 92  < previous residue 298 
Skipped atom 764 because residue number 92  < previous residue 298 
Skipped atom 765 because residue number 92  < previous residue 298 
Skipped atom 766 because residue number 92  < previous residue 298 
Skipped atom 767 because residue number 92  < previous residue 298 
Skipped atom 768 because residue number 92  < previous residue 298 
Skipped atom 769 because residue number 93  < previous residue 298 
Skipped atom 770 because residue number 93  < previous residue 298 
Skipped atom 771 because residue number 93  < previous residue 298 
Skipped atom 772 because residue number 93  < previous residue 298 
Skipped atom 773 because residue number 93  < previous residue 298 
Skipped atom 774 because residue number 93  < previous residue 298 
Skipped atom 775 because residue number 93  < previous residue 298 
Skipped atom 776 because residue number 93  < previous residue 298 
Skipped atom 777 because residue number 93  < previous residue 298 
Skipped atom 778 because residue number 94  < previous residue 298 
Skipped atom 779 because residue number 94  < previous residue 298 
Skipped atom 780 because residue number 94  < previous residue 298 
Skipped atom 781 because residue number 94  < previous residue 298 
Skipped atom 782 because residue number 94  < previous residue 298 
Skipped atom 783 because residue number 94  < previous residue 298 
Skipped atom 784 because residue number 94  < previous residue 298 
Skipped atom 785 because residue number 94  < previous residue 298 
Skipped atom 786 because residue number 94  < previous residue 298 
Skipped atom 787 because residue number 95  < previous residue 298 
Skipped atom 788 because residue number 95  < previous residue 298 
Skipped atom 789 because residue number 95  < previous residue 298 
Skipped atom 790 because residue number 95  < previous residue 298 
Skipped atom 791 because residue number 95  < previous residue 298 
Skipped atom 792 because residue number 95  < previous residue 298 
Skipped atom 793 because residue number 95  < previous residue 298 
Skipped atom 794 because residue number 96  < previous residue 298 
Skipped atom 795 because residue number 96  < previous residue 298 
Skipped atom 796 because residue number 96  < previous residue 298 
Skipped atom 797 because residue number 96  < previous residue 298 
Skipped atom 798 because residue number 96  < previous residue 298 
Skipped atom 799 because residue number 96  < previous residue 298 
Skipped atom 800 because residue number 96  < previous residue 298 
Skipped atom 801 because residue number 96  < previous residue 298 
Skipped atom 802 because residue number 96  < previous residue 298 
Skipped atom 803 because residue number 96  < previous residue 298 
Skipped atom 804 because residue number 97  < previous residue 298 
Skipped atom 805 because residue number 97  < previous residue 298 
Skipped atom 806 because residue number 97  < previous residue 298 
Skipped atom 807 because residue number 97  < previous residue 298 
Skipped atom 808 because residue number 97  < previous residue 298 
Skipped atom 809 because residue number 97  < previous residue 298 
Skipped atom 810 because residue number 97  < previous residue 298 
Skipped atom 811 because residue number 97  < previous residue 298 
Skipped atom 812 because residue number 98  < previous residue 298 
Skipped atom 813 because residue number 98  < previous residue 298 
Skipped atom 814 because residue number 98  < previous residue 298 
Skipped atom 815 because residue number 98  < previous residue 298 
Skipped atom 816 because residue number 98  < previous residue 298 
Skipped atom 817 because residue number 98  < previous residue 298 
Skipped atom 818 because residue number 98  < previous residue 298 
Skipped atom 819 because residue number 98  < previous residue 298 
Skipped atom 820 because residue number 99  < previous residue 298 
Skipped atom 821 because residue number 99  < previous residue 298 
Skipped atom 822 because residue number 99  < previous residue 298 
Skipped atom 823 because residue number 99  < previous residue 298 
Skipped atom 824 because residue number 99  < previous residue 298 
Skipped atom 825 because residue number 99  < previous residue 298 
Skipped atom 826 because residue number 99  < previous residue 298 
Skipped atom 827 because residue number 99  < previous residue 298 
Skipped atom 828 because residue number 99  < previous residue 298 
Skipped atom 829 because residue number 100  < previous residue 298 
Skipped atom 830 because residue number 100  < previous residue 298 
Skipped atom 831 because residue number 100  < previous residue 298 
Skipped atom 832 because residue number 100  < previous residue 298 
Skipped atom 833 because residue number 100  < previous residue 298 
Skipped atom 834 because residue number 100  < previous residue 298 
Skipped atom 835 because residue number 100  < previous residue 298 
Skipped atom 836 because residue number 100  < previous residue 298 
Skipped atom 837 because residue number 101  < previous residue 298 
Skipped atom 838 because residue number 101  < previous residue 298 
Skipped atom 839 because residue number 101  < previous residue 298 
Skipped atom 840 because residue number 101  < previous residue 298 
Skipped atom 841 because residue number 101  < previous residue 298 
Skipped atom 842 because residue number 101  < previous residue 298 
Skipped atom 843 because residue number 101  < previous residue 298 
Skipped atom 844 because residue number 101  < previous residue 298 
Skipped atom 845 because residue number 102  < previous residue 298 
Skipped atom 846 because residue number 102  < previous residue 298 
Skipped atom 847 because residue number 102  < previous residue 298 
Skipped atom 848 because residue number 102  < previous residue 298 
Skipped atom 849 because residue number 102  < previous residue 298 
Skipped atom 850 because residue number 102  < previous residue 298 
Skipped atom 851 because residue number 102  < previous residue 298 
Skipped atom 852 because residue number 102  < previous residue 298 
Skipped atom 853 because residue number 103  < previous residue 298 
Skipped atom 854 because residue number 103  < previous residue 298 
Skipped atom 855 because residue number 103  < previous residue 298 
Skipped atom 856 because residue number 103  < previous residue 298 
Skipped atom 857 because residue number 103  < previous residue 298 
Skipped atom 858 because residue number 103  < previous residue 298 
Skipped atom 859 because residue number 103  < previous residue 298 
Skipped atom 860 because residue number 104  < previous residue 298 
Skipped atom 861 because residue number 104  < previous residue 298 
Skipped atom 862 because residue number 104  < previous residue 298 
Skipped atom 863 because residue number 104  < previous residue 298 
Skipped atom 864 because residue number 104  < previous residue 298 
Skipped atom 865 because residue number 105  < previous residue 298 
Skipped atom 866 because residue number 105  < previous residue 298 
Skipped atom 867 because residue number 105  < previous residue 298 
Skipped atom 868 because residue number 105  < previous residue 298 
Skipped atom 869 because residue number 105  < previous residue 298 
Skipped atom 870 because residue number 105  < previous residue 298 
Skipped atom 871 because residue number 105  < previous residue 298 
Skipped atom 872 because residue number 105  < previous residue 298 
Skipped atom 873 because residue number 105  < previous residue 298 
Skipped atom 874 because residue number 105  < previous residue 298 
Skipped atom 875 because residue number 105  < previous residue 298 
Skipped atom 876 because residue number 105  < previous residue 298 
Skipped atom 877 because residue number 106  < previous residue 298 
Skipped atom 878 because residue number 106  < previous residue 298 
Skipped atom 879 because residue number 106  < previous residue 298 
Skipped atom 880 because residue number 106  < previous residue 298 
Skipped atom 881 because residue number 106  < previous residue 298 
Skipped atom 882 because residue number 106  < previous residue 298 
Skipped atom 883 because residue number 107  < previous residue 298 
Skipped atom 884 because residue number 107  < previous residue 298 
Skipped atom 885 because residue number 107  < previous residue 298 
Skipped atom 886 because residue number 107  < previous residue 298 
Skipped atom 887 because residue number 107  < previous residue 298 
Skipped atom 888 because residue number 107  < previous residue 298 
Skipped atom 889 because residue number 107  < previous residue 298 
Skipped atom 890 because residue number 108  < previous residue 298 
Skipped atom 891 because residue number 108  < previous residue 298 
Skipped atom 892 because residue number 108  < previous residue 298 
Skipped atom 893 because residue number 108  < previous residue 298 
Skipped atom 894 because residue number 108  < previous residue 298 
Skipped atom 895 because residue number 108  < previous residue 298 
Skipped atom 896 because residue number 108  < previous residue 298 
Skipped atom 897 because residue number 108  < previous residue 298 
Skipped atom 898 because residue number 109  < previous residue 298 
Skipped atom 899 because residue number 109  < previous residue 298 
Skipped atom 900 because residue number 109  < previous residue 298 
Skipped atom 901 because residue number 109  < previous residue 298 
Skipped atom 902 because residue number 109  < previous residue 298 
Skipped atom 903 because residue number 109  < previous residue 298 
Skipped atom 904 because residue number 109  < previous residue 298 
Skipped atom 905 because residue number 109  < previous residue 298 
Skipped atom 906 because residue number 110  < previous residue 298 
Skipped atom 907 because residue number 110  < previous residue 298 
Skipped atom 908 because residue number 110  < previous residue 298 
Skipped atom 909 because residue number 110  < previous residue 298 
Skipped atom 910 because residue number 110  < previous residue 298 
Skipped atom 911 because residue number 110  < previous residue 298 
Skipped atom 912 because residue number 110  < previous residue 298 
Skipped atom 913 because residue number 110  < previous residue 298 
Skipped atom 914 because residue number 110  < previous residue 298 
Skipped atom 915 because residue number 111  < previous residue 298 
Skipped atom 916 because residue number 111  < previous residue 298 
Skipped atom 917 because residue number 111  < previous residue 298 
Skipped atom 918 because residue number 111  < previous residue 298 
Skipped atom 919 because residue number 111  < previous residue 298 
Skipped atom 920 because residue number 111  < previous residue 298 
Skipped atom 921 because residue number 111  < previous residue 298 
Skipped atom 922 because residue number 111  < previous residue 298 
Skipped atom 923 because residue number 111  < previous residue 298 
Skipped atom 924 because residue number 112  < previous residue 298 
Skipped atom 925 because residue number 112  < previous residue 298 
Skipped atom 926 because residue number 112  < previous residue 298 
Skipped atom 927 because residue number 112  < previous residue 298 
Skipped atom 928 because residue number 112  < previous residue 298 
Skipped atom 929 because residue number 112  < previous residue 298 
Skipped atom 930 because residue number 112  < previous residue 298 
Skipped atom 931 because residue number 112  < previous residue 298 
Skipped atom 932 because residue number 112  < previous residue 298 
Skipped atom 933 because residue number 112  < previous residue 298 
Skipped atom 934 because residue number 112  < previous residue 298 
Skipped atom 935 because residue number 112  < previous residue 298 
Skipped atom 936 because residue number 113  < previous residue 298 
Skipped atom 937 because residue number 113  < previous residue 298 
Skipped atom 938 because residue number 113  < previous residue 298 
Skipped atom 939 because residue number 113  < previous residue 298 
Skipped atom 940 because residue number 113  < previous residue 298 
Skipped atom 941 because residue number 113  < previous residue 298 
Skipped atom 942 because residue number 113  < previous residue 298 
Skipped atom 943 because residue number 114  < previous residue 298 
Skipped atom 944 because residue number 114  < previous residue 298 
Skipped atom 945 because residue number 114  < previous residue 298 
Skipped atom 946 because residue number 114  < previous residue 298 
Skipped atom 947 because residue number 115  < previous residue 298 
Skipped atom 948 because residue number 115  < previous residue 298 
Skipped atom 949 because residue number 115  < previous residue 298 
Skipped atom 950 because residue number 115  < previous residue 298 
Skipped atom 951 because residue number 115  < previous residue 298 
Skipped atom 952 because residue number 115  < previous residue 298 
Skipped atom 953 because residue number 115  < previous residue 298 
Skipped atom 954 because residue number 115  < previous residue 298 
Skipped atom 955 because residue number 115  < previous residue 298 
Skipped atom 956 because residue number 116  < previous residue 298 
Skipped atom 957 because residue number 116  < previous residue 298 
Skipped atom 958 because residue number 116  < previous residue 298 
Skipped atom 959 because residue number 116  < previous residue 298 
Skipped atom 960 because residue number 116  < previous residue 298 
Skipped atom 961 because residue number 116  < previous residue 298 
Skipped atom 962 because residue number 116  < previous residue 298 
Skipped atom 963 because residue number 116  < previous residue 298 
Skipped atom 964 because residue number 117  < previous residue 298 
Skipped atom 965 because residue number 117  < previous residue 298 
Skipped atom 966 because residue number 117  < previous residue 298 
Skipped atom 967 because residue number 117  < previous residue 298 
Skipped atom 968 because residue number 117  < previous residue 298 
Skipped atom 969 because residue number 117  < previous residue 298 
Skipped atom 970 because residue number 117  < previous residue 298 
Skipped atom 971 because residue number 117  < previous residue 298 
Skipped atom 972 because residue number 118  < previous residue 298 
Skipped atom 973 because residue number 118  < previous residue 298 
Skipped atom 974 because residue number 118  < previous residue 298 
Skipped atom 975 because residue number 118  < previous residue 298 
Skipped atom 976 because residue number 118  < previous residue 298 
Skipped atom 977 because residue number 118  < previous residue 298 
Skipped atom 978 because residue number 118  < previous residue 298 
Skipped atom 979 because residue number 119  < previous residue 298 
Skipped atom 980 because residue number 119  < previous residue 298 
Skipped atom 981 because residue number 119  < previous residue 298 
Skipped atom 982 because residue number 119  < previous residue 298 
Skipped atom 983 because residue number 119  < previous residue 298 
Skipped atom 984 because residue number 119  < previous residue 298 
Skipped atom 985 because residue number 119  < previous residue 298 
Skipped atom 986 because residue number 119  < previous residue 298 
Skipped atom 987 because residue number 120  < previous residue 298 
Skipped atom 988 because residue number 120  < previous residue 298 
Skipped atom 989 because residue number 120  < previous residue 298 
Skipped atom 990 because residue number 120  < previous residue 298 
Skipped atom 991 because residue number 120  < previous residue 298 
Skipped atom 992 because residue number 120  < previous residue 298 
Skipped atom 993 because residue number 120  < previous residue 298 
Skipped atom 994 because residue number 120  < previous residue 298 
Skipped atom 995 because residue number 120  < previous residue 298 
Skipped atom 996 because residue number 121  < previous residue 298 
Skipped atom 997 because residue number 121  < previous residue 298 
Skipped atom 998 because residue number 121  < previous residue 298 
Skipped atom 999 because residue number 121  < previous residue 298 
Skipped atom 1000 because residue number 121  < previous residue 298 
Skipped atom 1001 because residue number 122  < previous residue 298 
Skipped atom 1002 because residue number 122  < previous residue 298 
Skipped atom 1003 because residue number 122  < previous residue 298 
Skipped atom 1004 because residue number 122  < previous residue 298 
Skipped atom 1005 because residue number 122  < previous residue 298 
Skipped atom 1006 because residue number 122  < previous residue 298 
Skipped atom 1007 because residue number 122  < previous residue 298 
Skipped atom 1008 because residue number 122  < previous residue 298 
Skipped atom 1009 because residue number 123  < previous residue 298 
Skipped atom 1010 because residue number 123  < previous residue 298 
Skipped atom 1011 because residue number 123  < previous residue 298 
Skipped atom 1012 because residue number 123  < previous residue 298 
Skipped atom 1013 because residue number 123  < previous residue 298 
Skipped atom 1014 because residue number 123  < previous residue 298 
Skipped atom 1015 because residue number 123  < previous residue 298 
Skipped atom 1016 because residue number 123  < previous residue 298 
Skipped atom 1017 because residue number 124  < previous residue 298 
Skipped atom 1018 because residue number 124  < previous residue 298 
Skipped atom 1019 because residue number 124  < previous residue 298 
Skipped atom 1020 because residue number 124  < previous residue 298 
Skipped atom 1021 because residue number 124  < previous residue 298 
Skipped atom 1022 because residue number 124  < previous residue 298 
Skipped atom 1023 because residue number 124  < previous residue 298 
Skipped atom 1024 because residue number 124  < previous residue 298 
Skipped atom 1025 because residue number 124  < previous residue 298 
Skipped atom 1026 because residue number 125  < previous residue 298 
Skipped atom 1027 because residue number 125  < previous residue 298 
Skipped atom 1028 because residue number 125  < previous residue 298 
Skipped atom 1029 because residue number 125  < previous residue 298 
Skipped atom 1030 because residue number 125  < previous residue 298 
Skipped atom 1031 because residue number 126  < previous residue 298 
Skipped atom 1032 because residue number 126  < previous residue 298 
Skipped atom 1033 because residue number 126  < previous residue 298 
Skipped atom 1034 because residue number 126  < previous residue 298 
Skipped atom 1035 because residue number 126  < previous residue 298 
Skipped atom 1036 because residue number 126  < previous residue 298 
Skipped atom 1037 because residue number 127  < previous residue 298 
Skipped atom 1038 because residue number 127  < previous residue 298 
Skipped atom 1039 because residue number 127  < previous residue 298 
Skipped atom 1040 because residue number 127  < previous residue 298 
Skipped atom 1041 because residue number 127  < previous residue 298 
Skipped atom 1042 because residue number 127  < previous residue 298 
Skipped atom 1043 because residue number 127  < previous residue 298 
Skipped atom 1044 because residue number 127  < previous residue 298 
Skipped atom 1045 because residue number 128  < previous residue 298 
Skipped atom 1046 because residue number 128  < previous residue 298 
Skipped atom 1047 because residue number 128  < previous residue 298 
Skipped atom 1048 because residue number 128  < previous residue 298 
Skipped atom 1049 because residue number 128  < previous residue 298 
Skipped atom 1050 because residue number 128  < previous residue 298 
Skipped atom 1051 because residue number 128  < previous residue 298 
Skipped atom 1052 because residue number 129  < previous residue 298 
Skipped atom 1053 because residue number 129  < previous residue 298 
Skipped atom 1054 because residue number 129  < previous residue 298 
Skipped atom 1055 because residue number 129  < previous residue 298 
Skipped atom 1056 because residue number 129  < previous residue 298 
Skipped atom 1057 because residue number 129  < previous residue 298 
Skipped atom 1058 because residue number 129  < previous residue 298 
Skipped atom 1059 because residue number 129  < previous residue 298 
Skipped atom 1060 because residue number 129  < previous residue 298 
Skipped atom 1061 because residue number 129  < previous residue 298 
Skipped atom 1062 because residue number 129  < previous residue 298 
Skipped atom 1063 because residue number 129  < previous residue 298 
Skipped atom 1064 because residue number 130  < previous residue 298 
Skipped atom 1065 because residue number 130  < previous residue 298 
Skipped atom 1066 because residue number 130  < previous residue 298 
Skipped atom 1067 because residue number 130  < previous residue 298 
Skipped atom 1068 because residue number 130  < previous residue 298 
Skipped atom 1069 because residue number 130  < previous residue 298 
Skipped atom 1070 because residue number 131  < previous residue 298 
Skipped atom 1071 because residue number 131  < previous residue 298 
Skipped atom 1072 because residue number 131  < previous residue 298 
Skipped atom 1073 because residue number 131  < previous residue 298 
Skipped atom 1074 because residue number 131  < previous residue 298 
Skipped atom 1075 because residue number 131  < previous residue 298 
Skipped atom 1076 because residue number 131  < previous residue 298 
Skipped atom 1077 because residue number 131  < previous residue 298 
Skipped atom 1078 because residue number 132  < previous residue 298 
Skipped atom 1079 because residue number 132  < previous residue 298 
Skipped atom 1080 because residue number 132  < previous residue 298 
Skipped atom 1081 because residue number 132  < previous residue 298 
Skipped atom 1082 because residue number 132  < previous residue 298 
Skipped atom 1083 because residue number 132  < previous residue 298 
Skipped atom 1084 because residue number 132  < previous residue 298 
Skipped atom 1085 because residue number 132  < previous residue 298 
Skipped atom 1086 because residue number 133  < previous residue 298 
Skipped atom 1087 because residue number 133  < previous residue 298 
Skipped atom 1088 because residue number 133  < previous residue 298 
Skipped atom 1089 because residue number 133  < previous residue 298 
Skipped atom 1090 because residue number 133  < previous residue 298 
Skipped atom 1091 because residue number 133  < previous residue 298 
Skipped atom 1092 because residue number 133  < previous residue 298 
Skipped atom 1093 because residue number 134  < previous residue 298 
Skipped atom 1094 because residue number 134  < previous residue 298 
Skipped atom 1095 because residue number 134  < previous residue 298 
Skipped atom 1096 because residue number 134  < previous residue 298 
Skipped atom 1097 because residue number 134  < previous residue 298 
Skipped atom 1098 because residue number 135  < previous residue 298 
Skipped atom 1099 because residue number 135  < previous residue 298 
Skipped atom 1100 because residue number 135  < previous residue 298 
Skipped atom 1101 because residue number 135  < previous residue 298 
Skipped atom 1102 because residue number 135  < previous residue 298 
Skipped atom 1103 because residue number 135  < previous residue 298 
Skipped atom 1104 because residue number 135  < previous residue 298 
Skipped atom 1105 because residue number 135  < previous residue 298 
Skipped atom 1106 because residue number 136  < previous residue 298 
Skipped atom 1107 because residue number 136  < previous residue 298 
Skipped atom 1108 because residue number 136  < previous residue 298 
Skipped atom 1109 because residue number 136  < previous residue 298 
Skipped atom 1110 because residue number 136  < previous residue 298 
Skipped atom 1111 because residue number 136  < previous residue 298 
Skipped atom 1112 because residue number 136  < previous residue 298 
Skipped atom 1113 because residue number 136  < previous residue 298 
Skipped atom 1114 because residue number 137  < previous residue 298 
Skipped atom 1115 because residue number 137  < previous residue 298 
Skipped atom 1116 because residue number 137  < previous residue 298 
Skipped atom 1117 because residue number 137  < previous residue 298 
Skipped atom 1118 because residue number 137  < previous residue 298 
Skipped atom 1119 because residue number 137  < previous residue 298 
Skipped atom 1120 because residue number 137  < previous residue 298 
Skipped atom 1121 because residue number 137  < previous residue 298 
Skipped atom 1122 because residue number 137  < previous residue 298 
Skipped atom 1123 because residue number 138  < previous residue 298 
Skipped atom 1124 because residue number 138  < previous residue 298 
Skipped atom 1125 because residue number 138  < previous residue 298 
Skipped atom 1126 because residue number 138  < previous residue 298 
Skipped atom 1127 because residue number 138  < previous residue 298 
Skipped atom 1128 because residue number 138  < previous residue 298 
Skipped atom 1129 because residue number 138  < previous residue 298 
Skipped atom 1130 because residue number 138  < previous residue 298 
Skipped atom 1131 because residue number 139  < previous residue 298 
Skipped atom 1132 because residue number 139  < previous residue 298 
Skipped atom 1133 because residue number 139  < previous residue 298 
Skipped atom 1134 because residue number 139  < previous residue 298 
Skipped atom 1135 because residue number 139  < previous residue 298 
Skipped atom 1136 because residue number 139  < previous residue 298 
Skipped atom 1137 because residue number 139  < previous residue 298 
Skipped atom 1138 because residue number 139  < previous residue 298 
Skipped atom 1139 because residue number 140  < previous residue 298 
Skipped atom 1140 because residue number 140  < previous residue 298 
Skipped atom 1141 because residue number 140  < previous residue 298 
Skipped atom 1142 because residue number 140  < previous residue 298 
Skipped atom 1143 because residue number 140  < previous residue 298 
Skipped atom 1144 because residue number 140  < previous residue 298 
Skipped atom 1145 because residue number 140  < previous residue 298 
Skipped atom 1146 because residue number 140  < previous residue 298 
Skipped atom 1147 because residue number 140  < previous residue 298 
Skipped atom 1148 because residue number 141  < previous residue 298 
Skipped atom 1149 because residue number 141  < previous residue 298 
Skipped atom 1150 because residue number 141  < previous residue 298 
Skipped atom 1151 because residue number 141  < previous residue 298 
Skipped atom 1152 because residue number 141  < previous residue 298 
Skipped atom 1153 because residue number 141  < previous residue 298 
Skipped atom 1154 because residue number 141  < previous residue 298 
Skipped atom 1155 because residue number 141  < previous residue 298 
Skipped atom 1156 because residue number 141  < previous residue 298 
Skipped atom 1157 because residue number 142  < previous residue 298 
Skipped atom 1158 because residue number 142  < previous residue 298 
Skipped atom 1159 because residue number 142  < previous residue 298 
Skipped atom 1160 because residue number 142  < previous residue 298 
Skipped atom 1161 because residue number 142  < previous residue 298 
Skipped atom 1162 because residue number 142  < previous residue 298 
Skipped atom 1163 because residue number 142  < previous residue 298 
Skipped atom 1164 because residue number 142  < previous residue 298 
Skipped atom 1165 because residue number 143  < previous residue 298 
Skipped atom 1166 because residue number 143  < previous residue 298 
Skipped atom 1167 because residue number 143  < previous residue 298 
Skipped atom 1168 because residue number 143  < previous residue 298 
Skipped atom 1169 because residue number 144  < previous residue 298 
Skipped atom 1170 because residue number 144  < previous residue 298 
Skipped atom 1171 because residue number 144  < previous residue 298 
Skipped atom 1172 because residue number 144  < previous residue 298 
Skipped atom 1173 because residue number 145  < previous residue 298 
Skipped atom 1174 because residue number 145  < previous residue 298 
Skipped atom 1175 because residue number 145  < previous residue 298 
Skipped atom 1176 because residue number 145  < previous residue 298 
Skipped atom 1177 because residue number 145  < previous residue 298 
Skipped atom 1178 because residue number 145  < previous residue 298 
Skipped atom 1179 because residue number 145  < previous residue 298 
Skipped atom 1180 because residue number 145  < previous residue 298 
Skipped atom 1181 because residue number 146  < previous residue 298 
Skipped atom 1182 because residue number 146  < previous residue 298 
Skipped atom 1183 because residue number 146  < previous residue 298 
Skipped atom 1184 because residue number 146  < previous residue 298 
Skipped atom 1185 because residue number 146  < previous residue 298 
Skipped atom 1186 because residue number 146  < previous residue 298 
Skipped atom 1187 because residue number 146  < previous residue 298 
Skipped atom 1188 because residue number 146  < previous residue 298 
Skipped atom 1189 because residue number 146  < previous residue 298 
Skipped atom 1190 because residue number 147  < previous residue 298 
Skipped atom 1191 because residue number 147  < previous residue 298 
Skipped atom 1192 because residue number 147  < previous residue 298 
Skipped atom 1193 because residue number 147  < previous residue 298 
Skipped atom 1194 because residue number 147  < previous residue 298 
Skipped atom 1195 because residue number 147  < previous residue 298 
Skipped atom 1196 because residue number 147  < previous residue 298 
Skipped atom 1197 because residue number 147  < previous residue 298 
Skipped atom 1198 because residue number 147  < previous residue 298 
Skipped atom 1199 because residue number 148  < previous residue 298 
Skipped atom 1200 because residue number 148  < previous residue 298 
Skipped atom 1201 because residue number 148  < previous residue 298 
Skipped atom 1202 because residue number 148  < previous residue 298 
Skipped atom 1203 because residue number 148  < previous residue 298 
Skipped atom 1204 because residue number 148  < previous residue 298 
Skipped atom 1205 because residue number 148  < previous residue 298 
Skipped atom 1206 because residue number 149  < previous residue 298 
Skipped atom 1207 because residue number 149  < previous residue 298 
Skipped atom 1208 because residue number 149  < previous residue 298 
Skipped atom 1209 because residue number 149  < previous residue 298 
Skipped atom 1210 because residue number 149  < previous residue 298 
Skipped atom 1211 because residue number 149  < previous residue 298 
Skipped atom 1212 because residue number 149  < previous residue 298 
Skipped atom 1213 because residue number 149  < previous residue 298 
Skipped atom 1214 because residue number 149  < previous residue 298 
Skipped atom 1215 because residue number 150  < previous residue 298 
Skipped atom 1216 because residue number 150  < previous residue 298 
Skipped atom 1217 because residue number 150  < previous residue 298 
Skipped atom 1218 because residue number 150  < previous residue 298 
Skipped atom 1219 because residue number 150  < previous residue 298 
Skipped atom 1220 because residue number 150  < previous residue 298 
Skipped atom 1221 because residue number 150  < previous residue 298 
Skipped atom 1222 because residue number 150  < previous residue 298 
Skipped atom 1223 because residue number 150  < previous residue 298 
Skipped atom 1224 because residue number 151  < previous residue 298 
Skipped atom 1225 because residue number 151  < previous residue 298 
Skipped atom 1226 because residue number 151  < previous residue 298 
Skipped atom 1227 because residue number 151  < previous residue 298 
Skipped atom 1228 because residue number 151  < previous residue 298 
Skipped atom 1229 because residue number 151  < previous residue 298 
Skipped atom 1230 because residue number 151  < previous residue 298 
Skipped atom 1231 because residue number 151  < previous residue 298 
Skipped atom 1232 because residue number 151  < previous residue 298 
Skipped atom 1233 because residue number 151  < previous residue 298 
Skipped atom 1234 because residue number 151  < previous residue 298 
Skipped atom 1235 because residue number 152  < previous residue 298 
Skipped atom 1236 because residue number 152  < previous residue 298 
Skipped atom 1237 because residue number 152  < previous residue 298 
Skipped atom 1238 because residue number 152  < previous residue 298 
Skipped atom 1239 because residue number 152  < previous residue 298 
Skipped atom 1240 because residue number 152  < previous residue 298 
Skipped atom 1241 because residue number 152  < previous residue 298 
Skipped atom 1242 because residue number 152  < previous residue 298 
Skipped atom 1243 because residue number 153  < previous residue 298 
Skipped atom 1244 because residue number 153  < previous residue 298 
Skipped atom 1245 because residue number 153  < previous residue 298 
Skipped atom 1246 because residue number 153  < previous residue 298 
Skipped atom 1247 because residue number 153  < previous residue 298 
Skipped atom 1248 because residue number 153  < previous residue 298 
Skipped atom 1249 because residue number 153  < previous residue 298 
Skipped atom 1250 because residue number 153  < previous residue 298 
Skipped atom 1251 because residue number 153  < previous residue 298 
Skipped atom 1252 because residue number 154  < previous residue 298 
Skipped atom 1253 because residue number 154  < previous residue 298 
Skipped atom 1254 because residue number 154  < previous residue 298 
Skipped atom 1255 because residue number 154  < previous residue 298 
Skipped atom 1256 because residue number 154  < previous residue 298 
Skipped atom 1257 because residue number 154  < previous residue 298 
Skipped atom 1258 because residue number 154  < previous residue 298 
Skipped atom 1259 because residue number 154  < previous residue 298 
Skipped atom 1260 because residue number 154  < previous residue 298 
Skipped atom 1261 because residue number 155  < previous residue 298 
Skipped atom 1262 because residue number 155  < previous residue 298 
Skipped atom 1263 because residue number 155  < previous residue 298 
Skipped atom 1264 because residue number 155  < previous residue 298 
Skipped atom 1265 because residue number 155  < previous residue 298 
Skipped atom 1266 because residue number 155  < previous residue 298 
Skipped atom 1267 because residue number 155  < previous residue 298 
Skipped atom 1268 because residue number 155  < previous residue 298 
Skipped atom 1269 because residue number 156  < previous residue 298 
Skipped atom 1270 because residue number 156  < previous residue 298 
Skipped atom 1271 because residue number 156  < previous residue 298 
Skipped atom 1272 because residue number 156  < previous residue 298 
Skipped atom 1273 because residue number 157  < previous residue 298 
Skipped atom 1274 because residue number 157  < previous residue 298 
Skipped atom 1275 because residue number 157  < previous residue 298 
Skipped atom 1276 because residue number 157  < previous residue 298 
Skipped atom 1277 because residue number 157  < previous residue 298 
Skipped atom 1278 because residue number 157  < previous residue 298 
Skipped atom 1279 because residue number 157  < previous residue 298 
Skipped atom 1280 because residue number 157  < previous residue 298 
Skipped atom 1281 because residue number 158  < previous residue 298 
Skipped atom 1282 because residue number 158  < previous residue 298 
Skipped atom 1283 because residue number 158  < previous residue 298 
Skipped atom 1284 because residue number 158  < previous residue 298 
Skipped atom 1285 because residue number 158  < previous residue 298 
Skipped atom 1286 because residue number 158  < previous residue 298 
Skipped atom 1287 because residue number 158  < previous residue 298 
Skipped atom 1288 because residue number 158  < previous residue 298 
Skipped atom 1289 because residue number 158  < previous residue 298 
Skipped atom 1290 because residue number 159  < previous residue 298 
Skipped atom 1291 because residue number 159  < previous residue 298 
Skipped atom 1292 because residue number 159  < previous residue 298 
Skipped atom 1293 because residue number 159  < previous residue 298 
Skipped atom 1294 because residue number 159  < previous residue 298 
Skipped atom 1295 because residue number 159  < previous residue 298 
Skipped atom 1296 because residue number 159  < previous residue 298 
Skipped atom 1297 because residue number 160  < previous residue 298 
Skipped atom 1298 because residue number 160  < previous residue 298 
Skipped atom 1299 because residue number 160  < previous residue 298 
Skipped atom 1300 because residue number 160  < previous residue 298 
Skipped atom 1301 because residue number 160  < previous residue 298 
Skipped atom 1302 because residue number 160  < previous residue 298 
Skipped atom 1303 because residue number 160  < previous residue 298 
Skipped atom 1304 because residue number 161  < previous residue 298 
Skipped atom 1305 because residue number 161  < previous residue 298 
Skipped atom 1306 because residue number 161  < previous residue 298 
Skipped atom 1307 because residue number 161  < previous residue 298 
Skipped atom 1308 because residue number 161  < previous residue 298 
Skipped atom 1309 because residue number 161  < previous residue 298 
Skipped atom 1310 because residue number 161  < previous residue 298 
Skipped atom 1311 because residue number 161  < previous residue 298 
Skipped atom 1312 because residue number 162  < previous residue 298 
Skipped atom 1313 because residue number 162  < previous residue 298 
Skipped atom 1314 because residue number 162  < previous residue 298 
Skipped atom 1315 because residue number 162  < previous residue 298 
Skipped atom 1316 because residue number 162  < previous residue 298 
Skipped atom 1317 because residue number 162  < previous residue 298 
Skipped atom 1318 because residue number 162  < previous residue 298 
Skipped atom 1319 because residue number 163  < previous residue 298 
Skipped atom 1320 because residue number 163  < previous residue 298 
Skipped atom 1321 because residue number 163  < previous residue 298 
Skipped atom 1322 because residue number 163  < previous residue 298 
Skipped atom 1323 because residue number 163  < previous residue 298 
Skipped atom 1324 because residue number 163  < previous residue 298 
Skipped atom 1325 because residue number 163  < previous residue 298 
Skipped atom 1326 because residue number 164  < previous residue 298 
Skipped atom 1327 because residue number 164  < previous residue 298 
Skipped atom 1328 because residue number 164  < previous residue 298 
Skipped atom 1329 because residue number 164  < previous residue 298 
Skipped atom 1330 because residue number 164  < previous residue 298 
Skipped atom 1331 because residue number 164  < previous residue 298 
Skipped atom 1332 because residue number 164  < previous residue 298 
Skipped atom 1333 because residue number 164  < previous residue 298 
Skipped atom 1334 because residue number 164  < previous residue 298 
Skipped atom 1335 because residue number 164  < previous residue 298 
Skipped atom 1336 because residue number 164  < previous residue 298 
Skipped atom 1337 because residue number 165  < previous residue 298 
Skipped atom 1338 because residue number 165  < previous residue 298 
Skipped atom 1339 because residue number 165  < previous residue 298 
Skipped atom 1340 because residue number 165  < previous residue 298 
Skipped atom 1341 because residue number 165  < previous residue 298 
Skipped atom 1342 because residue number 165  < previous residue 298 
Skipped atom 1343 because residue number 165  < previous residue 298 
Skipped atom 1344 because residue number 165  < previous residue 298 
Skipped atom 1345 because residue number 165  < previous residue 298 
Skipped atom 1346 because residue number 165  < previous residue 298 
Skipped atom 1347 because residue number 165  < previous residue 298 
Skipped atom 1348 because residue number 165  < previous residue 298 
Skipped atom 1349 because residue number 166  < previous residue 298 
Skipped atom 1350 because residue number 166  < previous residue 298 
Skipped atom 1351 because residue number 166  < previous residue 298 
Skipped atom 1352 because residue number 166  < previous residue 298 
Skipped atom 1353 because residue number 166  < previous residue 298 
Skipped atom 1354 because residue number 166  < previous residue 298 
Skipped atom 1355 because residue number 166  < previous residue 298 
Skipped atom 1356 because residue number 166  < previous residue 298 
Skipped atom 1357 because residue number 166  < previous residue 298 
Skipped atom 1358 because residue number 167  < previous residue 298 
Skipped atom 1359 because residue number 167  < previous residue 298 
Skipped atom 1360 because residue number 167  < previous residue 298 
Skipped atom 1361 because residue number 167  < previous residue 298 
Skipped atom 1362 because residue number 167  < previous residue 298 
Skipped atom 1363 because residue number 167  < previous residue 298 
Skipped atom 1364 because residue number 167  < previous residue 298 
Skipped atom 1365 because residue number 167  < previous residue 298 
Skipped atom 1366 because residue number 168  < previous residue 298 
Skipped atom 1367 because residue number 168  < previous residue 298 
Skipped atom 1368 because residue number 168  < previous residue 298 
Skipped atom 1369 because residue number 168  < previous residue 298 
Skipped atom 1370 because residue number 168  < previous residue 298 
Skipped atom 1371 because residue number 168  < previous residue 298 
Skipped atom 1372 because residue number 168  < previous residue 298 
Skipped atom 1373 because residue number 168  < previous residue 298 
Skipped atom 1374 because residue number 168  < previous residue 298 
Skipped atom 1375 because residue number 169  < previous residue 298 
Skipped atom 1376 because residue number 169  < previous residue 298 
Skipped atom 1377 because residue number 169  < previous residue 298 
Skipped atom 1378 because residue number 169  < previous residue 298 
Skipped atom 1379 because residue number 169  < previous residue 298 
Skipped atom 1380 because residue number 169  < previous residue 298 
Skipped atom 1381 because residue number 169  < previous residue 298 
Skipped atom 1382 because residue number 169  < previous residue 298 
Skipped atom 1383 because residue number 170  < previous residue 298 
Skipped atom 1384 because residue number 170  < previous residue 298 
Skipped atom 1385 because residue number 170  < previous residue 298 
Skipped atom 1386 because residue number 170  < previous residue 298 
Skipped atom 1387 because residue number 170  < previous residue 298 
Skipped atom 1388 because residue number 170  < previous residue 298 
Skipped atom 1389 because residue number 170  < previous residue 298 
Skipped atom 1390 because residue number 170  < previous residue 298 
Skipped atom 1391 because residue number 171  < previous residue 298 
Skipped atom 1392 because residue number 171  < previous residue 298 
Skipped atom 1393 because residue number 171  < previous residue 298 
Skipped atom 1394 because residue number 171  < previous residue 298 
Skipped atom 1395 because residue number 171  < previous residue 298 
Skipped atom 1396 because residue number 171  < previous residue 298 
Skipped atom 1397 because residue number 171  < previous residue 298 
Skipped atom 1398 because residue number 171  < previous residue 298 
Skipped atom 1399 because residue number 171  < previous residue 298 
Skipped atom 1400 because residue number 171  < previous residue 298 
Skipped atom 1401 because residue number 171  < previous residue 298 
Skipped atom 1402 because residue number 171  < previous residue 298 
Skipped atom 1403 because residue number 172  < previous residue 298 
Skipped atom 1404 because residue number 172  < previous residue 298 
Skipped atom 1405 because residue number 172  < previous residue 298 
Skipped atom 1406 because residue number 172  < previous residue 298 
Skipped atom 1407 because residue number 172  < previous residue 298 
Skipped atom 1408 because residue number 172  < previous residue 298 
Skipped atom 1409 because residue number 172  < previous residue 298 
Skipped atom 1410 because residue number 172  < previous residue 298 
Skipped atom 1411 because residue number 172  < previous residue 298 
Skipped atom 1412 because residue number 172  < previous residue 298 
Skipped atom 1413 because residue number 172  < previous residue 298 
Skipped atom 1414 because residue number 172  < previous residue 298 
Skipped atom 1415 because residue number 173  < previous residue 298 
Skipped atom 1416 because residue number 173  < previous residue 298 
Skipped atom 1417 because residue number 173  < previous residue 298 
Skipped atom 1418 because residue number 173  < previous residue 298 
Skipped atom 1419 because residue number 173  < previous residue 298 
Skipped atom 1420 because residue number 173  < previous residue 298 
Skipped atom 1421 because residue number 174  < previous residue 298 
Skipped atom 1422 because residue number 174  < previous residue 298 
Skipped atom 1423 because residue number 174  < previous residue 298 
Skipped atom 1424 because residue number 174  < previous residue 298 
Skipped atom 1425 because residue number 174  < previous residue 298 
Skipped atom 1426 because residue number 174  < previous residue 298 
Skipped atom 1427 because residue number 174  < previous residue 298 
Skipped atom 1428 because residue number 175  < previous residue 298 
Skipped atom 1429 because residue number 175  < previous residue 298 
Skipped atom 1430 because residue number 175  < previous residue 298 
Skipped atom 1431 because residue number 175  < previous residue 298 
Skipped atom 1432 because residue number 175  < previous residue 298 
Skipped atom 1433 because residue number 175  < previous residue 298 
Skipped atom 1434 because residue number 175  < previous residue 298 
Skipped atom 1435 because residue number 175  < previous residue 298 
Skipped atom 1436 because residue number 175  < previous residue 298 
Skipped atom 1437 because residue number 176  < previous residue 298 
Skipped atom 1438 because residue number 176  < previous residue 298 
Skipped atom 1439 because residue number 176  < previous residue 298 
Skipped atom 1440 because residue number 176  < previous residue 298 
Skipped atom 1441 because residue number 176  < previous residue 298 
Skipped atom 1442 because residue number 176  < previous residue 298 
Skipped atom 1443 because residue number 177  < previous residue 298 
Skipped atom 1444 because residue number 177  < previous residue 298 
Skipped atom 1445 because residue number 177  < previous residue 298 
Skipped atom 1446 because residue number 177  < previous residue 298 
Skipped atom 1447 because residue number 177  < previous residue 298 
Skipped atom 1448 because residue number 177  < previous residue 298 
Skipped atom 1449 because residue number 177  < previous residue 298 
Skipped atom 1450 because residue number 177  < previous residue 298 
Skipped atom 1451 because residue number 177  < previous residue 298 
Skipped atom 1452 because residue number 178  < previous residue 298 
Skipped atom 1453 because residue number 178  < previous residue 298 
Skipped atom 1454 because residue number 178  < previous residue 298 
Skipped atom 1455 because residue number 178  < previous residue 298 
Skipped atom 1456 because residue number 178  < previous residue 298 
Skipped atom 1457 because residue number 178  < previous residue 298 
Skipped atom 1458 because residue number 178  < previous residue 298 
Skipped atom 1459 because residue number 178  < previous residue 298 
Skipped atom 1460 because residue number 178  < previous residue 298 
Skipped atom 1461 because residue number 179  < previous residue 298 
Skipped atom 1462 because residue number 179  < previous residue 298 
Skipped atom 1463 because residue number 179  < previous residue 298 
Skipped atom 1464 because residue number 179  < previous residue 298 
Skipped atom 1465 because residue number 179  < previous residue 298 
Skipped atom 1466 because residue number 179  < previous residue 298 
Skipped atom 1467 because residue number 179  < previous residue 298 
Skipped atom 1468 because residue number 179  < previous residue 298 
Skipped atom 1469 because residue number 180  < previous residue 298 
Skipped atom 1470 because residue number 180  < previous residue 298 
Skipped atom 1471 because residue number 180  < previous residue 298 
Skipped atom 1472 because residue number 180  < previous residue 298 
Skipped atom 1473 because residue number 180  < previous residue 298 
Skipped atom 1474 because residue number 180  < previous residue 298 
Skipped atom 1475 because residue number 180  < previous residue 298 
Skipped atom 1476 because residue number 181  < previous residue 298 
Skipped atom 1477 because residue number 181  < previous residue 298 
Skipped atom 1478 because residue number 181  < previous residue 298 
Skipped atom 1479 because residue number 181  < previous residue 298 
Skipped atom 1480 because residue number 181  < previous residue 298 
Skipped atom 1481 because residue number 181  < previous residue 298 
Skipped atom 1482 because residue number 182  < previous residue 298 
Skipped atom 1483 because residue number 182  < previous residue 298 
Skipped atom 1484 because residue number 182  < previous residue 298 
Skipped atom 1485 because residue number 182  < previous residue 298 
Skipped atom 1486 because residue number 182  < previous residue 298 
Skipped atom 1487 because residue number 182  < previous residue 298 
Skipped atom 1488 because residue number 182  < previous residue 298 
Skipped atom 1489 because residue number 183  < previous residue 298 
Skipped atom 1490 because residue number 183  < previous residue 298 
Skipped atom 1491 because residue number 183  < previous residue 298 
Skipped atom 1492 because residue number 183  < previous residue 298 
Skipped atom 1493 because residue number 183  < previous residue 298 
Skipped atom 1494 because residue number 183  < previous residue 298 
Skipped atom 1495 because residue number 183  < previous residue 298 
Skipped atom 1496 because residue number 184  < previous residue 298 
Skipped atom 1497 because residue number 184  < previous residue 298 
Skipped atom 1498 because residue number 184  < previous residue 298 
Skipped atom 1499 because residue number 184  < previous residue 298 
Skipped atom 1500 because residue number 184  < previous residue 298 
Skipped atom 1501 because residue number 185  < previous residue 298 
Skipped atom 1502 because residue number 185  < previous residue 298 
Skipped atom 1503 because residue number 185  < previous residue 298 
Skipped atom 1504 because residue number 185  < previous residue 298 
Skipped atom 1505 because residue number 185  < previous residue 298 
Skipped atom 1506 because residue number 186  < previous residue 298 
Skipped atom 1507 because residue number 186  < previous residue 298 
Skipped atom 1508 because residue number 186  < previous residue 298 
Skipped atom 1509 because residue number 186  < previous residue 298 
Skipped atom 1510 because residue number 186  < previous residue 298 
Skipped atom 1511 because residue number 186  < previous residue 298 
Skipped atom 1512 because residue number 186  < previous residue 298 
Skipped atom 1513 because residue number 186  < previous residue 298 
Skipped atom 1514 because residue number 186  < previous residue 298 
Skipped atom 1515 because residue number 186  < previous residue 298 
Skipped atom 1516 because residue number 186  < previous residue 298 
Skipped atom 1517 because residue number 187  < previous residue 298 
Skipped atom 1518 because residue number 187  < previous residue 298 
Skipped atom 1519 because residue number 187  < previous residue 298 
Skipped atom 1520 because residue number 187  < previous residue 298 
Skipped atom 1521 because residue number 188  < previous residue 298 
Skipped atom 1522 because residue number 188  < previous residue 298 
Skipped atom 1523 because residue number 188  < previous residue 298 
Skipped atom 1524 because residue number 188  < previous residue 298 
Skipped atom 1525 because residue number 188  < previous residue 298 
Skipped atom 1526 because residue number 188  < previous residue 298 
Skipped atom 1527 because residue number 188  < previous residue 298 
Skipped atom 1528 because residue number 188  < previous residue 298 
Skipped atom 1529 because residue number 188  < previous residue 298 
Skipped atom 1530 because residue number 189  < previous residue 298 
Skipped atom 1531 because residue number 189  < previous residue 298 
Skipped atom 1532 because residue number 189  < previous residue 298 
Skipped atom 1533 because residue number 189  < previous residue 298 
Skipped atom 1534 because residue number 189  < previous residue 298 
Skipped atom 1535 because residue number 189  < previous residue 298 
Skipped atom 1536 because residue number 189  < previous residue 298 
Skipped atom 1537 because residue number 190  < previous residue 298 
Skipped atom 1538 because residue number 190  < previous residue 298 
Skipped atom 1539 because residue number 190  < previous residue 298 
Skipped atom 1540 because residue number 190  < previous residue 298 
Skipped atom 1541 because residue number 190  < previous residue 298 
Skipped atom 1542 because residue number 190  < previous residue 298 
Skipped atom 1543 because residue number 190  < previous residue 298 
Skipped atom 1544 because residue number 190  < previous residue 298 
Skipped atom 1545 because residue number 191  < previous residue 298 
Skipped atom 1546 because residue number 191  < previous residue 298 
Skipped atom 1547 because residue number 191  < previous residue 298 
Skipped atom 1548 because residue number 191  < previous residue 298 
Skipped atom 1549 because residue number 191  < previous residue 298 
Skipped atom 1550 because residue number 191  < previous residue 298 
Skipped atom 1551 because residue number 191  < previous residue 298 
Skipped atom 1552 because residue number 191  < previous residue 298 
Skipped atom 1553 because residue number 192  < previous residue 298 
Skipped atom 1554 because residue number 192  < previous residue 298 
Skipped atom 1555 because residue number 192  < previous residue 298 
Skipped atom 1556 because residue number 192  < previous residue 298 
Skipped atom 1557 because residue number 192  < previous residue 298 
Skipped atom 1558 because residue number 192  < previous residue 298 
Skipped atom 1559 because residue number 192  < previous residue 298 
Skipped atom 1560 because residue number 192  < previous residue 298 
Skipped atom 1561 because residue number 192  < previous residue 298 
Skipped atom 1562 because residue number 193  < previous residue 298 
Skipped atom 1563 because residue number 193  < previous residue 298 
Skipped atom 1564 because residue number 193  < previous residue 298 
Skipped atom 1565 because residue number 193  < previous residue 298 
Skipped atom 1566 because residue number 193  < previous residue 298 
Skipped atom 1567 because residue number 193  < previous residue 298 
Skipped atom 1568 because residue number 193  < previous residue 298 
Skipped atom 1569 because residue number 193  < previous residue 298 
Skipped atom 1570 because residue number 194  < previous residue 298 
Skipped atom 1571 because residue number 194  < previous residue 298 
Skipped atom 1572 because residue number 194  < previous residue 298 
Skipped atom 1573 because residue number 194  < previous residue 298 
Skipped atom 1574 because residue number 194  < previous residue 298 
Skipped atom 1575 because residue number 194  < previous residue 298 
Skipped atom 1576 because residue number 194  < previous residue 298 
Skipped atom 1577 because residue number 194  < previous residue 298 
Skipped atom 1578 because residue number 195  < previous residue 298 
Skipped atom 1579 because residue number 195  < previous residue 298 
Skipped atom 1580 because residue number 195  < previous residue 298 
Skipped atom 1581 because residue number 195  < previous residue 298 
Skipped atom 1582 because residue number 195  < previous residue 298 
Skipped atom 1583 because residue number 196  < previous residue 298 
Skipped atom 1584 because residue number 196  < previous residue 298 
Skipped atom 1585 because residue number 196  < previous residue 298 
Skipped atom 1586 because residue number 196  < previous residue 298 
Skipped atom 1587 because residue number 196  < previous residue 298 
Skipped atom 1588 because residue number 196  < previous residue 298 
Skipped atom 1589 because residue number 196  < previous residue 298 
Skipped atom 1590 because residue number 196  < previous residue 298 
Skipped atom 1591 because residue number 197  < previous residue 298 
Skipped atom 1592 because residue number 197  < previous residue 298 
Skipped atom 1593 because residue number 197  < previous residue 298 
Skipped atom 1594 because residue number 197  < previous residue 298 
Skipped atom 1595 because residue number 198  < previous residue 298 
Skipped atom 1596 because residue number 198  < previous residue 298 
Skipped atom 1597 because residue number 198  < previous residue 298 
Skipped atom 1598 because residue number 198  < previous residue 298 
Skipped atom 1599 because residue number 198  < previous residue 298 
Skipped atom 1600 because residue number 198  < previous residue 298 
Skipped atom 1601 because residue number 198  < previous residue 298 
Skipped atom 1602 because residue number 198  < previous residue 298 
Skipped atom 1603 because residue number 198  < previous residue 298 
Skipped atom 1604 because residue number 199  < previous residue 298 
Skipped atom 1605 because residue number 199  < previous residue 298 
Skipped atom 1606 because residue number 199  < previous residue 298 
Skipped atom 1607 because residue number 199  < previous residue 298 
Skipped atom 1608 because residue number 199  < previous residue 298 
Skipped atom 1609 because residue number 199  < previous residue 298 
Skipped atom 1610 because residue number 199  < previous residue 298 
Skipped atom 1611 because residue number 199  < previous residue 298 
Skipped atom 1612 because residue number 200  < previous residue 298 
Skipped atom 1613 because residue number 200  < previous residue 298 
Skipped atom 1614 because residue number 200  < previous residue 298 
Skipped atom 1615 because residue number 200  < previous residue 298 
Skipped atom 1616 because residue number 200  < previous residue 298 
Skipped atom 1617 because residue number 200  < previous residue 298 
Skipped atom 1618 because residue number 201  < previous residue 298 
Skipped atom 1619 because residue number 201  < previous residue 298 
Skipped atom 1620 because residue number 201  < previous residue 298 
Skipped atom 1621 because residue number 201  < previous residue 298 
Skipped atom 1622 because residue number 201  < previous residue 298 
Skipped atom 1623 because residue number 201  < previous residue 298 
Skipped atom 1624 because residue number 201  < previous residue 298 
Skipped atom 1625 because residue number 201  < previous residue 298 
Skipped atom 1626 because residue number 201  < previous residue 298 
Skipped atom 1627 because residue number 202  < previous residue 298 
Skipped atom 1628 because residue number 202  < previous residue 298 
Skipped atom 1629 because residue number 202  < previous residue 298 
Skipped atom 1630 because residue number 202  < previous residue 298 
Skipped atom 1631 because residue number 202  < previous residue 298 
Skipped atom 1632 because residue number 202  < previous residue 298 
Skipped atom 1633 because residue number 202  < previous residue 298 
Skipped atom 1634 because residue number 202  < previous residue 298 
Skipped atom 1635 because residue number 202  < previous residue 298 
Skipped atom 1636 because residue number 203  < previous residue 298 
Skipped atom 1637 because residue number 203  < previous residue 298 
Skipped atom 1638 because residue number 203  < previous residue 298 
Skipped atom 1639 because residue number 203  < previous residue 298 
Skipped atom 1640 because residue number 203  < previous residue 298 
Skipped atom 1641 because residue number 203  < previous residue 298 
Skipped atom 1642 because residue number 203  < previous residue 298 
Skipped atom 1643 because residue number 203  < previous residue 298 
Skipped atom 1644 because residue number 204  < previous residue 298 
Skipped atom 1645 because residue number 204  < previous residue 298 
Skipped atom 1646 because residue number 204  < previous residue 298 
Skipped atom 1647 because residue number 204  < previous residue 298 
Skipped atom 1648 because residue number 204  < previous residue 298 
Skipped atom 1649 because residue number 204  < previous residue 298 
Skipped atom 1650 because residue number 204  < previous residue 298 
Skipped atom 1651 because residue number 204  < previous residue 298 
Skipped atom 1652 because residue number 204  < previous residue 298 
Skipped atom 1653 because residue number 205  < previous residue 298 
Skipped atom 1654 because residue number 205  < previous residue 298 
Skipped atom 1655 because residue number 205  < previous residue 298 
Skipped atom 1656 because residue number 205  < previous residue 298 
Skipped atom 1657 because residue number 205  < previous residue 298 
Skipped atom 1658 because residue number 205  < previous residue 298 
Skipped atom 1659 because residue number 205  < previous residue 298 
Skipped atom 1660 because residue number 205  < previous residue 298 
Skipped atom 1661 because residue number 205  < previous residue 298 
Skipped atom 1662 because residue number 206  < previous residue 298 
Skipped atom 1663 because residue number 206  < previous residue 298 
Skipped atom 1664 because residue number 206  < previous residue 298 
Skipped atom 1665 because residue number 206  < previous residue 298 
Skipped atom 1666 because residue number 206  < previous residue 298 
Skipped atom 1667 because residue number 206  < previous residue 298 
Skipped atom 1668 because residue number 206  < previous residue 298 
Skipped atom 1669 because residue number 206  < previous residue 298 
Skipped atom 1670 because residue number 206  < previous residue 298 
Skipped atom 1671 because residue number 206  < previous residue 298 
Skipped atom 1672 because residue number 206  < previous residue 298 
Skipped atom 1673 because residue number 207  < previous residue 298 
Skipped atom 1674 because residue number 207  < previous residue 298 
Skipped atom 1675 because residue number 207  < previous residue 298 
Skipped atom 1676 because residue number 207  < previous residue 298 
Skipped atom 1677 because residue number 207  < previous residue 298 
Skipped atom 1678 because residue number 207  < previous residue 298 
Skipped atom 1679 because residue number 207  < previous residue 298 
Skipped atom 1680 because residue number 207  < previous residue 298 
Skipped atom 1681 because residue number 208  < previous residue 298 
Skipped atom 1682 because residue number 208  < previous residue 298 
Skipped atom 1683 because residue number 208  < previous residue 298 
Skipped atom 1684 because residue number 208  < previous residue 298 
Skipped atom 1685 because residue number 208  < previous residue 298 
Skipped atom 1686 because residue number 208  < previous residue 298 
Skipped atom 1687 because residue number 208  < previous residue 298 
Skipped atom 1688 because residue number 208  < previous residue 298 
Skipped atom 1689 because residue number 209  < previous residue 298 
Skipped atom 1690 because residue number 209  < previous residue 298 
Skipped atom 1691 because residue number 209  < previous residue 298 
Skipped atom 1692 because residue number 209  < previous residue 298 
Skipped atom 1693 because residue number 209  < previous residue 298 
Skipped atom 1694 because residue number 209  < previous residue 298 
Skipped atom 1695 because residue number 209  < previous residue 298 
Skipped atom 1696 because residue number 209  < previous residue 298 
Skipped atom 1697 because residue number 210  < previous residue 298 
Skipped atom 1698 because residue number 210  < previous residue 298 
Skipped atom 1699 because residue number 210  < previous residue 298 
Skipped atom 1700 because residue number 210  < previous residue 298 
Skipped atom 1701 because residue number 210  < previous residue 298 
Skipped atom 1702 because residue number 210  < previous residue 298 
Skipped atom 1703 because residue number 210  < previous residue 298 
Skipped atom 1704 because residue number 210  < previous residue 298 
Skipped atom 1705 because residue number 211  < previous residue 298 
Skipped atom 1706 because residue number 211  < previous residue 298 
Skipped atom 1707 because residue number 211  < previous residue 298 
Skipped atom 1708 because residue number 211  < previous residue 298 
Skipped atom 1709 because residue number 211  < previous residue 298 
Skipped atom 1710 because residue number 211  < previous residue 298 
Skipped atom 1711 because residue number 211  < previous residue 298 
Skipped atom 1712 because residue number 211  < previous residue 298 
Skipped atom 1713 because residue number 212  < previous residue 298 
Skipped atom 1714 because residue number 212  < previous residue 298 
Skipped atom 1715 because residue number 212  < previous residue 298 
Skipped atom 1716 because residue number 212  < previous residue 298 
Skipped atom 1717 because residue number 212  < previous residue 298 
Skipped atom 1718 because residue number 212  < previous residue 298 
Skipped atom 1719 because residue number 212  < previous residue 298 
Skipped atom 1720 because residue number 212  < previous residue 298 
Skipped atom 1721 because residue number 213  < previous residue 298 
Skipped atom 1722 because residue number 213  < previous residue 298 
Skipped atom 1723 because residue number 213  < previous residue 298 
Skipped atom 1724 because residue number 213  < previous residue 298 
Skipped atom 1725 because residue number 213  < previous residue 298 
Skipped atom 1726 because residue number 213  < previous residue 298 
Skipped atom 1727 because residue number 213  < previous residue 298 
Skipped atom 1728 because residue number 213  < previous residue 298 
Skipped atom 1729 because residue number 214  < previous residue 298 
Skipped atom 1730 because residue number 214  < previous residue 298 
Skipped atom 1731 because residue number 214  < previous residue 298 
Skipped atom 1732 because residue number 214  < previous residue 298 
Skipped atom 1733 because residue number 214  < previous residue 298 
Skipped atom 1734 because residue number 214  < previous residue 298 
Skipped atom 1735 because residue number 214  < previous residue 298 
Skipped atom 1736 because residue number 214  < previous residue 298 
Skipped atom 1737 because residue number 215  < previous residue 298 
Skipped atom 1738 because residue number 215  < previous residue 298 
Skipped atom 1739 because residue number 215  < previous residue 298 
Skipped atom 1740 because residue number 215  < previous residue 298 
Skipped atom 1741 because residue number 215  < previous residue 298 
Skipped atom 1742 because residue number 215  < previous residue 298 
Skipped atom 1743 because residue number 215  < previous residue 298 
Skipped atom 1744 because residue number 215  < previous residue 298 
Skipped atom 1745 because residue number 215  < previous residue 298 
Skipped atom 1746 because residue number 216  < previous residue 298 
Skipped atom 1747 because residue number 216  < previous residue 298 
Skipped atom 1748 because residue number 216  < previous residue 298 
Skipped atom 1749 because residue number 216  < previous residue 298 
Skipped atom 1750 because residue number 216  < previous residue 298 
Skipped atom 1751 because residue number 216  < previous residue 298 
Skipped atom 1752 because residue number 217  < previous residue 298 
Skipped atom 1753 because residue number 217  < previous residue 298 
Skipped atom 1754 because residue number 217  < previous residue 298 
Skipped atom 1755 because residue number 217  < previous residue 298 
Skipped atom 1756 because residue number 218  < previous residue 298 
Skipped atom 1757 because residue number 218  < previous residue 298 
Skipped atom 1758 because residue number 218  < previous residue 298 
Skipped atom 1759 because residue number 218  < previous residue 298 
Skipped atom 1760 because residue number 218  < previous residue 298 
Skipped atom 1761 because residue number 218  < previous residue 298 
Skipped atom 1762 because residue number 218  < previous residue 298 
Skipped atom 1763 because residue number 218  < previous residue 298 
Skipped atom 1764 because residue number 219  < previous residue 298 
Skipped atom 1765 because residue number 219  < previous residue 298 
Skipped atom 1766 because residue number 219  < previous residue 298 
Skipped atom 1767 because residue number 219  < previous residue 298 
Skipped atom 1768 because residue number 219  < previous residue 298 
Skipped atom 1769 because residue number 219  < previous residue 298 
Skipped atom 1770 because residue number 219  < previous residue 298 
Skipped atom 1771 because residue number 220  < previous residue 298 
Skipped atom 1772 because residue number 220  < previous residue 298 
Skipped atom 1773 because residue number 220  < previous residue 298 
Skipped atom 1774 because residue number 220  < previous residue 298 
Skipped atom 1775 because residue number 220  < previous residue 298 
Skipped atom 1776 because residue number 220  < previous residue 298 
Skipped atom 1777 because residue number 220  < previous residue 298 
Skipped atom 1778 because residue number 220  < previous residue 298 
Skipped atom 1779 because residue number 221  < previous residue 298 
Skipped atom 1780 because residue number 221  < previous residue 298 
Skipped atom 1781 because residue number 221  < previous residue 298 
Skipped atom 1782 because residue number 221  < previous residue 298 
Skipped atom 1783 because residue number 221  < previous residue 298 
Skipped atom 1784 because residue number 221  < previous residue 298 
Skipped atom 1785 because residue number 221  < previous residue 298 
Skipped atom 1786 because residue number 221  < previous residue 298 
Skipped atom 1787 because residue number 222  < previous residue 298 
Skipped atom 1788 because residue number 222  < previous residue 298 
Skipped atom 1789 because residue number 222  < previous residue 298 
Skipped atom 1790 because residue number 222  < previous residue 298 
Skipped atom 1791 because residue number 222  < previous residue 298 
Skipped atom 1792 because residue number 222  < previous residue 298 
Skipped atom 1793 because residue number 222  < previous residue 298 
Skipped atom 1794 because residue number 222  < previous residue 298 
Skipped atom 1795 because residue number 222  < previous residue 298 
Skipped atom 1796 because residue number 223  < previous residue 298 
Skipped atom 1797 because residue number 223  < previous residue 298 
Skipped atom 1798 because residue number 223  < previous residue 298 
Skipped atom 1799 because residue number 223  < previous residue 298 
Skipped atom 1800 because residue number 223  < previous residue 298 
Skipped atom 1801 because residue number 223  < previous residue 298 
Skipped atom 1802 because residue number 223  < previous residue 298 
Skipped atom 1803 because residue number 223  < previous residue 298 
Skipped atom 1804 because residue number 224  < previous residue 298 
Skipped atom 1805 because residue number 224  < previous residue 298 
Skipped atom 1806 because residue number 224  < previous residue 298 
Skipped atom 1807 because residue number 224  < previous residue 298 
Skipped atom 1808 because residue number 225  < previous residue 298 
Skipped atom 1809 because residue number 225  < previous residue 298 
Skipped atom 1810 because residue number 225  < previous residue 298 
Skipped atom 1811 because residue number 225  < previous residue 298 
Skipped atom 1812 because residue number 225  < previous residue 298 
Skipped atom 1813 because residue number 225  < previous residue 298 
Skipped atom 1814 because residue number 225  < previous residue 298 
Skipped atom 1815 because residue number 226  < previous residue 298 
Skipped atom 1816 because residue number 226  < previous residue 298 
Skipped atom 1817 because residue number 226  < previous residue 298 
Skipped atom 1818 because residue number 226  < previous residue 298 
Skipped atom 1819 because residue number 226  < previous residue 298 
Skipped atom 1820 because residue number 226  < previous residue 298 
Skipped atom 1821 because residue number 226  < previous residue 298 
Skipped atom 1822 because residue number 227  < previous residue 298 
Skipped atom 1823 because residue number 227  < previous residue 298 
Skipped atom 1824 because residue number 227  < previous residue 298 
Skipped atom 1825 because residue number 227  < previous residue 298 
Skipped atom 1826 because residue number 227  < previous residue 298 
Skipped atom 1827 because residue number 227  < previous residue 298 
Skipped atom 1828 because residue number 228  < previous residue 298 
Skipped atom 1829 because residue number 228  < previous residue 298 
Skipped atom 1830 because residue number 228  < previous residue 298 
Skipped atom 1831 because residue number 228  < previous residue 298 
Skipped atom 1832 because residue number 228  < previous residue 298 
Skipped atom 1833 because residue number 228  < previous residue 298 
Skipped atom 1834 because residue number 228  < previous residue 298 
Skipped atom 1835 because residue number 228  < previous residue 298 
Skipped atom 1836 because residue number 229  < previous residue 298 
Skipped atom 1837 because residue number 229  < previous residue 298 
Skipped atom 1838 because residue number 229  < previous residue 298 
Skipped atom 1839 because residue number 229  < previous residue 298 
Skipped atom 1840 because residue number 229  < previous residue 298 
Skipped atom 1841 because residue number 229  < previous residue 298 
Skipped atom 1842 because residue number 229  < previous residue 298 
Skipped atom 1843 because residue number 229  < previous residue 298 
Skipped atom 1844 because residue number 229  < previous residue 298 
Skipped atom 1845 because residue number 229  < previous residue 298 
Skipped atom 1846 because residue number 229  < previous residue 298 
Skipped atom 1847 because residue number 229  < previous residue 298 
Skipped atom 1848 because residue number 230  < previous residue 298 
Skipped atom 1849 because residue number 230  < previous residue 298 
Skipped atom 1850 because residue number 230  < previous residue 298 
Skipped atom 1851 because residue number 230  < previous residue 298 
Skipped atom 1852 because residue number 230  < previous residue 298 
Skipped atom 1853 because residue number 230  < previous residue 298 
Skipped atom 1854 because residue number 230  < previous residue 298 
Skipped atom 1855 because residue number 230  < previous residue 298 
Skipped atom 1856 because residue number 230  < previous residue 298 
Skipped atom 1857 because residue number 231  < previous residue 298 
Skipped atom 1858 because residue number 231  < previous residue 298 
Skipped atom 1859 because residue number 231  < previous residue 298 
Skipped atom 1860 because residue number 231  < previous residue 298 
Skipped atom 1861 because residue number 231  < previous residue 298 
Skipped atom 1862 because residue number 231  < previous residue 298 
Skipped atom 1863 because residue number 231  < previous residue 298 
Skipped atom 1864 because residue number 232  < previous residue 298 
Skipped atom 1865 because residue number 232  < previous residue 298 
Skipped atom 1866 because residue number 232  < previous residue 298 
Skipped atom 1867 because residue number 232  < previous residue 298 
Skipped atom 1868 because residue number 232  < previous residue 298 
Skipped atom 1869 because residue number 233  < previous residue 298 
Skipped atom 1870 because residue number 233  < previous residue 298 
Skipped atom 1871 because residue number 233  < previous residue 298 
Skipped atom 1872 because residue number 233  < previous residue 298 
Skipped atom 1873 because residue number 233  < previous residue 298 
Skipped atom 1874 because residue number 233  < previous residue 298 
Skipped atom 1875 because residue number 233  < previous residue 298 
Skipped atom 1876 because residue number 233  < previous residue 298 
Skipped atom 1877 because residue number 234  < previous residue 298 
Skipped atom 1878 because residue number 234  < previous residue 298 
Skipped atom 1879 because residue number 234  < previous residue 298 
Skipped atom 1880 because residue number 234  < previous residue 298 
Skipped atom 1881 because residue number 234  < previous residue 298 
Skipped atom 1882 because residue number 234  < previous residue 298 
Skipped atom 1883 because residue number 234  < previous residue 298 
Skipped atom 1884 because residue number 234  < previous residue 298 
Skipped atom 1885 because residue number 234  < previous residue 298 
Skipped atom 1886 because residue number 235  < previous residue 298 
Skipped atom 1887 because residue number 235  < previous residue 298 
Skipped atom 1888 because residue number 235  < previous residue 298 
Skipped atom 1889 because residue number 235  < previous residue 298 
Skipped atom 1890 because residue number 235  < previous residue 298 
Skipped atom 1891 because residue number 235  < previous residue 298 
Skipped atom 1892 because residue number 236  < previous residue 298 
Skipped atom 1893 because residue number 236  < previous residue 298 
Skipped atom 1894 because residue number 236  < previous residue 298 
Skipped atom 1895 because residue number 236  < previous residue 298 
Skipped atom 1896 because residue number 237  < previous residue 298 
Skipped atom 1897 because residue number 237  < previous residue 298 
Skipped atom 1898 because residue number 237  < previous residue 298 
Skipped atom 1899 because residue number 237  < previous residue 298 
Skipped atom 1900 because residue number 237  < previous residue 298 
Skipped atom 1901 because residue number 237  < previous residue 298 
Skipped atom 1902 because residue number 237  < previous residue 298 
Skipped atom 1903 because residue number 237  < previous residue 298 
Skipped atom 1904 because residue number 237  < previous residue 298 
Skipped atom 1905 because residue number 238  < previous residue 298 
Skipped atom 1906 because residue number 238  < previous residue 298 
Skipped atom 1907 because residue number 238  < previous residue 298 
Skipped atom 1908 because residue number 238  < previous residue 298 
Skipped atom 1909 because residue number 238  < previous residue 298 
Skipped atom 1910 because residue number 239  < previous residue 298 
Skipped atom 1911 because residue number 239  < previous residue 298 
Skipped atom 1912 because residue number 239  < previous residue 298 
Skipped atom 1913 because residue number 239  < previous residue 298 
Skipped atom 1914 because residue number 239  < previous residue 298 
Skipped atom 1915 because residue number 239  < previous residue 298 
Skipped atom 1916 because residue number 239  < previous residue 298 
Skipped atom 1917 because residue number 239  < previous residue 298 
Skipped atom 1918 because residue number 240  < previous residue 298 
Skipped atom 1919 because residue number 240  < previous residue 298 
Skipped atom 1920 because residue number 240  < previous residue 298 
Skipped atom 1921 because residue number 240  < previous residue 298 
Skipped atom 1922 because residue number 240  < previous residue 298 
Skipped atom 1923 because residue number 240  < previous residue 298 
Skipped atom 1924 because residue number 240  < previous residue 298 
Skipped atom 1925 because residue number 241  < previous residue 298 
Skipped atom 1926 because residue number 241  < previous residue 298 
Skipped atom 1927 because residue number 241  < previous residue 298 
Skipped atom 1928 because residue number 241  < previous residue 298 
Skipped atom 1929 because residue number 241  < previous residue 298 
Skipped atom 1930 because residue number 241  < previous residue 298 
Skipped atom 1931 because residue number 241  < previous residue 298 
Skipped atom 1932 because residue number 241  < previous residue 298 
Skipped atom 1933 because residue number 241  < previous residue 298 
Skipped atom 1934 because residue number 241  < previous residue 298 
Skipped atom 1935 because residue number 241  < previous residue 298 
Skipped atom 1936 because residue number 241  < previous residue 298 
Skipped atom 1937 because residue number 242  < previous residue 298 
Skipped atom 1938 because residue number 242  < previous residue 298 
Skipped atom 1939 because residue number 242  < previous residue 298 
Skipped atom 1940 because residue number 242  < previous residue 298 
Skipped atom 1941 because residue number 242  < previous residue 298 
Skipped atom 1942 because residue number 243  < previous residue 298 
Skipped atom 1943 because residue number 243  < previous residue 298 
Skipped atom 1944 because residue number 243  < previous residue 298 
Skipped atom 1945 because residue number 243  < previous residue 298 
Skipped atom 1946 because residue number 243  < previous residue 298 
Skipped atom 1947 because residue number 243  < previous residue 298 
Skipped atom 1948 because residue number 244  < previous residue 298 
Skipped atom 1949 because residue number 244  < previous residue 298 
Skipped atom 1950 because residue number 244  < previous residue 298 
Skipped atom 1951 because residue number 244  < previous residue 298 
Skipped atom 1952 because residue number 244  < previous residue 298 
Skipped atom 1953 because residue number 244  < previous residue 298 
Skipped atom 1954 because residue number 244  < previous residue 298 
Skipped atom 1955 because residue number 244  < previous residue 298 
Skipped atom 1956 because residue number 244  < previous residue 298 
Skipped atom 1957 because residue number 244  < previous residue 298 
Skipped atom 1958 because residue number 244  < previous residue 298 
Skipped atom 1959 because residue number 245  < previous residue 298 
Skipped atom 1960 because residue number 245  < previous residue 298 
Skipped atom 1961 because residue number 245  < previous residue 298 
Skipped atom 1962 because residue number 245  < previous residue 298 
Skipped atom 1963 because residue number 245  < previous residue 298 
Skipped atom 1964 because residue number 245  < previous residue 298 
Skipped atom 1965 because residue number 245  < previous residue 298 
Skipped atom 1966 because residue number 245  < previous residue 298 
Skipped atom 1967 because residue number 246  < previous residue 298 
Skipped atom 1968 because residue number 246  < previous residue 298 
Skipped atom 1969 because residue number 246  < previous residue 298 
Skipped atom 1970 because residue number 246  < previous residue 298 
Skipped atom 1971 because residue number 246  < previous residue 298 
Skipped atom 1972 because residue number 246  < previous residue 298 
Skipped atom 1973 because residue number 246  < previous residue 298 
Skipped atom 1974 because residue number 246  < previous residue 298 
Skipped atom 1975 because residue number 247  < previous residue 298 
Skipped atom 1976 because residue number 247  < previous residue 298 
Skipped atom 1977 because residue number 247  < previous residue 298 
Skipped atom 1978 because residue number 247  < previous residue 298 
Skipped atom 1979 because residue number 247  < previous residue 298 
Skipped atom 1980 because residue number 247  < previous residue 298 
Skipped atom 1981 because residue number 247  < previous residue 298 
Skipped atom 1982 because residue number 248  < previous residue 298 
Skipped atom 1983 because residue number 248  < previous residue 298 
Skipped atom 1984 because residue number 248  < previous residue 298 
Skipped atom 1985 because residue number 248  < previous residue 298 
Skipped atom 1986 because residue number 248  < previous residue 298 
Skipped atom 1987 because residue number 249  < previous residue 298 
Skipped atom 1988 because residue number 249  < previous residue 298 
Skipped atom 1989 because residue number 249  < previous residue 298 
Skipped atom 1990 because residue number 249  < previous residue 298 
Skipped atom 1991 because residue number 249  < previous residue 298 
Skipped atom 1992 because residue number 249  < previous residue 298 
Skipped atom 1993 because residue number 249  < previous residue 298 
Skipped atom 1994 because residue number 249  < previous residue 298 
Skipped atom 1995 because residue number 249  < previous residue 298 
Skipped atom 1996 because residue number 249  < previous residue 298 
Skipped atom 1997 because residue number 249  < previous residue 298 
Skipped atom 1998 because residue number 250  < previous residue 298 
Skipped atom 1999 because residue number 250  < previous residue 298 
Skipped atom 2000 because residue number 250  < previous residue 298 
Skipped atom 2001 because residue number 250  < previous residue 298 
Skipped atom 2002 because residue number 250  < previous residue 298 
Skipped atom 2003 because residue number 250  < previous residue 298 
Skipped atom 2004 because residue number 250  < previous residue 298 
Skipped atom 2005 because residue number 251  < previous residue 298 
Skipped atom 2006 because residue number 251  < previous residue 298 
Skipped atom 2007 because residue number 251  < previous residue 298 
Skipped atom 2008 because residue number 251  < previous residue 298 
Skipped atom 2009 because residue number 251  < previous residue 298 
Skipped atom 2010 because residue number 251  < previous residue 298 
Skipped atom 2011 because residue number 251  < previous residue 298 
Skipped atom 2012 because residue number 251  < previous residue 298 
Skipped atom 2013 because residue number 251  < previous residue 298 
Skipped atom 2014 because residue number 251  < previous residue 298 
Skipped atom 2015 because residue number 251  < previous residue 298 
Skipped atom 2016 because residue number 251  < previous residue 298 
Skipped atom 2017 because residue number 252  < previous residue 298 
Skipped atom 2018 because residue number 252  < previous residue 298 
Skipped atom 2019 because residue number 252  < previous residue 298 
Skipped atom 2020 because residue number 252  < previous residue 298 
Skipped atom 2021 because residue number 252  < previous residue 298 
Skipped atom 2022 because residue number 252  < previous residue 298 
Skipped atom 2023 because residue number 252  < previous residue 298 
Skipped atom 2024 because residue number 253  < previous residue 298 
Skipped atom 2025 because residue number 253  < previous residue 298 
Skipped atom 2026 because residue number 253  < previous residue 298 
Skipped atom 2027 because residue number 253  < previous residue 298 
Skipped atom 2028 because residue number 253  < previous residue 298 
Skipped atom 2029 because residue number 253  < previous residue 298 
Skipped atom 2030 because residue number 253  < previous residue 298 
Skipped atom 2031 because residue number 253  < previous residue 298 
Skipped atom 2032 because residue number 253  < previous residue 298 
Skipped atom 2033 because residue number 253  < previous residue 298 
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1alq-orig.a2m
Writing a2m file: tmp/1alq-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23064


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23064/tmp -alignfile tmp/1alq-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1alq-orig.a2m (1 sequences, 266 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23064/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23064/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23064/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23064/tmp.a2m (1 sequences, 266 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23064/tmp.mod tmp/1alq-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23064 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1alq-align.mod
tmp/1alq-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23064/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1alq-orig.a2m tmp/1alq-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1alq-align.mod
Running w0.5 tmp/1alq-orig.a2m tmp/1alq-align.mod
Running align2model tmp/1alq-align -i tmp/1alq-align.mod -db tmp/1alq-orig.a2m -db tmp/1alq-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1alq.143.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1alq.144.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1alq.144.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1alq.144.0.a2m \
	-target T0124 -template 1alq \
	-out T0124-1alq.144.0 -outdir und
Skipped atom 298 because residue number 31  < previous residue 298 
Skipped atom 299 because residue number 31  < previous residue 298 
Skipped atom 300 because residue number 31  < previous residue 298 
Skipped atom 301 because residue number 31  < previous residue 298 
Skipped atom 302 because residue number 31  < previous residue 298 
Skipped atom 303 because residue number 31  < previous residue 298 
Skipped atom 304 because residue number 31  < previous residue 298 
Skipped atom 305 because residue number 31  < previous residue 298 
Skipped atom 306 because residue number 31  < previous residue 298 
Skipped atom 307 because residue number 32  < previous residue 298 
Skipped atom 308 because residue number 32  < previous residue 298 
Skipped atom 309 because residue number 32  < previous residue 298 
Skipped atom 310 because residue number 32  < previous residue 298 
Skipped atom 311 because residue number 32  < previous residue 298 
Skipped atom 312 because residue number 32  < previous residue 298 
Skipped atom 313 because residue number 32  < previous residue 298 
Skipped atom 314 because residue number 32  < previous residue 298 
Skipped atom 315 because residue number 32  < previous residue 298 
Skipped atom 316 because residue number 33  < previous residue 298 
Skipped atom 317 because residue number 33  < previous residue 298 
Skipped atom 318 because residue number 33  < previous residue 298 
Skipped atom 319 because residue number 33  < previous residue 298 
Skipped atom 320 because residue number 33  < previous residue 298 
Skipped atom 321 because residue number 33  < previous residue 298 
Skipped atom 322 because residue number 33  < previous residue 298 
Skipped atom 323 because residue number 33  < previous residue 298 
Skipped atom 324 because residue number 34  < previous residue 298 
Skipped atom 325 because residue number 34  < previous residue 298 
Skipped atom 326 because residue number 34  < previous residue 298 
Skipped atom 327 because residue number 34  < previous residue 298 
Skipped atom 328 because residue number 34  < previous residue 298 
Skipped atom 329 because residue number 34  < previous residue 298 
Skipped atom 330 because residue number 34  < previous residue 298 
Skipped atom 331 because residue number 34  < previous residue 298 
Skipped atom 332 because residue number 35  < previous residue 298 
Skipped atom 333 because residue number 35  < previous residue 298 
Skipped atom 334 because residue number 35  < previous residue 298 
Skipped atom 335 because residue number 35  < previous residue 298 
Skipped atom 336 because residue number 35  < previous residue 298 
Skipped atom 337 because residue number 35  < previous residue 298 
Skipped atom 338 because residue number 35  < previous residue 298 
Skipped atom 339 because residue number 35  < previous residue 298 
Skipped atom 340 because residue number 36  < previous residue 298 
Skipped atom 341 because residue number 36  < previous residue 298 
Skipped atom 342 because residue number 36  < previous residue 298 
Skipped atom 343 because residue number 36  < previous residue 298 
Skipped atom 344 because residue number 36  < previous residue 298 
Skipped atom 345 because residue number 36  < previous residue 298 
Skipped atom 346 because residue number 36  < previous residue 298 
Skipped atom 347 because residue number 36  < previous residue 298 
Skipped atom 348 because residue number 37  < previous residue 298 
Skipped atom 349 because residue number 37  < previous residue 298 
Skipped atom 350 because residue number 37  < previous residue 298 
Skipped atom 351 because residue number 37  < previous residue 298 
Skipped atom 352 because residue number 37  < previous residue 298 
Skipped atom 353 because residue number 37  < previous residue 298 
Skipped atom 354 because residue number 37  < previous residue 298 
Skipped atom 355 because residue number 37  < previous residue 298 
Skipped atom 356 because residue number 37  < previous residue 298 
Skipped atom 357 because residue number 38  < previous residue 298 
Skipped atom 358 because residue number 38  < previous residue 298 
Skipped atom 359 because residue number 38  < previous residue 298 
Skipped atom 360 because residue number 38  < previous residue 298 
Skipped atom 361 because residue number 38  < previous residue 298 
Skipped atom 362 because residue number 38  < previous residue 298 
Skipped atom 363 because residue number 38  < previous residue 298 
Skipped atom 364 because residue number 38  < previous residue 298 
Skipped atom 365 because residue number 38  < previous residue 298 
Skipped atom 366 because residue number 39  < previous residue 298 
Skipped atom 367 because residue number 39  < previous residue 298 
Skipped atom 368 because residue number 39  < previous residue 298 
Skipped atom 369 because residue number 39  < previous residue 298 
Skipped atom 370 because residue number 39  < previous residue 298 
Skipped atom 371 because residue number 39  < previous residue 298 
Skipped atom 372 because residue number 39  < previous residue 298 
Skipped atom 373 because residue number 39  < previous residue 298 
Skipped atom 374 because residue number 39  < previous residue 298 
Skipped atom 375 because residue number 40  < previous residue 298 
Skipped atom 376 because residue number 40  < previous residue 298 
Skipped atom 377 because residue number 40  < previous residue 298 
Skipped atom 378 because residue number 40  < previous residue 298 
Skipped atom 379 because residue number 40  < previous residue 298 
Skipped atom 380 because residue number 40  < previous residue 298 
Skipped atom 381 because residue number 40  < previous residue 298 
Skipped atom 382 because residue number 40  < previous residue 298 
Skipped atom 383 because residue number 40  < previous residue 298 
Skipped atom 384 because residue number 40  < previous residue 298 
Skipped atom 385 because residue number 40  < previous residue 298 
Skipped atom 386 because residue number 40  < previous residue 298 
Skipped atom 387 because residue number 41  < previous residue 298 
Skipped atom 388 because residue number 41  < previous residue 298 
Skipped atom 389 because residue number 41  < previous residue 298 
Skipped atom 390 because residue number 41  < previous residue 298 
Skipped atom 391 because residue number 41  < previous residue 298 
Skipped atom 392 because residue number 41  < previous residue 298 
Skipped atom 393 because residue number 41  < previous residue 298 
Skipped atom 394 because residue number 41  < previous residue 298 
Skipped atom 395 because residue number 42  < previous residue 298 
Skipped atom 396 because residue number 42  < previous residue 298 
Skipped atom 397 because residue number 42  < previous residue 298 
Skipped atom 398 because residue number 42  < previous residue 298 
Skipped atom 399 because residue number 42  < previous residue 298 
Skipped atom 400 because residue number 43  < previous residue 298 
Skipped atom 401 because residue number 43  < previous residue 298 
Skipped atom 402 because residue number 43  < previous residue 298 
Skipped atom 403 because residue number 43  < previous residue 298 
Skipped atom 404 because residue number 43  < previous residue 298 
Skipped atom 405 because residue number 43  < previous residue 298 
Skipped atom 406 because residue number 43  < previous residue 298 
Skipped atom 407 because residue number 43  < previous residue 298 
Skipped atom 408 because residue number 43  < previous residue 298 
Skipped atom 409 because residue number 43  < previous residue 298 
Skipped atom 410 because residue number 44  < previous residue 298 
Skipped atom 411 because residue number 44  < previous residue 298 
Skipped atom 412 because residue number 44  < previous residue 298 
Skipped atom 413 because residue number 44  < previous residue 298 
Skipped atom 414 because residue number 44  < previous residue 298 
Skipped atom 415 because residue number 44  < previous residue 298 
Skipped atom 416 because residue number 44  < previous residue 298 
Skipped atom 417 because residue number 44  < previous residue 298 
Skipped atom 418 because residue number 45  < previous residue 298 
Skipped atom 419 because residue number 45  < previous residue 298 
Skipped atom 420 because residue number 45  < previous residue 298 
Skipped atom 421 because residue number 45  < previous residue 298 
Skipped atom 422 because residue number 46  < previous residue 298 
Skipped atom 423 because residue number 46  < previous residue 298 
Skipped atom 424 because residue number 46  < previous residue 298 
Skipped atom 425 because residue number 46  < previous residue 298 
Skipped atom 426 because residue number 46  < previous residue 298 
Skipped atom 427 because residue number 46  < previous residue 298 
Skipped atom 428 because residue number 46  < previous residue 298 
Skipped atom 429 because residue number 47  < previous residue 298 
Skipped atom 430 because residue number 47  < previous residue 298 
Skipped atom 431 because residue number 47  < previous residue 298 
Skipped atom 432 because residue number 47  < previous residue 298 
Skipped atom 433 because residue number 47  < previous residue 298 
Skipped atom 434 because residue number 47  < previous residue 298 
Skipped atom 435 because residue number 47  < previous residue 298 
Skipped atom 436 because residue number 47  < previous residue 298 
Skipped atom 437 because residue number 47  < previous residue 298 
Skipped atom 438 because residue number 47  < previous residue 298 
Skipped atom 439 because residue number 47  < previous residue 298 
Skipped atom 440 because residue number 47  < previous residue 298 
Skipped atom 441 because residue number 48  < previous residue 298 
Skipped atom 442 because residue number 48  < previous residue 298 
Skipped atom 443 because residue number 48  < previous residue 298 
Skipped atom 444 because residue number 48  < previous residue 298 
Skipped atom 445 because residue number 48  < previous residue 298 
Skipped atom 446 because residue number 49  < previous residue 298 
Skipped atom 447 because residue number 49  < previous residue 298 
Skipped atom 448 because residue number 49  < previous residue 298 
Skipped atom 449 because residue number 49  < previous residue 298 
Skipped atom 450 because residue number 49  < previous residue 298 
Skipped atom 451 because residue number 49  < previous residue 298 
Skipped atom 452 because residue number 49  < previous residue 298 
Skipped atom 453 because residue number 49  < previous residue 298 
Skipped atom 454 because residue number 50  < previous residue 298 
Skipped atom 455 because residue number 50  < previous residue 298 
Skipped atom 456 because residue number 50  < previous residue 298 
Skipped atom 457 because residue number 50  < previous residue 298 
Skipped atom 458 because residue number 50  < previous residue 298 
Skipped atom 459 because residue number 50  < previous residue 298 
Skipped atom 460 because residue number 50  < previous residue 298 
Skipped atom 461 because residue number 50  < previous residue 298 
Skipped atom 462 because residue number 51  < previous residue 298 
Skipped atom 463 because residue number 51  < previous residue 298 
Skipped atom 464 because residue number 51  < previous residue 298 
Skipped atom 465 because residue number 51  < previous residue 298 
Skipped atom 466 because residue number 51  < previous residue 298 
Skipped atom 467 because residue number 51  < previous residue 298 
Skipped atom 468 because residue number 51  < previous residue 298 
Skipped atom 469 because residue number 52  < previous residue 298 
Skipped atom 470 because residue number 52  < previous residue 298 
Skipped atom 471 because residue number 52  < previous residue 298 
Skipped atom 472 because residue number 52  < previous residue 298 
Skipped atom 473 because residue number 52  < previous residue 298 
Skipped atom 474 because residue number 52  < previous residue 298 
Skipped atom 475 because residue number 52  < previous residue 298 
Skipped atom 476 because residue number 52  < previous residue 298 
Skipped atom 477 because residue number 52  < previous residue 298 
Skipped atom 478 because residue number 53  < previous residue 298 
Skipped atom 479 because residue number 53  < previous residue 298 
Skipped atom 480 because residue number 53  < previous residue 298 
Skipped atom 481 because residue number 53  < previous residue 298 
Skipped atom 482 because residue number 53  < previous residue 298 
Skipped atom 483 because residue number 53  < previous residue 298 
Skipped atom 484 because residue number 54  < previous residue 298 
Skipped atom 485 because residue number 54  < previous residue 298 
Skipped atom 486 because residue number 54  < previous residue 298 
Skipped atom 487 because residue number 54  < previous residue 298 
Skipped atom 488 because residue number 55  < previous residue 298 
Skipped atom 489 because residue number 55  < previous residue 298 
Skipped atom 490 because residue number 55  < previous residue 298 
Skipped atom 491 because residue number 55  < previous residue 298 
Skipped atom 492 because residue number 55  < previous residue 298 
Skipped atom 493 because residue number 55  < previous residue 298 
Skipped atom 494 because residue number 55  < previous residue 298 
Skipped atom 495 because residue number 55  < previous residue 298 
Skipped atom 496 because residue number 55  < previous residue 298 
Skipped atom 497 because residue number 56  < previous residue 298 
Skipped atom 498 because residue number 56  < previous residue 298 
Skipped atom 499 because residue number 56  < previous residue 298 
Skipped atom 500 because residue number 56  < previous residue 298 
Skipped atom 501 because residue number 56  < previous residue 298 
Skipped atom 502 because residue number 56  < previous residue 298 
Skipped atom 503 because residue number 56  < previous residue 298 
Skipped atom 504 because residue number 56  < previous residue 298 
Skipped atom 505 because residue number 56  < previous residue 298 
Skipped atom 506 because residue number 57  < previous residue 298 
Skipped atom 507 because residue number 57  < previous residue 298 
Skipped atom 508 because residue number 57  < previous residue 298 
Skipped atom 509 because residue number 57  < previous residue 298 
Skipped atom 510 because residue number 57  < previous residue 298 
Skipped atom 511 because residue number 57  < previous residue 298 
Skipped atom 512 because residue number 57  < previous residue 298 
Skipped atom 513 because residue number 59  < previous residue 298 
Skipped atom 514 because residue number 59  < previous residue 298 
Skipped atom 515 because residue number 59  < previous residue 298 
Skipped atom 516 because residue number 59  < previous residue 298 
Skipped atom 517 because residue number 59  < previous residue 298 
Skipped atom 518 because residue number 59  < previous residue 298 
Skipped atom 519 because residue number 59  < previous residue 298 
Skipped atom 520 because residue number 59  < previous residue 298 
Skipped atom 521 because residue number 59  < previous residue 298 
Skipped atom 522 because residue number 60  < previous residue 298 
Skipped atom 523 because residue number 60  < previous residue 298 
Skipped atom 524 because residue number 60  < previous residue 298 
Skipped atom 525 because residue number 60  < previous residue 298 
Skipped atom 526 because residue number 60  < previous residue 298 
Skipped atom 527 because residue number 60  < previous residue 298 
Skipped atom 528 because residue number 60  < previous residue 298 
Skipped atom 529 because residue number 60  < previous residue 298 
Skipped atom 530 because residue number 60  < previous residue 298 
Skipped atom 531 because residue number 60  < previous residue 298 
Skipped atom 532 because residue number 60  < previous residue 298 
Skipped atom 533 because residue number 61  < previous residue 298 
Skipped atom 534 because residue number 61  < previous residue 298 
Skipped atom 535 because residue number 61  < previous residue 298 
Skipped atom 536 because residue number 61  < previous residue 298 
Skipped atom 537 because residue number 61  < previous residue 298 
Skipped atom 538 because residue number 61  < previous residue 298 
Skipped atom 539 because residue number 61  < previous residue 298 
Skipped atom 540 because residue number 61  < previous residue 298 
Skipped atom 541 because residue number 62  < previous residue 298 
Skipped atom 542 because residue number 62  < previous residue 298 
Skipped atom 543 because residue number 62  < previous residue 298 
Skipped atom 544 because residue number 62  < previous residue 298 
Skipped atom 545 because residue number 62  < previous residue 298 
Skipped atom 546 because residue number 62  < previous residue 298 
Skipped atom 547 because residue number 63  < previous residue 298 
Skipped atom 548 because residue number 63  < previous residue 298 
Skipped atom 549 because residue number 63  < previous residue 298 
Skipped atom 550 because residue number 63  < previous residue 298 
Skipped atom 551 because residue number 63  < previous residue 298 
Skipped atom 552 because residue number 63  < previous residue 298 
Skipped atom 553 because residue number 63  < previous residue 298 
Skipped atom 554 because residue number 63  < previous residue 298 
Skipped atom 555 because residue number 64  < previous residue 298 
Skipped atom 556 because residue number 64  < previous residue 298 
Skipped atom 557 because residue number 64  < previous residue 298 
Skipped atom 558 because residue number 64  < previous residue 298 
Skipped atom 559 because residue number 64  < previous residue 298 
Skipped atom 560 because residue number 64  < previous residue 298 
Skipped atom 561 because residue number 64  < previous residue 298 
Skipped atom 562 because residue number 64  < previous residue 298 
Skipped atom 563 because residue number 64  < previous residue 298 
Skipped atom 564 because residue number 65  < previous residue 298 
Skipped atom 565 because residue number 65  < previous residue 298 
Skipped atom 566 because residue number 65  < previous residue 298 
Skipped atom 567 because residue number 65  < previous residue 298 
Skipped atom 568 because residue number 65  < previous residue 298 
Skipped atom 569 because residue number 65  < previous residue 298 
Skipped atom 570 because residue number 65  < previous residue 298 
Skipped atom 571 because residue number 65  < previous residue 298 
Skipped atom 572 because residue number 65  < previous residue 298 
Skipped atom 573 because residue number 65  < previous residue 298 
Skipped atom 574 because residue number 65  < previous residue 298 
Skipped atom 575 because residue number 66  < previous residue 298 
Skipped atom 576 because residue number 66  < previous residue 298 
Skipped atom 577 because residue number 66  < previous residue 298 
Skipped atom 578 because residue number 66  < previous residue 298 
Skipped atom 579 because residue number 66  < previous residue 298 
Skipped atom 580 because residue number 66  < previous residue 298 
Skipped atom 581 because residue number 66  < previous residue 298 
Skipped atom 582 because residue number 66  < previous residue 298 
Skipped atom 583 because residue number 66  < previous residue 298 
Skipped atom 584 because residue number 66  < previous residue 298 
Skipped atom 585 because residue number 66  < previous residue 298 
Skipped atom 586 because residue number 67  < previous residue 298 
Skipped atom 587 because residue number 67  < previous residue 298 
Skipped atom 588 because residue number 67  < previous residue 298 
Skipped atom 589 because residue number 67  < previous residue 298 
Skipped atom 590 because residue number 67  < previous residue 298 
Skipped atom 591 because residue number 68  < previous residue 298 
Skipped atom 592 because residue number 68  < previous residue 298 
Skipped atom 593 because residue number 68  < previous residue 298 
Skipped atom 594 because residue number 68  < previous residue 298 
Skipped atom 595 because residue number 68  < previous residue 298 
Skipped atom 596 because residue number 68  < previous residue 298 
Skipped atom 597 because residue number 68  < previous residue 298 
Skipped atom 598 because residue number 68  < previous residue 298 
Skipped atom 599 because residue number 68  < previous residue 298 
Skipped atom 600 because residue number 68  < previous residue 298 
Skipped atom 601 because residue number 68  < previous residue 298 
Skipped atom 602 because residue number 68  < previous residue 298 
Skipped atom 603 because residue number 69  < previous residue 298 
Skipped atom 604 because residue number 69  < previous residue 298 
Skipped atom 605 because residue number 69  < previous residue 298 
Skipped atom 606 because residue number 69  < previous residue 298 
Skipped atom 607 because residue number 69  < previous residue 298 
Skipped atom 608 because residue number 70  < previous residue 298 
Skipped atom 609 because residue number 70  < previous residue 298 
Skipped atom 610 because residue number 70  < previous residue 298 
Skipped atom 611 because residue number 70  < previous residue 298 
Skipped atom 612 because residue number 70  < previous residue 298 
Skipped atom 613 because residue number 70  < previous residue 298 
Skipped atom 614 because residue number 71  < previous residue 298 
Skipped atom 615 because residue number 71  < previous residue 298 
Skipped atom 616 because residue number 71  < previous residue 298 
Skipped atom 617 because residue number 71  < previous residue 298 
Skipped atom 618 because residue number 71  < previous residue 298 
Skipped atom 619 because residue number 71  < previous residue 298 
Skipped atom 620 because residue number 71  < previous residue 298 
Skipped atom 621 because residue number 72  < previous residue 298 
Skipped atom 622 because residue number 72  < previous residue 298 
Skipped atom 623 because residue number 72  < previous residue 298 
Skipped atom 624 because residue number 72  < previous residue 298 
Skipped atom 625 because residue number 72  < previous residue 298 
Skipped atom 626 because residue number 72  < previous residue 298 
Skipped atom 627 because residue number 73  < previous residue 298 
Skipped atom 628 because residue number 73  < previous residue 298 
Skipped atom 629 because residue number 73  < previous residue 298 
Skipped atom 630 because residue number 73  < previous residue 298 
Skipped atom 631 because residue number 73  < previous residue 298 
Skipped atom 632 because residue number 73  < previous residue 298 
Skipped atom 633 because residue number 73  < previous residue 298 
Skipped atom 634 because residue number 73  < previous residue 298 
Skipped atom 635 because residue number 73  < previous residue 298 
Skipped atom 636 because residue number 74  < previous residue 298 
Skipped atom 637 because residue number 74  < previous residue 298 
Skipped atom 638 because residue number 74  < previous residue 298 
Skipped atom 639 because residue number 74  < previous residue 298 
Skipped atom 640 because residue number 74  < previous residue 298 
Skipped atom 641 because residue number 75  < previous residue 298 
Skipped atom 642 because residue number 75  < previous residue 298 
Skipped atom 643 because residue number 75  < previous residue 298 
Skipped atom 644 because residue number 75  < previous residue 298 
Skipped atom 645 because residue number 75  < previous residue 298 
Skipped atom 646 because residue number 75  < previous residue 298 
Skipped atom 647 because residue number 75  < previous residue 298 
Skipped atom 648 because residue number 75  < previous residue 298 
Skipped atom 649 because residue number 76  < previous residue 298 
Skipped atom 650 because residue number 76  < previous residue 298 
Skipped atom 651 because residue number 76  < previous residue 298 
Skipped atom 652 because residue number 76  < previous residue 298 
Skipped atom 653 because residue number 76  < previous residue 298 
Skipped atom 654 because residue number 76  < previous residue 298 
Skipped atom 655 because residue number 76  < previous residue 298 
Skipped atom 656 because residue number 76  < previous residue 298 
Skipped atom 657 because residue number 77  < previous residue 298 
Skipped atom 658 because residue number 77  < previous residue 298 
Skipped atom 659 because residue number 77  < previous residue 298 
Skipped atom 660 because residue number 77  < previous residue 298 
Skipped atom 661 because residue number 77  < previous residue 298 
Skipped atom 662 because residue number 77  < previous residue 298 
Skipped atom 663 because residue number 78  < previous residue 298 
Skipped atom 664 because residue number 78  < previous residue 298 
Skipped atom 665 because residue number 78  < previous residue 298 
Skipped atom 666 because residue number 78  < previous residue 298 
Skipped atom 667 because residue number 78  < previous residue 298 
Skipped atom 668 because residue number 79  < previous residue 298 
Skipped atom 669 because residue number 79  < previous residue 298 
Skipped atom 670 because residue number 79  < previous residue 298 
Skipped atom 671 because residue number 79  < previous residue 298 
Skipped atom 672 because residue number 79  < previous residue 298 
Skipped atom 673 because residue number 79  < previous residue 298 
Skipped atom 674 because residue number 79  < previous residue 298 
Skipped atom 675 because residue number 79  < previous residue 298 
Skipped atom 676 because residue number 80  < previous residue 298 
Skipped atom 677 because residue number 80  < previous residue 298 
Skipped atom 678 because residue number 80  < previous residue 298 
Skipped atom 679 because residue number 80  < previous residue 298 
Skipped atom 680 because residue number 80  < previous residue 298 
Skipped atom 681 because residue number 80  < previous residue 298 
Skipped atom 682 because residue number 80  < previous residue 298 
Skipped atom 683 because residue number 80  < previous residue 298 
Skipped atom 684 because residue number 81  < previous residue 298 
Skipped atom 685 because residue number 81  < previous residue 298 
Skipped atom 686 because residue number 81  < previous residue 298 
Skipped atom 687 because residue number 81  < previous residue 298 
Skipped atom 688 because residue number 81  < previous residue 298 
Skipped atom 689 because residue number 81  < previous residue 298 
Skipped atom 690 because residue number 81  < previous residue 298 
Skipped atom 691 because residue number 81  < previous residue 298 
Skipped atom 692 because residue number 82  < previous residue 298 
Skipped atom 693 because residue number 82  < previous residue 298 
Skipped atom 694 because residue number 82  < previous residue 298 
Skipped atom 695 because residue number 82  < previous residue 298 
Skipped atom 696 because residue number 82  < previous residue 298 
Skipped atom 697 because residue number 82  < previous residue 298 
Skipped atom 698 because residue number 82  < previous residue 298 
Skipped atom 699 because residue number 82  < previous residue 298 
Skipped atom 700 because residue number 82  < previous residue 298 
Skipped atom 701 because residue number 83  < previous residue 298 
Skipped atom 702 because residue number 83  < previous residue 298 
Skipped atom 703 because residue number 83  < previous residue 298 
Skipped atom 704 because residue number 83  < previous residue 298 
Skipped atom 705 because residue number 83  < previous residue 298 
Skipped atom 706 because residue number 83  < previous residue 298 
Skipped atom 707 because residue number 83  < previous residue 298 
Skipped atom 708 because residue number 83  < previous residue 298 
Skipped atom 709 because residue number 83  < previous residue 298 
Skipped atom 710 because residue number 84  < previous residue 298 
Skipped atom 711 because residue number 84  < previous residue 298 
Skipped atom 712 because residue number 84  < previous residue 298 
Skipped atom 713 because residue number 84  < previous residue 298 
Skipped atom 714 because residue number 84  < previous residue 298 
Skipped atom 715 because residue number 84  < previous residue 298 
Skipped atom 716 because residue number 84  < previous residue 298 
Skipped atom 717 because residue number 87  < previous residue 298 
Skipped atom 718 because residue number 87  < previous residue 298 
Skipped atom 719 because residue number 87  < previous residue 298 
Skipped atom 720 because residue number 87  < previous residue 298 
Skipped atom 721 because residue number 87  < previous residue 298 
Skipped atom 722 because residue number 87  < previous residue 298 
Skipped atom 723 because residue number 87  < previous residue 298 
Skipped atom 724 because residue number 88  < previous residue 298 
Skipped atom 725 because residue number 88  < previous residue 298 
Skipped atom 726 because residue number 88  < previous residue 298 
Skipped atom 727 because residue number 88  < previous residue 298 
Skipped atom 728 because residue number 88  < previous residue 298 
Skipped atom 729 because residue number 88  < previous residue 298 
Skipped atom 730 because residue number 88  < previous residue 298 
Skipped atom 731 because residue number 88  < previous residue 298 
Skipped atom 732 because residue number 88  < previous residue 298 
Skipped atom 733 because residue number 88  < previous residue 298 
Skipped atom 734 because residue number 88  < previous residue 298 
Skipped atom 735 because residue number 88  < previous residue 298 
Skipped atom 736 because residue number 89  < previous residue 298 
Skipped atom 737 because residue number 89  < previous residue 298 
Skipped atom 738 because residue number 89  < previous residue 298 
Skipped atom 739 because residue number 89  < previous residue 298 
Skipped atom 740 because residue number 89  < previous residue 298 
Skipped atom 741 because residue number 89  < previous residue 298 
Skipped atom 742 because residue number 89  < previous residue 298 
Skipped atom 743 because residue number 89  < previous residue 298 
Skipped atom 744 because residue number 90  < previous residue 298 
Skipped atom 745 because residue number 90  < previous residue 298 
Skipped atom 746 because residue number 90  < previous residue 298 
Skipped atom 747 because residue number 90  < previous residue 298 
Skipped atom 748 because residue number 90  < previous residue 298 
Skipped atom 749 because residue number 90  < previous residue 298 
Skipped atom 750 because residue number 90  < previous residue 298 
Skipped atom 751 because residue number 90  < previous residue 298 
Skipped atom 752 because residue number 90  < previous residue 298 
Skipped atom 753 because residue number 91  < previous residue 298 
Skipped atom 754 because residue number 91  < previous residue 298 
Skipped atom 755 because residue number 91  < previous residue 298 
Skipped atom 756 because residue number 91  < previous residue 298 
Skipped atom 757 because residue number 91  < previous residue 298 
Skipped atom 758 because residue number 91  < previous residue 298 
Skipped atom 759 because residue number 91  < previous residue 298 
Skipped atom 760 because residue number 91  < previous residue 298 
Skipped atom 761 because residue number 92  < previous residue 298 
Skipped atom 762 because residue number 92  < previous residue 298 
Skipped atom 763 because residue number 92  < previous residue 298 
Skipped atom 764 because residue number 92  < previous residue 298 
Skipped atom 765 because residue number 92  < previous residue 298 
Skipped atom 766 because residue number 92  < previous residue 298 
Skipped atom 767 because residue number 92  < previous residue 298 
Skipped atom 768 because residue number 92  < previous residue 298 
Skipped atom 769 because residue number 93  < previous residue 298 
Skipped atom 770 because residue number 93  < previous residue 298 
Skipped atom 771 because residue number 93  < previous residue 298 
Skipped atom 772 because residue number 93  < previous residue 298 
Skipped atom 773 because residue number 93  < previous residue 298 
Skipped atom 774 because residue number 93  < previous residue 298 
Skipped atom 775 because residue number 93  < previous residue 298 
Skipped atom 776 because residue number 93  < previous residue 298 
Skipped atom 777 because residue number 93  < previous residue 298 
Skipped atom 778 because residue number 94  < previous residue 298 
Skipped atom 779 because residue number 94  < previous residue 298 
Skipped atom 780 because residue number 94  < previous residue 298 
Skipped atom 781 because residue number 94  < previous residue 298 
Skipped atom 782 because residue number 94  < previous residue 298 
Skipped atom 783 because residue number 94  < previous residue 298 
Skipped atom 784 because residue number 94  < previous residue 298 
Skipped atom 785 because residue number 94  < previous residue 298 
Skipped atom 786 because residue number 94  < previous residue 298 
Skipped atom 787 because residue number 95  < previous residue 298 
Skipped atom 788 because residue number 95  < previous residue 298 
Skipped atom 789 because residue number 95  < previous residue 298 
Skipped atom 790 because residue number 95  < previous residue 298 
Skipped atom 791 because residue number 95  < previous residue 298 
Skipped atom 792 because residue number 95  < previous residue 298 
Skipped atom 793 because residue number 95  < previous residue 298 
Skipped atom 794 because residue number 96  < previous residue 298 
Skipped atom 795 because residue number 96  < previous residue 298 
Skipped atom 796 because residue number 96  < previous residue 298 
Skipped atom 797 because residue number 96  < previous residue 298 
Skipped atom 798 because residue number 96  < previous residue 298 
Skipped atom 799 because residue number 96  < previous residue 298 
Skipped atom 800 because residue number 96  < previous residue 298 
Skipped atom 801 because residue number 96  < previous residue 298 
Skipped atom 802 because residue number 96  < previous residue 298 
Skipped atom 803 because residue number 96  < previous residue 298 
Skipped atom 804 because residue number 97  < previous residue 298 
Skipped atom 805 because residue number 97  < previous residue 298 
Skipped atom 806 because residue number 97  < previous residue 298 
Skipped atom 807 because residue number 97  < previous residue 298 
Skipped atom 808 because residue number 97  < previous residue 298 
Skipped atom 809 because residue number 97  < previous residue 298 
Skipped atom 810 because residue number 97  < previous residue 298 
Skipped atom 811 because residue number 97  < previous residue 298 
Skipped atom 812 because residue number 98  < previous residue 298 
Skipped atom 813 because residue number 98  < previous residue 298 
Skipped atom 814 because residue number 98  < previous residue 298 
Skipped atom 815 because residue number 98  < previous residue 298 
Skipped atom 816 because residue number 98  < previous residue 298 
Skipped atom 817 because residue number 98  < previous residue 298 
Skipped atom 818 because residue number 98  < previous residue 298 
Skipped atom 819 because residue number 98  < previous residue 298 
Skipped atom 820 because residue number 99  < previous residue 298 
Skipped atom 821 because residue number 99  < previous residue 298 
Skipped atom 822 because residue number 99  < previous residue 298 
Skipped atom 823 because residue number 99  < previous residue 298 
Skipped atom 824 because residue number 99  < previous residue 298 
Skipped atom 825 because residue number 99  < previous residue 298 
Skipped atom 826 because residue number 99  < previous residue 298 
Skipped atom 827 because residue number 99  < previous residue 298 
Skipped atom 828 because residue number 99  < previous residue 298 
Skipped atom 829 because residue number 100  < previous residue 298 
Skipped atom 830 because residue number 100  < previous residue 298 
Skipped atom 831 because residue number 100  < previous residue 298 
Skipped atom 832 because residue number 100  < previous residue 298 
Skipped atom 833 because residue number 100  < previous residue 298 
Skipped atom 834 because residue number 100  < previous residue 298 
Skipped atom 835 because residue number 100  < previous residue 298 
Skipped atom 836 because residue number 100  < previous residue 298 
Skipped atom 837 because residue number 101  < previous residue 298 
Skipped atom 838 because residue number 101  < previous residue 298 
Skipped atom 839 because residue number 101  < previous residue 298 
Skipped atom 840 because residue number 101  < previous residue 298 
Skipped atom 841 because residue number 101  < previous residue 298 
Skipped atom 842 because residue number 101  < previous residue 298 
Skipped atom 843 because residue number 101  < previous residue 298 
Skipped atom 844 because residue number 101  < previous residue 298 
Skipped atom 845 because residue number 102  < previous residue 298 
Skipped atom 846 because residue number 102  < previous residue 298 
Skipped atom 847 because residue number 102  < previous residue 298 
Skipped atom 848 because residue number 102  < previous residue 298 
Skipped atom 849 because residue number 102  < previous residue 298 
Skipped atom 850 because residue number 102  < previous residue 298 
Skipped atom 851 because residue number 102  < previous residue 298 
Skipped atom 852 because residue number 102  < previous residue 298 
Skipped atom 853 because residue number 103  < previous residue 298 
Skipped atom 854 because residue number 103  < previous residue 298 
Skipped atom 855 because residue number 103  < previous residue 298 
Skipped atom 856 because residue number 103  < previous residue 298 
Skipped atom 857 because residue number 103  < previous residue 298 
Skipped atom 858 because residue number 103  < previous residue 298 
Skipped atom 859 because residue number 103  < previous residue 298 
Skipped atom 860 because residue number 104  < previous residue 298 
Skipped atom 861 because residue number 104  < previous residue 298 
Skipped atom 862 because residue number 104  < previous residue 298 
Skipped atom 863 because residue number 104  < previous residue 298 
Skipped atom 864 because residue number 104  < previous residue 298 
Skipped atom 865 because residue number 105  < previous residue 298 
Skipped atom 866 because residue number 105  < previous residue 298 
Skipped atom 867 because residue number 105  < previous residue 298 
Skipped atom 868 because residue number 105  < previous residue 298 
Skipped atom 869 because residue number 105  < previous residue 298 
Skipped atom 870 because residue number 105  < previous residue 298 
Skipped atom 871 because residue number 105  < previous residue 298 
Skipped atom 872 because residue number 105  < previous residue 298 
Skipped atom 873 because residue number 105  < previous residue 298 
Skipped atom 874 because residue number 105  < previous residue 298 
Skipped atom 875 because residue number 105  < previous residue 298 
Skipped atom 876 because residue number 105  < previous residue 298 
Skipped atom 877 because residue number 106  < previous residue 298 
Skipped atom 878 because residue number 106  < previous residue 298 
Skipped atom 879 because residue number 106  < previous residue 298 
Skipped atom 880 because residue number 106  < previous residue 298 
Skipped atom 881 because residue number 106  < previous residue 298 
Skipped atom 882 because residue number 106  < previous residue 298 
Skipped atom 883 because residue number 107  < previous residue 298 
Skipped atom 884 because residue number 107  < previous residue 298 
Skipped atom 885 because residue number 107  < previous residue 298 
Skipped atom 886 because residue number 107  < previous residue 298 
Skipped atom 887 because residue number 107  < previous residue 298 
Skipped atom 888 because residue number 107  < previous residue 298 
Skipped atom 889 because residue number 107  < previous residue 298 
Skipped atom 890 because residue number 108  < previous residue 298 
Skipped atom 891 because residue number 108  < previous residue 298 
Skipped atom 892 because residue number 108  < previous residue 298 
Skipped atom 893 because residue number 108  < previous residue 298 
Skipped atom 894 because residue number 108  < previous residue 298 
Skipped atom 895 because residue number 108  < previous residue 298 
Skipped atom 896 because residue number 108  < previous residue 298 
Skipped atom 897 because residue number 108  < previous residue 298 
Skipped atom 898 because residue number 109  < previous residue 298 
Skipped atom 899 because residue number 109  < previous residue 298 
Skipped atom 900 because residue number 109  < previous residue 298 
Skipped atom 901 because residue number 109  < previous residue 298 
Skipped atom 902 because residue number 109  < previous residue 298 
Skipped atom 903 because residue number 109  < previous residue 298 
Skipped atom 904 because residue number 109  < previous residue 298 
Skipped atom 905 because residue number 109  < previous residue 298 
Skipped atom 906 because residue number 110  < previous residue 298 
Skipped atom 907 because residue number 110  < previous residue 298 
Skipped atom 908 because residue number 110  < previous residue 298 
Skipped atom 909 because residue number 110  < previous residue 298 
Skipped atom 910 because residue number 110  < previous residue 298 
Skipped atom 911 because residue number 110  < previous residue 298 
Skipped atom 912 because residue number 110  < previous residue 298 
Skipped atom 913 because residue number 110  < previous residue 298 
Skipped atom 914 because residue number 110  < previous residue 298 
Skipped atom 915 because residue number 111  < previous residue 298 
Skipped atom 916 because residue number 111  < previous residue 298 
Skipped atom 917 because residue number 111  < previous residue 298 
Skipped atom 918 because residue number 111  < previous residue 298 
Skipped atom 919 because residue number 111  < previous residue 298 
Skipped atom 920 because residue number 111  < previous residue 298 
Skipped atom 921 because residue number 111  < previous residue 298 
Skipped atom 922 because residue number 111  < previous residue 298 
Skipped atom 923 because residue number 111  < previous residue 298 
Skipped atom 924 because residue number 112  < previous residue 298 
Skipped atom 925 because residue number 112  < previous residue 298 
Skipped atom 926 because residue number 112  < previous residue 298 
Skipped atom 927 because residue number 112  < previous residue 298 
Skipped atom 928 because residue number 112  < previous residue 298 
Skipped atom 929 because residue number 112  < previous residue 298 
Skipped atom 930 because residue number 112  < previous residue 298 
Skipped atom 931 because residue number 112  < previous residue 298 
Skipped atom 932 because residue number 112  < previous residue 298 
Skipped atom 933 because residue number 112  < previous residue 298 
Skipped atom 934 because residue number 112  < previous residue 298 
Skipped atom 935 because residue number 112  < previous residue 298 
Skipped atom 936 because residue number 113  < previous residue 298 
Skipped atom 937 because residue number 113  < previous residue 298 
Skipped atom 938 because residue number 113  < previous residue 298 
Skipped atom 939 because residue number 113  < previous residue 298 
Skipped atom 940 because residue number 113  < previous residue 298 
Skipped atom 941 because residue number 113  < previous residue 298 
Skipped atom 942 because residue number 113  < previous residue 298 
Skipped atom 943 because residue number 114  < previous residue 298 
Skipped atom 944 because residue number 114  < previous residue 298 
Skipped atom 945 because residue number 114  < previous residue 298 
Skipped atom 946 because residue number 114  < previous residue 298 
Skipped atom 947 because residue number 115  < previous residue 298 
Skipped atom 948 because residue number 115  < previous residue 298 
Skipped atom 949 because residue number 115  < previous residue 298 
Skipped atom 950 because residue number 115  < previous residue 298 
Skipped atom 951 because residue number 115  < previous residue 298 
Skipped atom 952 because residue number 115  < previous residue 298 
Skipped atom 953 because residue number 115  < previous residue 298 
Skipped atom 954 because residue number 115  < previous residue 298 
Skipped atom 955 because residue number 115  < previous residue 298 
Skipped atom 956 because residue number 116  < previous residue 298 
Skipped atom 957 because residue number 116  < previous residue 298 
Skipped atom 958 because residue number 116  < previous residue 298 
Skipped atom 959 because residue number 116  < previous residue 298 
Skipped atom 960 because residue number 116  < previous residue 298 
Skipped atom 961 because residue number 116  < previous residue 298 
Skipped atom 962 because residue number 116  < previous residue 298 
Skipped atom 963 because residue number 116  < previous residue 298 
Skipped atom 964 because residue number 117  < previous residue 298 
Skipped atom 965 because residue number 117  < previous residue 298 
Skipped atom 966 because residue number 117  < previous residue 298 
Skipped atom 967 because residue number 117  < previous residue 298 
Skipped atom 968 because residue number 117  < previous residue 298 
Skipped atom 969 because residue number 117  < previous residue 298 
Skipped atom 970 because residue number 117  < previous residue 298 
Skipped atom 971 because residue number 117  < previous residue 298 
Skipped atom 972 because residue number 118  < previous residue 298 
Skipped atom 973 because residue number 118  < previous residue 298 
Skipped atom 974 because residue number 118  < previous residue 298 
Skipped atom 975 because residue number 118  < previous residue 298 
Skipped atom 976 because residue number 118  < previous residue 298 
Skipped atom 977 because residue number 118  < previous residue 298 
Skipped atom 978 because residue number 118  < previous residue 298 
Skipped atom 979 because residue number 119  < previous residue 298 
Skipped atom 980 because residue number 119  < previous residue 298 
Skipped atom 981 because residue number 119  < previous residue 298 
Skipped atom 982 because residue number 119  < previous residue 298 
Skipped atom 983 because residue number 119  < previous residue 298 
Skipped atom 984 because residue number 119  < previous residue 298 
Skipped atom 985 because residue number 119  < previous residue 298 
Skipped atom 986 because residue number 119  < previous residue 298 
Skipped atom 987 because residue number 120  < previous residue 298 
Skipped atom 988 because residue number 120  < previous residue 298 
Skipped atom 989 because residue number 120  < previous residue 298 
Skipped atom 990 because residue number 120  < previous residue 298 
Skipped atom 991 because residue number 120  < previous residue 298 
Skipped atom 992 because residue number 120  < previous residue 298 
Skipped atom 993 because residue number 120  < previous residue 298 
Skipped atom 994 because residue number 120  < previous residue 298 
Skipped atom 995 because residue number 120  < previous residue 298 
Skipped atom 996 because residue number 121  < previous residue 298 
Skipped atom 997 because residue number 121  < previous residue 298 
Skipped atom 998 because residue number 121  < previous residue 298 
Skipped atom 999 because residue number 121  < previous residue 298 
Skipped atom 1000 because residue number 121  < previous residue 298 
Skipped atom 1001 because residue number 122  < previous residue 298 
Skipped atom 1002 because residue number 122  < previous residue 298 
Skipped atom 1003 because residue number 122  < previous residue 298 
Skipped atom 1004 because residue number 122  < previous residue 298 
Skipped atom 1005 because residue number 122  < previous residue 298 
Skipped atom 1006 because residue number 122  < previous residue 298 
Skipped atom 1007 because residue number 122  < previous residue 298 
Skipped atom 1008 because residue number 122  < previous residue 298 
Skipped atom 1009 because residue number 123  < previous residue 298 
Skipped atom 1010 because residue number 123  < previous residue 298 
Skipped atom 1011 because residue number 123  < previous residue 298 
Skipped atom 1012 because residue number 123  < previous residue 298 
Skipped atom 1013 because residue number 123  < previous residue 298 
Skipped atom 1014 because residue number 123  < previous residue 298 
Skipped atom 1015 because residue number 123  < previous residue 298 
Skipped atom 1016 because residue number 123  < previous residue 298 
Skipped atom 1017 because residue number 124  < previous residue 298 
Skipped atom 1018 because residue number 124  < previous residue 298 
Skipped atom 1019 because residue number 124  < previous residue 298 
Skipped atom 1020 because residue number 124  < previous residue 298 
Skipped atom 1021 because residue number 124  < previous residue 298 
Skipped atom 1022 because residue number 124  < previous residue 298 
Skipped atom 1023 because residue number 124  < previous residue 298 
Skipped atom 1024 because residue number 124  < previous residue 298 
Skipped atom 1025 because residue number 124  < previous residue 298 
Skipped atom 1026 because residue number 125  < previous residue 298 
Skipped atom 1027 because residue number 125  < previous residue 298 
Skipped atom 1028 because residue number 125  < previous residue 298 
Skipped atom 1029 because residue number 125  < previous residue 298 
Skipped atom 1030 because residue number 125  < previous residue 298 
Skipped atom 1031 because residue number 126  < previous residue 298 
Skipped atom 1032 because residue number 126  < previous residue 298 
Skipped atom 1033 because residue number 126  < previous residue 298 
Skipped atom 1034 because residue number 126  < previous residue 298 
Skipped atom 1035 because residue number 126  < previous residue 298 
Skipped atom 1036 because residue number 126  < previous residue 298 
Skipped atom 1037 because residue number 127  < previous residue 298 
Skipped atom 1038 because residue number 127  < previous residue 298 
Skipped atom 1039 because residue number 127  < previous residue 298 
Skipped atom 1040 because residue number 127  < previous residue 298 
Skipped atom 1041 because residue number 127  < previous residue 298 
Skipped atom 1042 because residue number 127  < previous residue 298 
Skipped atom 1043 because residue number 127  < previous residue 298 
Skipped atom 1044 because residue number 127  < previous residue 298 
Skipped atom 1045 because residue number 128  < previous residue 298 
Skipped atom 1046 because residue number 128  < previous residue 298 
Skipped atom 1047 because residue number 128  < previous residue 298 
Skipped atom 1048 because residue number 128  < previous residue 298 
Skipped atom 1049 because residue number 128  < previous residue 298 
Skipped atom 1050 because residue number 128  < previous residue 298 
Skipped atom 1051 because residue number 128  < previous residue 298 
Skipped atom 1052 because residue number 129  < previous residue 298 
Skipped atom 1053 because residue number 129  < previous residue 298 
Skipped atom 1054 because residue number 129  < previous residue 298 
Skipped atom 1055 because residue number 129  < previous residue 298 
Skipped atom 1056 because residue number 129  < previous residue 298 
Skipped atom 1057 because residue number 129  < previous residue 298 
Skipped atom 1058 because residue number 129  < previous residue 298 
Skipped atom 1059 because residue number 129  < previous residue 298 
Skipped atom 1060 because residue number 129  < previous residue 298 
Skipped atom 1061 because residue number 129  < previous residue 298 
Skipped atom 1062 because residue number 129  < previous residue 298 
Skipped atom 1063 because residue number 129  < previous residue 298 
Skipped atom 1064 because residue number 130  < previous residue 298 
Skipped atom 1065 because residue number 130  < previous residue 298 
Skipped atom 1066 because residue number 130  < previous residue 298 
Skipped atom 1067 because residue number 130  < previous residue 298 
Skipped atom 1068 because residue number 130  < previous residue 298 
Skipped atom 1069 because residue number 130  < previous residue 298 
Skipped atom 1070 because residue number 131  < previous residue 298 
Skipped atom 1071 because residue number 131  < previous residue 298 
Skipped atom 1072 because residue number 131  < previous residue 298 
Skipped atom 1073 because residue number 131  < previous residue 298 
Skipped atom 1074 because residue number 131  < previous residue 298 
Skipped atom 1075 because residue number 131  < previous residue 298 
Skipped atom 1076 because residue number 131  < previous residue 298 
Skipped atom 1077 because residue number 131  < previous residue 298 
Skipped atom 1078 because residue number 132  < previous residue 298 
Skipped atom 1079 because residue number 132  < previous residue 298 
Skipped atom 1080 because residue number 132  < previous residue 298 
Skipped atom 1081 because residue number 132  < previous residue 298 
Skipped atom 1082 because residue number 132  < previous residue 298 
Skipped atom 1083 because residue number 132  < previous residue 298 
Skipped atom 1084 because residue number 132  < previous residue 298 
Skipped atom 1085 because residue number 132  < previous residue 298 
Skipped atom 1086 because residue number 133  < previous residue 298 
Skipped atom 1087 because residue number 133  < previous residue 298 
Skipped atom 1088 because residue number 133  < previous residue 298 
Skipped atom 1089 because residue number 133  < previous residue 298 
Skipped atom 1090 because residue number 133  < previous residue 298 
Skipped atom 1091 because residue number 133  < previous residue 298 
Skipped atom 1092 because residue number 133  < previous residue 298 
Skipped atom 1093 because residue number 134  < previous residue 298 
Skipped atom 1094 because residue number 134  < previous residue 298 
Skipped atom 1095 because residue number 134  < previous residue 298 
Skipped atom 1096 because residue number 134  < previous residue 298 
Skipped atom 1097 because residue number 134  < previous residue 298 
Skipped atom 1098 because residue number 135  < previous residue 298 
Skipped atom 1099 because residue number 135  < previous residue 298 
Skipped atom 1100 because residue number 135  < previous residue 298 
Skipped atom 1101 because residue number 135  < previous residue 298 
Skipped atom 1102 because residue number 135  < previous residue 298 
Skipped atom 1103 because residue number 135  < previous residue 298 
Skipped atom 1104 because residue number 135  < previous residue 298 
Skipped atom 1105 because residue number 135  < previous residue 298 
Skipped atom 1106 because residue number 136  < previous residue 298 
Skipped atom 1107 because residue number 136  < previous residue 298 
Skipped atom 1108 because residue number 136  < previous residue 298 
Skipped atom 1109 because residue number 136  < previous residue 298 
Skipped atom 1110 because residue number 136  < previous residue 298 
Skipped atom 1111 because residue number 136  < previous residue 298 
Skipped atom 1112 because residue number 136  < previous residue 298 
Skipped atom 1113 because residue number 136  < previous residue 298 
Skipped atom 1114 because residue number 137  < previous residue 298 
Skipped atom 1115 because residue number 137  < previous residue 298 
Skipped atom 1116 because residue number 137  < previous residue 298 
Skipped atom 1117 because residue number 137  < previous residue 298 
Skipped atom 1118 because residue number 137  < previous residue 298 
Skipped atom 1119 because residue number 137  < previous residue 298 
Skipped atom 1120 because residue number 137  < previous residue 298 
Skipped atom 1121 because residue number 137  < previous residue 298 
Skipped atom 1122 because residue number 137  < previous residue 298 
Skipped atom 1123 because residue number 138  < previous residue 298 
Skipped atom 1124 because residue number 138  < previous residue 298 
Skipped atom 1125 because residue number 138  < previous residue 298 
Skipped atom 1126 because residue number 138  < previous residue 298 
Skipped atom 1127 because residue number 138  < previous residue 298 
Skipped atom 1128 because residue number 138  < previous residue 298 
Skipped atom 1129 because residue number 138  < previous residue 298 
Skipped atom 1130 because residue number 138  < previous residue 298 
Skipped atom 1131 because residue number 139  < previous residue 298 
Skipped atom 1132 because residue number 139  < previous residue 298 
Skipped atom 1133 because residue number 139  < previous residue 298 
Skipped atom 1134 because residue number 139  < previous residue 298 
Skipped atom 1135 because residue number 139  < previous residue 298 
Skipped atom 1136 because residue number 139  < previous residue 298 
Skipped atom 1137 because residue number 139  < previous residue 298 
Skipped atom 1138 because residue number 139  < previous residue 298 
Skipped atom 1139 because residue number 140  < previous residue 298 
Skipped atom 1140 because residue number 140  < previous residue 298 
Skipped atom 1141 because residue number 140  < previous residue 298 
Skipped atom 1142 because residue number 140  < previous residue 298 
Skipped atom 1143 because residue number 140  < previous residue 298 
Skipped atom 1144 because residue number 140  < previous residue 298 
Skipped atom 1145 because residue number 140  < previous residue 298 
Skipped atom 1146 because residue number 140  < previous residue 298 
Skipped atom 1147 because residue number 140  < previous residue 298 
Skipped atom 1148 because residue number 141  < previous residue 298 
Skipped atom 1149 because residue number 141  < previous residue 298 
Skipped atom 1150 because residue number 141  < previous residue 298 
Skipped atom 1151 because residue number 141  < previous residue 298 
Skipped atom 1152 because residue number 141  < previous residue 298 
Skipped atom 1153 because residue number 141  < previous residue 298 
Skipped atom 1154 because residue number 141  < previous residue 298 
Skipped atom 1155 because residue number 141  < previous residue 298 
Skipped atom 1156 because residue number 141  < previous residue 298 
Skipped atom 1157 because residue number 142  < previous residue 298 
Skipped atom 1158 because residue number 142  < previous residue 298 
Skipped atom 1159 because residue number 142  < previous residue 298 
Skipped atom 1160 because residue number 142  < previous residue 298 
Skipped atom 1161 because residue number 142  < previous residue 298 
Skipped atom 1162 because residue number 142  < previous residue 298 
Skipped atom 1163 because residue number 142  < previous residue 298 
Skipped atom 1164 because residue number 142  < previous residue 298 
Skipped atom 1165 because residue number 143  < previous residue 298 
Skipped atom 1166 because residue number 143  < previous residue 298 
Skipped atom 1167 because residue number 143  < previous residue 298 
Skipped atom 1168 because residue number 143  < previous residue 298 
Skipped atom 1169 because residue number 144  < previous residue 298 
Skipped atom 1170 because residue number 144  < previous residue 298 
Skipped atom 1171 because residue number 144  < previous residue 298 
Skipped atom 1172 because residue number 144  < previous residue 298 
Skipped atom 1173 because residue number 145  < previous residue 298 
Skipped atom 1174 because residue number 145  < previous residue 298 
Skipped atom 1175 because residue number 145  < previous residue 298 
Skipped atom 1176 because residue number 145  < previous residue 298 
Skipped atom 1177 because residue number 145  < previous residue 298 
Skipped atom 1178 because residue number 145  < previous residue 298 
Skipped atom 1179 because residue number 145  < previous residue 298 
Skipped atom 1180 because residue number 145  < previous residue 298 
Skipped atom 1181 because residue number 146  < previous residue 298 
Skipped atom 1182 because residue number 146  < previous residue 298 
Skipped atom 1183 because residue number 146  < previous residue 298 
Skipped atom 1184 because residue number 146  < previous residue 298 
Skipped atom 1185 because residue number 146  < previous residue 298 
Skipped atom 1186 because residue number 146  < previous residue 298 
Skipped atom 1187 because residue number 146  < previous residue 298 
Skipped atom 1188 because residue number 146  < previous residue 298 
Skipped atom 1189 because residue number 146  < previous residue 298 
Skipped atom 1190 because residue number 147  < previous residue 298 
Skipped atom 1191 because residue number 147  < previous residue 298 
Skipped atom 1192 because residue number 147  < previous residue 298 
Skipped atom 1193 because residue number 147  < previous residue 298 
Skipped atom 1194 because residue number 147  < previous residue 298 
Skipped atom 1195 because residue number 147  < previous residue 298 
Skipped atom 1196 because residue number 147  < previous residue 298 
Skipped atom 1197 because residue number 147  < previous residue 298 
Skipped atom 1198 because residue number 147  < previous residue 298 
Skipped atom 1199 because residue number 148  < previous residue 298 
Skipped atom 1200 because residue number 148  < previous residue 298 
Skipped atom 1201 because residue number 148  < previous residue 298 
Skipped atom 1202 because residue number 148  < previous residue 298 
Skipped atom 1203 because residue number 148  < previous residue 298 
Skipped atom 1204 because residue number 148  < previous residue 298 
Skipped atom 1205 because residue number 148  < previous residue 298 
Skipped atom 1206 because residue number 149  < previous residue 298 
Skipped atom 1207 because residue number 149  < previous residue 298 
Skipped atom 1208 because residue number 149  < previous residue 298 
Skipped atom 1209 because residue number 149  < previous residue 298 
Skipped atom 1210 because residue number 149  < previous residue 298 
Skipped atom 1211 because residue number 149  < previous residue 298 
Skipped atom 1212 because residue number 149  < previous residue 298 
Skipped atom 1213 because residue number 149  < previous residue 298 
Skipped atom 1214 because residue number 149  < previous residue 298 
Skipped atom 1215 because residue number 150  < previous residue 298 
Skipped atom 1216 because residue number 150  < previous residue 298 
Skipped atom 1217 because residue number 150  < previous residue 298 
Skipped atom 1218 because residue number 150  < previous residue 298 
Skipped atom 1219 because residue number 150  < previous residue 298 
Skipped atom 1220 because residue number 150  < previous residue 298 
Skipped atom 1221 because residue number 150  < previous residue 298 
Skipped atom 1222 because residue number 150  < previous residue 298 
Skipped atom 1223 because residue number 150  < previous residue 298 
Skipped atom 1224 because residue number 151  < previous residue 298 
Skipped atom 1225 because residue number 151  < previous residue 298 
Skipped atom 1226 because residue number 151  < previous residue 298 
Skipped atom 1227 because residue number 151  < previous residue 298 
Skipped atom 1228 because residue number 151  < previous residue 298 
Skipped atom 1229 because residue number 151  < previous residue 298 
Skipped atom 1230 because residue number 151  < previous residue 298 
Skipped atom 1231 because residue number 151  < previous residue 298 
Skipped atom 1232 because residue number 151  < previous residue 298 
Skipped atom 1233 because residue number 151  < previous residue 298 
Skipped atom 1234 because residue number 151  < previous residue 298 
Skipped atom 1235 because residue number 152  < previous residue 298 
Skipped atom 1236 because residue number 152  < previous residue 298 
Skipped atom 1237 because residue number 152  < previous residue 298 
Skipped atom 1238 because residue number 152  < previous residue 298 
Skipped atom 1239 because residue number 152  < previous residue 298 
Skipped atom 1240 because residue number 152  < previous residue 298 
Skipped atom 1241 because residue number 152  < previous residue 298 
Skipped atom 1242 because residue number 152  < previous residue 298 
Skipped atom 1243 because residue number 153  < previous residue 298 
Skipped atom 1244 because residue number 153  < previous residue 298 
Skipped atom 1245 because residue number 153  < previous residue 298 
Skipped atom 1246 because residue number 153  < previous residue 298 
Skipped atom 1247 because residue number 153  < previous residue 298 
Skipped atom 1248 because residue number 153  < previous residue 298 
Skipped atom 1249 because residue number 153  < previous residue 298 
Skipped atom 1250 because residue number 153  < previous residue 298 
Skipped atom 1251 because residue number 153  < previous residue 298 
Skipped atom 1252 because residue number 154  < previous residue 298 
Skipped atom 1253 because residue number 154  < previous residue 298 
Skipped atom 1254 because residue number 154  < previous residue 298 
Skipped atom 1255 because residue number 154  < previous residue 298 
Skipped atom 1256 because residue number 154  < previous residue 298 
Skipped atom 1257 because residue number 154  < previous residue 298 
Skipped atom 1258 because residue number 154  < previous residue 298 
Skipped atom 1259 because residue number 154  < previous residue 298 
Skipped atom 1260 because residue number 154  < previous residue 298 
Skipped atom 1261 because residue number 155  < previous residue 298 
Skipped atom 1262 because residue number 155  < previous residue 298 
Skipped atom 1263 because residue number 155  < previous residue 298 
Skipped atom 1264 because residue number 155  < previous residue 298 
Skipped atom 1265 because residue number 155  < previous residue 298 
Skipped atom 1266 because residue number 155  < previous residue 298 
Skipped atom 1267 because residue number 155  < previous residue 298 
Skipped atom 1268 because residue number 155  < previous residue 298 
Skipped atom 1269 because residue number 156  < previous residue 298 
Skipped atom 1270 because residue number 156  < previous residue 298 
Skipped atom 1271 because residue number 156  < previous residue 298 
Skipped atom 1272 because residue number 156  < previous residue 298 
Skipped atom 1273 because residue number 157  < previous residue 298 
Skipped atom 1274 because residue number 157  < previous residue 298 
Skipped atom 1275 because residue number 157  < previous residue 298 
Skipped atom 1276 because residue number 157  < previous residue 298 
Skipped atom 1277 because residue number 157  < previous residue 298 
Skipped atom 1278 because residue number 157  < previous residue 298 
Skipped atom 1279 because residue number 157  < previous residue 298 
Skipped atom 1280 because residue number 157  < previous residue 298 
Skipped atom 1281 because residue number 158  < previous residue 298 
Skipped atom 1282 because residue number 158  < previous residue 298 
Skipped atom 1283 because residue number 158  < previous residue 298 
Skipped atom 1284 because residue number 158  < previous residue 298 
Skipped atom 1285 because residue number 158  < previous residue 298 
Skipped atom 1286 because residue number 158  < previous residue 298 
Skipped atom 1287 because residue number 158  < previous residue 298 
Skipped atom 1288 because residue number 158  < previous residue 298 
Skipped atom 1289 because residue number 158  < previous residue 298 
Skipped atom 1290 because residue number 159  < previous residue 298 
Skipped atom 1291 because residue number 159  < previous residue 298 
Skipped atom 1292 because residue number 159  < previous residue 298 
Skipped atom 1293 because residue number 159  < previous residue 298 
Skipped atom 1294 because residue number 159  < previous residue 298 
Skipped atom 1295 because residue number 159  < previous residue 298 
Skipped atom 1296 because residue number 159  < previous residue 298 
Skipped atom 1297 because residue number 160  < previous residue 298 
Skipped atom 1298 because residue number 160  < previous residue 298 
Skipped atom 1299 because residue number 160  < previous residue 298 
Skipped atom 1300 because residue number 160  < previous residue 298 
Skipped atom 1301 because residue number 160  < previous residue 298 
Skipped atom 1302 because residue number 160  < previous residue 298 
Skipped atom 1303 because residue number 160  < previous residue 298 
Skipped atom 1304 because residue number 161  < previous residue 298 
Skipped atom 1305 because residue number 161  < previous residue 298 
Skipped atom 1306 because residue number 161  < previous residue 298 
Skipped atom 1307 because residue number 161  < previous residue 298 
Skipped atom 1308 because residue number 161  < previous residue 298 
Skipped atom 1309 because residue number 161  < previous residue 298 
Skipped atom 1310 because residue number 161  < previous residue 298 
Skipped atom 1311 because residue number 161  < previous residue 298 
Skipped atom 1312 because residue number 162  < previous residue 298 
Skipped atom 1313 because residue number 162  < previous residue 298 
Skipped atom 1314 because residue number 162  < previous residue 298 
Skipped atom 1315 because residue number 162  < previous residue 298 
Skipped atom 1316 because residue number 162  < previous residue 298 
Skipped atom 1317 because residue number 162  < previous residue 298 
Skipped atom 1318 because residue number 162  < previous residue 298 
Skipped atom 1319 because residue number 163  < previous residue 298 
Skipped atom 1320 because residue number 163  < previous residue 298 
Skipped atom 1321 because residue number 163  < previous residue 298 
Skipped atom 1322 because residue number 163  < previous residue 298 
Skipped atom 1323 because residue number 163  < previous residue 298 
Skipped atom 1324 because residue number 163  < previous residue 298 
Skipped atom 1325 because residue number 163  < previous residue 298 
Skipped atom 1326 because residue number 164  < previous residue 298 
Skipped atom 1327 because residue number 164  < previous residue 298 
Skipped atom 1328 because residue number 164  < previous residue 298 
Skipped atom 1329 because residue number 164  < previous residue 298 
Skipped atom 1330 because residue number 164  < previous residue 298 
Skipped atom 1331 because residue number 164  < previous residue 298 
Skipped atom 1332 because residue number 164  < previous residue 298 
Skipped atom 1333 because residue number 164  < previous residue 298 
Skipped atom 1334 because residue number 164  < previous residue 298 
Skipped atom 1335 because residue number 164  < previous residue 298 
Skipped atom 1336 because residue number 164  < previous residue 298 
Skipped atom 1337 because residue number 165  < previous residue 298 
Skipped atom 1338 because residue number 165  < previous residue 298 
Skipped atom 1339 because residue number 165  < previous residue 298 
Skipped atom 1340 because residue number 165  < previous residue 298 
Skipped atom 1341 because residue number 165  < previous residue 298 
Skipped atom 1342 because residue number 165  < previous residue 298 
Skipped atom 1343 because residue number 165  < previous residue 298 
Skipped atom 1344 because residue number 165  < previous residue 298 
Skipped atom 1345 because residue number 165  < previous residue 298 
Skipped atom 1346 because residue number 165  < previous residue 298 
Skipped atom 1347 because residue number 165  < previous residue 298 
Skipped atom 1348 because residue number 165  < previous residue 298 
Skipped atom 1349 because residue number 166  < previous residue 298 
Skipped atom 1350 because residue number 166  < previous residue 298 
Skipped atom 1351 because residue number 166  < previous residue 298 
Skipped atom 1352 because residue number 166  < previous residue 298 
Skipped atom 1353 because residue number 166  < previous residue 298 
Skipped atom 1354 because residue number 166  < previous residue 298 
Skipped atom 1355 because residue number 166  < previous residue 298 
Skipped atom 1356 because residue number 166  < previous residue 298 
Skipped atom 1357 because residue number 166  < previous residue 298 
Skipped atom 1358 because residue number 167  < previous residue 298 
Skipped atom 1359 because residue number 167  < previous residue 298 
Skipped atom 1360 because residue number 167  < previous residue 298 
Skipped atom 1361 because residue number 167  < previous residue 298 
Skipped atom 1362 because residue number 167  < previous residue 298 
Skipped atom 1363 because residue number 167  < previous residue 298 
Skipped atom 1364 because residue number 167  < previous residue 298 
Skipped atom 1365 because residue number 167  < previous residue 298 
Skipped atom 1366 because residue number 168  < previous residue 298 
Skipped atom 1367 because residue number 168  < previous residue 298 
Skipped atom 1368 because residue number 168  < previous residue 298 
Skipped atom 1369 because residue number 168  < previous residue 298 
Skipped atom 1370 because residue number 168  < previous residue 298 
Skipped atom 1371 because residue number 168  < previous residue 298 
Skipped atom 1372 because residue number 168  < previous residue 298 
Skipped atom 1373 because residue number 168  < previous residue 298 
Skipped atom 1374 because residue number 168  < previous residue 298 
Skipped atom 1375 because residue number 169  < previous residue 298 
Skipped atom 1376 because residue number 169  < previous residue 298 
Skipped atom 1377 because residue number 169  < previous residue 298 
Skipped atom 1378 because residue number 169  < previous residue 298 
Skipped atom 1379 because residue number 169  < previous residue 298 
Skipped atom 1380 because residue number 169  < previous residue 298 
Skipped atom 1381 because residue number 169  < previous residue 298 
Skipped atom 1382 because residue number 169  < previous residue 298 
Skipped atom 1383 because residue number 170  < previous residue 298 
Skipped atom 1384 because residue number 170  < previous residue 298 
Skipped atom 1385 because residue number 170  < previous residue 298 
Skipped atom 1386 because residue number 170  < previous residue 298 
Skipped atom 1387 because residue number 170  < previous residue 298 
Skipped atom 1388 because residue number 170  < previous residue 298 
Skipped atom 1389 because residue number 170  < previous residue 298 
Skipped atom 1390 because residue number 170  < previous residue 298 
Skipped atom 1391 because residue number 171  < previous residue 298 
Skipped atom 1392 because residue number 171  < previous residue 298 
Skipped atom 1393 because residue number 171  < previous residue 298 
Skipped atom 1394 because residue number 171  < previous residue 298 
Skipped atom 1395 because residue number 171  < previous residue 298 
Skipped atom 1396 because residue number 171  < previous residue 298 
Skipped atom 1397 because residue number 171  < previous residue 298 
Skipped atom 1398 because residue number 171  < previous residue 298 
Skipped atom 1399 because residue number 171  < previous residue 298 
Skipped atom 1400 because residue number 171  < previous residue 298 
Skipped atom 1401 because residue number 171  < previous residue 298 
Skipped atom 1402 because residue number 171  < previous residue 298 
Skipped atom 1403 because residue number 172  < previous residue 298 
Skipped atom 1404 because residue number 172  < previous residue 298 
Skipped atom 1405 because residue number 172  < previous residue 298 
Skipped atom 1406 because residue number 172  < previous residue 298 
Skipped atom 1407 because residue number 172  < previous residue 298 
Skipped atom 1408 because residue number 172  < previous residue 298 
Skipped atom 1409 because residue number 172  < previous residue 298 
Skipped atom 1410 because residue number 172  < previous residue 298 
Skipped atom 1411 because residue number 172  < previous residue 298 
Skipped atom 1412 because residue number 172  < previous residue 298 
Skipped atom 1413 because residue number 172  < previous residue 298 
Skipped atom 1414 because residue number 172  < previous residue 298 
Skipped atom 1415 because residue number 173  < previous residue 298 
Skipped atom 1416 because residue number 173  < previous residue 298 
Skipped atom 1417 because residue number 173  < previous residue 298 
Skipped atom 1418 because residue number 173  < previous residue 298 
Skipped atom 1419 because residue number 173  < previous residue 298 
Skipped atom 1420 because residue number 173  < previous residue 298 
Skipped atom 1421 because residue number 174  < previous residue 298 
Skipped atom 1422 because residue number 174  < previous residue 298 
Skipped atom 1423 because residue number 174  < previous residue 298 
Skipped atom 1424 because residue number 174  < previous residue 298 
Skipped atom 1425 because residue number 174  < previous residue 298 
Skipped atom 1426 because residue number 174  < previous residue 298 
Skipped atom 1427 because residue number 174  < previous residue 298 
Skipped atom 1428 because residue number 175  < previous residue 298 
Skipped atom 1429 because residue number 175  < previous residue 298 
Skipped atom 1430 because residue number 175  < previous residue 298 
Skipped atom 1431 because residue number 175  < previous residue 298 
Skipped atom 1432 because residue number 175  < previous residue 298 
Skipped atom 1433 because residue number 175  < previous residue 298 
Skipped atom 1434 because residue number 175  < previous residue 298 
Skipped atom 1435 because residue number 175  < previous residue 298 
Skipped atom 1436 because residue number 175  < previous residue 298 
Skipped atom 1437 because residue number 176  < previous residue 298 
Skipped atom 1438 because residue number 176  < previous residue 298 
Skipped atom 1439 because residue number 176  < previous residue 298 
Skipped atom 1440 because residue number 176  < previous residue 298 
Skipped atom 1441 because residue number 176  < previous residue 298 
Skipped atom 1442 because residue number 176  < previous residue 298 
Skipped atom 1443 because residue number 177  < previous residue 298 
Skipped atom 1444 because residue number 177  < previous residue 298 
Skipped atom 1445 because residue number 177  < previous residue 298 
Skipped atom 1446 because residue number 177  < previous residue 298 
Skipped atom 1447 because residue number 177  < previous residue 298 
Skipped atom 1448 because residue number 177  < previous residue 298 
Skipped atom 1449 because residue number 177  < previous residue 298 
Skipped atom 1450 because residue number 177  < previous residue 298 
Skipped atom 1451 because residue number 177  < previous residue 298 
Skipped atom 1452 because residue number 178  < previous residue 298 
Skipped atom 1453 because residue number 178  < previous residue 298 
Skipped atom 1454 because residue number 178  < previous residue 298 
Skipped atom 1455 because residue number 178  < previous residue 298 
Skipped atom 1456 because residue number 178  < previous residue 298 
Skipped atom 1457 because residue number 178  < previous residue 298 
Skipped atom 1458 because residue number 178  < previous residue 298 
Skipped atom 1459 because residue number 178  < previous residue 298 
Skipped atom 1460 because residue number 178  < previous residue 298 
Skipped atom 1461 because residue number 179  < previous residue 298 
Skipped atom 1462 because residue number 179  < previous residue 298 
Skipped atom 1463 because residue number 179  < previous residue 298 
Skipped atom 1464 because residue number 179  < previous residue 298 
Skipped atom 1465 because residue number 179  < previous residue 298 
Skipped atom 1466 because residue number 179  < previous residue 298 
Skipped atom 1467 because residue number 179  < previous residue 298 
Skipped atom 1468 because residue number 179  < previous residue 298 
Skipped atom 1469 because residue number 180  < previous residue 298 
Skipped atom 1470 because residue number 180  < previous residue 298 
Skipped atom 1471 because residue number 180  < previous residue 298 
Skipped atom 1472 because residue number 180  < previous residue 298 
Skipped atom 1473 because residue number 180  < previous residue 298 
Skipped atom 1474 because residue number 180  < previous residue 298 
Skipped atom 1475 because residue number 180  < previous residue 298 
Skipped atom 1476 because residue number 181  < previous residue 298 
Skipped atom 1477 because residue number 181  < previous residue 298 
Skipped atom 1478 because residue number 181  < previous residue 298 
Skipped atom 1479 because residue number 181  < previous residue 298 
Skipped atom 1480 because residue number 181  < previous residue 298 
Skipped atom 1481 because residue number 181  < previous residue 298 
Skipped atom 1482 because residue number 182  < previous residue 298 
Skipped atom 1483 because residue number 182  < previous residue 298 
Skipped atom 1484 because residue number 182  < previous residue 298 
Skipped atom 1485 because residue number 182  < previous residue 298 
Skipped atom 1486 because residue number 182  < previous residue 298 
Skipped atom 1487 because residue number 182  < previous residue 298 
Skipped atom 1488 because residue number 182  < previous residue 298 
Skipped atom 1489 because residue number 183  < previous residue 298 
Skipped atom 1490 because residue number 183  < previous residue 298 
Skipped atom 1491 because residue number 183  < previous residue 298 
Skipped atom 1492 because residue number 183  < previous residue 298 
Skipped atom 1493 because residue number 183  < previous residue 298 
Skipped atom 1494 because residue number 183  < previous residue 298 
Skipped atom 1495 because residue number 183  < previous residue 298 
Skipped atom 1496 because residue number 184  < previous residue 298 
Skipped atom 1497 because residue number 184  < previous residue 298 
Skipped atom 1498 because residue number 184  < previous residue 298 
Skipped atom 1499 because residue number 184  < previous residue 298 
Skipped atom 1500 because residue number 184  < previous residue 298 
Skipped atom 1501 because residue number 185  < previous residue 298 
Skipped atom 1502 because residue number 185  < previous residue 298 
Skipped atom 1503 because residue number 185  < previous residue 298 
Skipped atom 1504 because residue number 185  < previous residue 298 
Skipped atom 1505 because residue number 185  < previous residue 298 
Skipped atom 1506 because residue number 186  < previous residue 298 
Skipped atom 1507 because residue number 186  < previous residue 298 
Skipped atom 1508 because residue number 186  < previous residue 298 
Skipped atom 1509 because residue number 186  < previous residue 298 
Skipped atom 1510 because residue number 186  < previous residue 298 
Skipped atom 1511 because residue number 186  < previous residue 298 
Skipped atom 1512 because residue number 186  < previous residue 298 
Skipped atom 1513 because residue number 186  < previous residue 298 
Skipped atom 1514 because residue number 186  < previous residue 298 
Skipped atom 1515 because residue number 186  < previous residue 298 
Skipped atom 1516 because residue number 186  < previous residue 298 
Skipped atom 1517 because residue number 187  < previous residue 298 
Skipped atom 1518 because residue number 187  < previous residue 298 
Skipped atom 1519 because residue number 187  < previous residue 298 
Skipped atom 1520 because residue number 187  < previous residue 298 
Skipped atom 1521 because residue number 188  < previous residue 298 
Skipped atom 1522 because residue number 188  < previous residue 298 
Skipped atom 1523 because residue number 188  < previous residue 298 
Skipped atom 1524 because residue number 188  < previous residue 298 
Skipped atom 1525 because residue number 188  < previous residue 298 
Skipped atom 1526 because residue number 188  < previous residue 298 
Skipped atom 1527 because residue number 188  < previous residue 298 
Skipped atom 1528 because residue number 188  < previous residue 298 
Skipped atom 1529 because residue number 188  < previous residue 298 
Skipped atom 1530 because residue number 189  < previous residue 298 
Skipped atom 1531 because residue number 189  < previous residue 298 
Skipped atom 1532 because residue number 189  < previous residue 298 
Skipped atom 1533 because residue number 189  < previous residue 298 
Skipped atom 1534 because residue number 189  < previous residue 298 
Skipped atom 1535 because residue number 189  < previous residue 298 
Skipped atom 1536 because residue number 189  < previous residue 298 
Skipped atom 1537 because residue number 190  < previous residue 298 
Skipped atom 1538 because residue number 190  < previous residue 298 
Skipped atom 1539 because residue number 190  < previous residue 298 
Skipped atom 1540 because residue number 190  < previous residue 298 
Skipped atom 1541 because residue number 190  < previous residue 298 
Skipped atom 1542 because residue number 190  < previous residue 298 
Skipped atom 1543 because residue number 190  < previous residue 298 
Skipped atom 1544 because residue number 190  < previous residue 298 
Skipped atom 1545 because residue number 191  < previous residue 298 
Skipped atom 1546 because residue number 191  < previous residue 298 
Skipped atom 1547 because residue number 191  < previous residue 298 
Skipped atom 1548 because residue number 191  < previous residue 298 
Skipped atom 1549 because residue number 191  < previous residue 298 
Skipped atom 1550 because residue number 191  < previous residue 298 
Skipped atom 1551 because residue number 191  < previous residue 298 
Skipped atom 1552 because residue number 191  < previous residue 298 
Skipped atom 1553 because residue number 192  < previous residue 298 
Skipped atom 1554 because residue number 192  < previous residue 298 
Skipped atom 1555 because residue number 192  < previous residue 298 
Skipped atom 1556 because residue number 192  < previous residue 298 
Skipped atom 1557 because residue number 192  < previous residue 298 
Skipped atom 1558 because residue number 192  < previous residue 298 
Skipped atom 1559 because residue number 192  < previous residue 298 
Skipped atom 1560 because residue number 192  < previous residue 298 
Skipped atom 1561 because residue number 192  < previous residue 298 
Skipped atom 1562 because residue number 193  < previous residue 298 
Skipped atom 1563 because residue number 193  < previous residue 298 
Skipped atom 1564 because residue number 193  < previous residue 298 
Skipped atom 1565 because residue number 193  < previous residue 298 
Skipped atom 1566 because residue number 193  < previous residue 298 
Skipped atom 1567 because residue number 193  < previous residue 298 
Skipped atom 1568 because residue number 193  < previous residue 298 
Skipped atom 1569 because residue number 193  < previous residue 298 
Skipped atom 1570 because residue number 194  < previous residue 298 
Skipped atom 1571 because residue number 194  < previous residue 298 
Skipped atom 1572 because residue number 194  < previous residue 298 
Skipped atom 1573 because residue number 194  < previous residue 298 
Skipped atom 1574 because residue number 194  < previous residue 298 
Skipped atom 1575 because residue number 194  < previous residue 298 
Skipped atom 1576 because residue number 194  < previous residue 298 
Skipped atom 1577 because residue number 194  < previous residue 298 
Skipped atom 1578 because residue number 195  < previous residue 298 
Skipped atom 1579 because residue number 195  < previous residue 298 
Skipped atom 1580 because residue number 195  < previous residue 298 
Skipped atom 1581 because residue number 195  < previous residue 298 
Skipped atom 1582 because residue number 195  < previous residue 298 
Skipped atom 1583 because residue number 196  < previous residue 298 
Skipped atom 1584 because residue number 196  < previous residue 298 
Skipped atom 1585 because residue number 196  < previous residue 298 
Skipped atom 1586 because residue number 196  < previous residue 298 
Skipped atom 1587 because residue number 196  < previous residue 298 
Skipped atom 1588 because residue number 196  < previous residue 298 
Skipped atom 1589 because residue number 196  < previous residue 298 
Skipped atom 1590 because residue number 196  < previous residue 298 
Skipped atom 1591 because residue number 197  < previous residue 298 
Skipped atom 1592 because residue number 197  < previous residue 298 
Skipped atom 1593 because residue number 197  < previous residue 298 
Skipped atom 1594 because residue number 197  < previous residue 298 
Skipped atom 1595 because residue number 198  < previous residue 298 
Skipped atom 1596 because residue number 198  < previous residue 298 
Skipped atom 1597 because residue number 198  < previous residue 298 
Skipped atom 1598 because residue number 198  < previous residue 298 
Skipped atom 1599 because residue number 198  < previous residue 298 
Skipped atom 1600 because residue number 198  < previous residue 298 
Skipped atom 1601 because residue number 198  < previous residue 298 
Skipped atom 1602 because residue number 198  < previous residue 298 
Skipped atom 1603 because residue number 198  < previous residue 298 
Skipped atom 1604 because residue number 199  < previous residue 298 
Skipped atom 1605 because residue number 199  < previous residue 298 
Skipped atom 1606 because residue number 199  < previous residue 298 
Skipped atom 1607 because residue number 199  < previous residue 298 
Skipped atom 1608 because residue number 199  < previous residue 298 
Skipped atom 1609 because residue number 199  < previous residue 298 
Skipped atom 1610 because residue number 199  < previous residue 298 
Skipped atom 1611 because residue number 199  < previous residue 298 
Skipped atom 1612 because residue number 200  < previous residue 298 
Skipped atom 1613 because residue number 200  < previous residue 298 
Skipped atom 1614 because residue number 200  < previous residue 298 
Skipped atom 1615 because residue number 200  < previous residue 298 
Skipped atom 1616 because residue number 200  < previous residue 298 
Skipped atom 1617 because residue number 200  < previous residue 298 
Skipped atom 1618 because residue number 201  < previous residue 298 
Skipped atom 1619 because residue number 201  < previous residue 298 
Skipped atom 1620 because residue number 201  < previous residue 298 
Skipped atom 1621 because residue number 201  < previous residue 298 
Skipped atom 1622 because residue number 201  < previous residue 298 
Skipped atom 1623 because residue number 201  < previous residue 298 
Skipped atom 1624 because residue number 201  < previous residue 298 
Skipped atom 1625 because residue number 201  < previous residue 298 
Skipped atom 1626 because residue number 201  < previous residue 298 
Skipped atom 1627 because residue number 202  < previous residue 298 
Skipped atom 1628 because residue number 202  < previous residue 298 
Skipped atom 1629 because residue number 202  < previous residue 298 
Skipped atom 1630 because residue number 202  < previous residue 298 
Skipped atom 1631 because residue number 202  < previous residue 298 
Skipped atom 1632 because residue number 202  < previous residue 298 
Skipped atom 1633 because residue number 202  < previous residue 298 
Skipped atom 1634 because residue number 202  < previous residue 298 
Skipped atom 1635 because residue number 202  < previous residue 298 
Skipped atom 1636 because residue number 203  < previous residue 298 
Skipped atom 1637 because residue number 203  < previous residue 298 
Skipped atom 1638 because residue number 203  < previous residue 298 
Skipped atom 1639 because residue number 203  < previous residue 298 
Skipped atom 1640 because residue number 203  < previous residue 298 
Skipped atom 1641 because residue number 203  < previous residue 298 
Skipped atom 1642 because residue number 203  < previous residue 298 
Skipped atom 1643 because residue number 203  < previous residue 298 
Skipped atom 1644 because residue number 204  < previous residue 298 
Skipped atom 1645 because residue number 204  < previous residue 298 
Skipped atom 1646 because residue number 204  < previous residue 298 
Skipped atom 1647 because residue number 204  < previous residue 298 
Skipped atom 1648 because residue number 204  < previous residue 298 
Skipped atom 1649 because residue number 204  < previous residue 298 
Skipped atom 1650 because residue number 204  < previous residue 298 
Skipped atom 1651 because residue number 204  < previous residue 298 
Skipped atom 1652 because residue number 204  < previous residue 298 
Skipped atom 1653 because residue number 205  < previous residue 298 
Skipped atom 1654 because residue number 205  < previous residue 298 
Skipped atom 1655 because residue number 205  < previous residue 298 
Skipped atom 1656 because residue number 205  < previous residue 298 
Skipped atom 1657 because residue number 205  < previous residue 298 
Skipped atom 1658 because residue number 205  < previous residue 298 
Skipped atom 1659 because residue number 205  < previous residue 298 
Skipped atom 1660 because residue number 205  < previous residue 298 
Skipped atom 1661 because residue number 205  < previous residue 298 
Skipped atom 1662 because residue number 206  < previous residue 298 
Skipped atom 1663 because residue number 206  < previous residue 298 
Skipped atom 1664 because residue number 206  < previous residue 298 
Skipped atom 1665 because residue number 206  < previous residue 298 
Skipped atom 1666 because residue number 206  < previous residue 298 
Skipped atom 1667 because residue number 206  < previous residue 298 
Skipped atom 1668 because residue number 206  < previous residue 298 
Skipped atom 1669 because residue number 206  < previous residue 298 
Skipped atom 1670 because residue number 206  < previous residue 298 
Skipped atom 1671 because residue number 206  < previous residue 298 
Skipped atom 1672 because residue number 206  < previous residue 298 
Skipped atom 1673 because residue number 207  < previous residue 298 
Skipped atom 1674 because residue number 207  < previous residue 298 
Skipped atom 1675 because residue number 207  < previous residue 298 
Skipped atom 1676 because residue number 207  < previous residue 298 
Skipped atom 1677 because residue number 207  < previous residue 298 
Skipped atom 1678 because residue number 207  < previous residue 298 
Skipped atom 1679 because residue number 207  < previous residue 298 
Skipped atom 1680 because residue number 207  < previous residue 298 
Skipped atom 1681 because residue number 208  < previous residue 298 
Skipped atom 1682 because residue number 208  < previous residue 298 
Skipped atom 1683 because residue number 208  < previous residue 298 
Skipped atom 1684 because residue number 208  < previous residue 298 
Skipped atom 1685 because residue number 208  < previous residue 298 
Skipped atom 1686 because residue number 208  < previous residue 298 
Skipped atom 1687 because residue number 208  < previous residue 298 
Skipped atom 1688 because residue number 208  < previous residue 298 
Skipped atom 1689 because residue number 209  < previous residue 298 
Skipped atom 1690 because residue number 209  < previous residue 298 
Skipped atom 1691 because residue number 209  < previous residue 298 
Skipped atom 1692 because residue number 209  < previous residue 298 
Skipped atom 1693 because residue number 209  < previous residue 298 
Skipped atom 1694 because residue number 209  < previous residue 298 
Skipped atom 1695 because residue number 209  < previous residue 298 
Skipped atom 1696 because residue number 209  < previous residue 298 
Skipped atom 1697 because residue number 210  < previous residue 298 
Skipped atom 1698 because residue number 210  < previous residue 298 
Skipped atom 1699 because residue number 210  < previous residue 298 
Skipped atom 1700 because residue number 210  < previous residue 298 
Skipped atom 1701 because residue number 210  < previous residue 298 
Skipped atom 1702 because residue number 210  < previous residue 298 
Skipped atom 1703 because residue number 210  < previous residue 298 
Skipped atom 1704 because residue number 210  < previous residue 298 
Skipped atom 1705 because residue number 211  < previous residue 298 
Skipped atom 1706 because residue number 211  < previous residue 298 
Skipped atom 1707 because residue number 211  < previous residue 298 
Skipped atom 1708 because residue number 211  < previous residue 298 
Skipped atom 1709 because residue number 211  < previous residue 298 
Skipped atom 1710 because residue number 211  < previous residue 298 
Skipped atom 1711 because residue number 211  < previous residue 298 
Skipped atom 1712 because residue number 211  < previous residue 298 
Skipped atom 1713 because residue number 212  < previous residue 298 
Skipped atom 1714 because residue number 212  < previous residue 298 
Skipped atom 1715 because residue number 212  < previous residue 298 
Skipped atom 1716 because residue number 212  < previous residue 298 
Skipped atom 1717 because residue number 212  < previous residue 298 
Skipped atom 1718 because residue number 212  < previous residue 298 
Skipped atom 1719 because residue number 212  < previous residue 298 
Skipped atom 1720 because residue number 212  < previous residue 298 
Skipped atom 1721 because residue number 213  < previous residue 298 
Skipped atom 1722 because residue number 213  < previous residue 298 
Skipped atom 1723 because residue number 213  < previous residue 298 
Skipped atom 1724 because residue number 213  < previous residue 298 
Skipped atom 1725 because residue number 213  < previous residue 298 
Skipped atom 1726 because residue number 213  < previous residue 298 
Skipped atom 1727 because residue number 213  < previous residue 298 
Skipped atom 1728 because residue number 213  < previous residue 298 
Skipped atom 1729 because residue number 214  < previous residue 298 
Skipped atom 1730 because residue number 214  < previous residue 298 
Skipped atom 1731 because residue number 214  < previous residue 298 
Skipped atom 1732 because residue number 214  < previous residue 298 
Skipped atom 1733 because residue number 214  < previous residue 298 
Skipped atom 1734 because residue number 214  < previous residue 298 
Skipped atom 1735 because residue number 214  < previous residue 298 
Skipped atom 1736 because residue number 214  < previous residue 298 
Skipped atom 1737 because residue number 215  < previous residue 298 
Skipped atom 1738 because residue number 215  < previous residue 298 
Skipped atom 1739 because residue number 215  < previous residue 298 
Skipped atom 1740 because residue number 215  < previous residue 298 
Skipped atom 1741 because residue number 215  < previous residue 298 
Skipped atom 1742 because residue number 215  < previous residue 298 
Skipped atom 1743 because residue number 215  < previous residue 298 
Skipped atom 1744 because residue number 215  < previous residue 298 
Skipped atom 1745 because residue number 215  < previous residue 298 
Skipped atom 1746 because residue number 216  < previous residue 298 
Skipped atom 1747 because residue number 216  < previous residue 298 
Skipped atom 1748 because residue number 216  < previous residue 298 
Skipped atom 1749 because residue number 216  < previous residue 298 
Skipped atom 1750 because residue number 216  < previous residue 298 
Skipped atom 1751 because residue number 216  < previous residue 298 
Skipped atom 1752 because residue number 217  < previous residue 298 
Skipped atom 1753 because residue number 217  < previous residue 298 
Skipped atom 1754 because residue number 217  < previous residue 298 
Skipped atom 1755 because residue number 217  < previous residue 298 
Skipped atom 1756 because residue number 218  < previous residue 298 
Skipped atom 1757 because residue number 218  < previous residue 298 
Skipped atom 1758 because residue number 218  < previous residue 298 
Skipped atom 1759 because residue number 218  < previous residue 298 
Skipped atom 1760 because residue number 218  < previous residue 298 
Skipped atom 1761 because residue number 218  < previous residue 298 
Skipped atom 1762 because residue number 218  < previous residue 298 
Skipped atom 1763 because residue number 218  < previous residue 298 
Skipped atom 1764 because residue number 219  < previous residue 298 
Skipped atom 1765 because residue number 219  < previous residue 298 
Skipped atom 1766 because residue number 219  < previous residue 298 
Skipped atom 1767 because residue number 219  < previous residue 298 
Skipped atom 1768 because residue number 219  < previous residue 298 
Skipped atom 1769 because residue number 219  < previous residue 298 
Skipped atom 1770 because residue number 219  < previous residue 298 
Skipped atom 1771 because residue number 220  < previous residue 298 
Skipped atom 1772 because residue number 220  < previous residue 298 
Skipped atom 1773 because residue number 220  < previous residue 298 
Skipped atom 1774 because residue number 220  < previous residue 298 
Skipped atom 1775 because residue number 220  < previous residue 298 
Skipped atom 1776 because residue number 220  < previous residue 298 
Skipped atom 1777 because residue number 220  < previous residue 298 
Skipped atom 1778 because residue number 220  < previous residue 298 
Skipped atom 1779 because residue number 221  < previous residue 298 
Skipped atom 1780 because residue number 221  < previous residue 298 
Skipped atom 1781 because residue number 221  < previous residue 298 
Skipped atom 1782 because residue number 221  < previous residue 298 
Skipped atom 1783 because residue number 221  < previous residue 298 
Skipped atom 1784 because residue number 221  < previous residue 298 
Skipped atom 1785 because residue number 221  < previous residue 298 
Skipped atom 1786 because residue number 221  < previous residue 298 
Skipped atom 1787 because residue number 222  < previous residue 298 
Skipped atom 1788 because residue number 222  < previous residue 298 
Skipped atom 1789 because residue number 222  < previous residue 298 
Skipped atom 1790 because residue number 222  < previous residue 298 
Skipped atom 1791 because residue number 222  < previous residue 298 
Skipped atom 1792 because residue number 222  < previous residue 298 
Skipped atom 1793 because residue number 222  < previous residue 298 
Skipped atom 1794 because residue number 222  < previous residue 298 
Skipped atom 1795 because residue number 222  < previous residue 298 
Skipped atom 1796 because residue number 223  < previous residue 298 
Skipped atom 1797 because residue number 223  < previous residue 298 
Skipped atom 1798 because residue number 223  < previous residue 298 
Skipped atom 1799 because residue number 223  < previous residue 298 
Skipped atom 1800 because residue number 223  < previous residue 298 
Skipped atom 1801 because residue number 223  < previous residue 298 
Skipped atom 1802 because residue number 223  < previous residue 298 
Skipped atom 1803 because residue number 223  < previous residue 298 
Skipped atom 1804 because residue number 224  < previous residue 298 
Skipped atom 1805 because residue number 224  < previous residue 298 
Skipped atom 1806 because residue number 224  < previous residue 298 
Skipped atom 1807 because residue number 224  < previous residue 298 
Skipped atom 1808 because residue number 225  < previous residue 298 
Skipped atom 1809 because residue number 225  < previous residue 298 
Skipped atom 1810 because residue number 225  < previous residue 298 
Skipped atom 1811 because residue number 225  < previous residue 298 
Skipped atom 1812 because residue number 225  < previous residue 298 
Skipped atom 1813 because residue number 225  < previous residue 298 
Skipped atom 1814 because residue number 225  < previous residue 298 
Skipped atom 1815 because residue number 226  < previous residue 298 
Skipped atom 1816 because residue number 226  < previous residue 298 
Skipped atom 1817 because residue number 226  < previous residue 298 
Skipped atom 1818 because residue number 226  < previous residue 298 
Skipped atom 1819 because residue number 226  < previous residue 298 
Skipped atom 1820 because residue number 226  < previous residue 298 
Skipped atom 1821 because residue number 226  < previous residue 298 
Skipped atom 1822 because residue number 227  < previous residue 298 
Skipped atom 1823 because residue number 227  < previous residue 298 
Skipped atom 1824 because residue number 227  < previous residue 298 
Skipped atom 1825 because residue number 227  < previous residue 298 
Skipped atom 1826 because residue number 227  < previous residue 298 
Skipped atom 1827 because residue number 227  < previous residue 298 
Skipped atom 1828 because residue number 228  < previous residue 298 
Skipped atom 1829 because residue number 228  < previous residue 298 
Skipped atom 1830 because residue number 228  < previous residue 298 
Skipped atom 1831 because residue number 228  < previous residue 298 
Skipped atom 1832 because residue number 228  < previous residue 298 
Skipped atom 1833 because residue number 228  < previous residue 298 
Skipped atom 1834 because residue number 228  < previous residue 298 
Skipped atom 1835 because residue number 228  < previous residue 298 
Skipped atom 1836 because residue number 229  < previous residue 298 
Skipped atom 1837 because residue number 229  < previous residue 298 
Skipped atom 1838 because residue number 229  < previous residue 298 
Skipped atom 1839 because residue number 229  < previous residue 298 
Skipped atom 1840 because residue number 229  < previous residue 298 
Skipped atom 1841 because residue number 229  < previous residue 298 
Skipped atom 1842 because residue number 229  < previous residue 298 
Skipped atom 1843 because residue number 229  < previous residue 298 
Skipped atom 1844 because residue number 229  < previous residue 298 
Skipped atom 1845 because residue number 229  < previous residue 298 
Skipped atom 1846 because residue number 229  < previous residue 298 
Skipped atom 1847 because residue number 229  < previous residue 298 
Skipped atom 1848 because residue number 230  < previous residue 298 
Skipped atom 1849 because residue number 230  < previous residue 298 
Skipped atom 1850 because residue number 230  < previous residue 298 
Skipped atom 1851 because residue number 230  < previous residue 298 
Skipped atom 1852 because residue number 230  < previous residue 298 
Skipped atom 1853 because residue number 230  < previous residue 298 
Skipped atom 1854 because residue number 230  < previous residue 298 
Skipped atom 1855 because residue number 230  < previous residue 298 
Skipped atom 1856 because residue number 230  < previous residue 298 
Skipped atom 1857 because residue number 231  < previous residue 298 
Skipped atom 1858 because residue number 231  < previous residue 298 
Skipped atom 1859 because residue number 231  < previous residue 298 
Skipped atom 1860 because residue number 231  < previous residue 298 
Skipped atom 1861 because residue number 231  < previous residue 298 
Skipped atom 1862 because residue number 231  < previous residue 298 
Skipped atom 1863 because residue number 231  < previous residue 298 
Skipped atom 1864 because residue number 232  < previous residue 298 
Skipped atom 1865 because residue number 232  < previous residue 298 
Skipped atom 1866 because residue number 232  < previous residue 298 
Skipped atom 1867 because residue number 232  < previous residue 298 
Skipped atom 1868 because residue number 232  < previous residue 298 
Skipped atom 1869 because residue number 233  < previous residue 298 
Skipped atom 1870 because residue number 233  < previous residue 298 
Skipped atom 1871 because residue number 233  < previous residue 298 
Skipped atom 1872 because residue number 233  < previous residue 298 
Skipped atom 1873 because residue number 233  < previous residue 298 
Skipped atom 1874 because residue number 233  < previous residue 298 
Skipped atom 1875 because residue number 233  < previous residue 298 
Skipped atom 1876 because residue number 233  < previous residue 298 
Skipped atom 1877 because residue number 234  < previous residue 298 
Skipped atom 1878 because residue number 234  < previous residue 298 
Skipped atom 1879 because residue number 234  < previous residue 298 
Skipped atom 1880 because residue number 234  < previous residue 298 
Skipped atom 1881 because residue number 234  < previous residue 298 
Skipped atom 1882 because residue number 234  < previous residue 298 
Skipped atom 1883 because residue number 234  < previous residue 298 
Skipped atom 1884 because residue number 234  < previous residue 298 
Skipped atom 1885 because residue number 234  < previous residue 298 
Skipped atom 1886 because residue number 235  < previous residue 298 
Skipped atom 1887 because residue number 235  < previous residue 298 
Skipped atom 1888 because residue number 235  < previous residue 298 
Skipped atom 1889 because residue number 235  < previous residue 298 
Skipped atom 1890 because residue number 235  < previous residue 298 
Skipped atom 1891 because residue number 235  < previous residue 298 
Skipped atom 1892 because residue number 236  < previous residue 298 
Skipped atom 1893 because residue number 236  < previous residue 298 
Skipped atom 1894 because residue number 236  < previous residue 298 
Skipped atom 1895 because residue number 236  < previous residue 298 
Skipped atom 1896 because residue number 237  < previous residue 298 
Skipped atom 1897 because residue number 237  < previous residue 298 
Skipped atom 1898 because residue number 237  < previous residue 298 
Skipped atom 1899 because residue number 237  < previous residue 298 
Skipped atom 1900 because residue number 237  < previous residue 298 
Skipped atom 1901 because residue number 237  < previous residue 298 
Skipped atom 1902 because residue number 237  < previous residue 298 
Skipped atom 1903 because residue number 237  < previous residue 298 
Skipped atom 1904 because residue number 237  < previous residue 298 
Skipped atom 1905 because residue number 238  < previous residue 298 
Skipped atom 1906 because residue number 238  < previous residue 298 
Skipped atom 1907 because residue number 238  < previous residue 298 
Skipped atom 1908 because residue number 238  < previous residue 298 
Skipped atom 1909 because residue number 238  < previous residue 298 
Skipped atom 1910 because residue number 239  < previous residue 298 
Skipped atom 1911 because residue number 239  < previous residue 298 
Skipped atom 1912 because residue number 239  < previous residue 298 
Skipped atom 1913 because residue number 239  < previous residue 298 
Skipped atom 1914 because residue number 239  < previous residue 298 
Skipped atom 1915 because residue number 239  < previous residue 298 
Skipped atom 1916 because residue number 239  < previous residue 298 
Skipped atom 1917 because residue number 239  < previous residue 298 
Skipped atom 1918 because residue number 240  < previous residue 298 
Skipped atom 1919 because residue number 240  < previous residue 298 
Skipped atom 1920 because residue number 240  < previous residue 298 
Skipped atom 1921 because residue number 240  < previous residue 298 
Skipped atom 1922 because residue number 240  < previous residue 298 
Skipped atom 1923 because residue number 240  < previous residue 298 
Skipped atom 1924 because residue number 240  < previous residue 298 
Skipped atom 1925 because residue number 241  < previous residue 298 
Skipped atom 1926 because residue number 241  < previous residue 298 
Skipped atom 1927 because residue number 241  < previous residue 298 
Skipped atom 1928 because residue number 241  < previous residue 298 
Skipped atom 1929 because residue number 241  < previous residue 298 
Skipped atom 1930 because residue number 241  < previous residue 298 
Skipped atom 1931 because residue number 241  < previous residue 298 
Skipped atom 1932 because residue number 241  < previous residue 298 
Skipped atom 1933 because residue number 241  < previous residue 298 
Skipped atom 1934 because residue number 241  < previous residue 298 
Skipped atom 1935 because residue number 241  < previous residue 298 
Skipped atom 1936 because residue number 241  < previous residue 298 
Skipped atom 1937 because residue number 242  < previous residue 298 
Skipped atom 1938 because residue number 242  < previous residue 298 
Skipped atom 1939 because residue number 242  < previous residue 298 
Skipped atom 1940 because residue number 242  < previous residue 298 
Skipped atom 1941 because residue number 242  < previous residue 298 
Skipped atom 1942 because residue number 243  < previous residue 298 
Skipped atom 1943 because residue number 243  < previous residue 298 
Skipped atom 1944 because residue number 243  < previous residue 298 
Skipped atom 1945 because residue number 243  < previous residue 298 
Skipped atom 1946 because residue number 243  < previous residue 298 
Skipped atom 1947 because residue number 243  < previous residue 298 
Skipped atom 1948 because residue number 244  < previous residue 298 
Skipped atom 1949 because residue number 244  < previous residue 298 
Skipped atom 1950 because residue number 244  < previous residue 298 
Skipped atom 1951 because residue number 244  < previous residue 298 
Skipped atom 1952 because residue number 244  < previous residue 298 
Skipped atom 1953 because residue number 244  < previous residue 298 
Skipped atom 1954 because residue number 244  < previous residue 298 
Skipped atom 1955 because residue number 244  < previous residue 298 
Skipped atom 1956 because residue number 244  < previous residue 298 
Skipped atom 1957 because residue number 244  < previous residue 298 
Skipped atom 1958 because residue number 244  < previous residue 298 
Skipped atom 1959 because residue number 245  < previous residue 298 
Skipped atom 1960 because residue number 245  < previous residue 298 
Skipped atom 1961 because residue number 245  < previous residue 298 
Skipped atom 1962 because residue number 245  < previous residue 298 
Skipped atom 1963 because residue number 245  < previous residue 298 
Skipped atom 1964 because residue number 245  < previous residue 298 
Skipped atom 1965 because residue number 245  < previous residue 298 
Skipped atom 1966 because residue number 245  < previous residue 298 
Skipped atom 1967 because residue number 246  < previous residue 298 
Skipped atom 1968 because residue number 246  < previous residue 298 
Skipped atom 1969 because residue number 246  < previous residue 298 
Skipped atom 1970 because residue number 246  < previous residue 298 
Skipped atom 1971 because residue number 246  < previous residue 298 
Skipped atom 1972 because residue number 246  < previous residue 298 
Skipped atom 1973 because residue number 246  < previous residue 298 
Skipped atom 1974 because residue number 246  < previous residue 298 
Skipped atom 1975 because residue number 247  < previous residue 298 
Skipped atom 1976 because residue number 247  < previous residue 298 
Skipped atom 1977 because residue number 247  < previous residue 298 
Skipped atom 1978 because residue number 247  < previous residue 298 
Skipped atom 1979 because residue number 247  < previous residue 298 
Skipped atom 1980 because residue number 247  < previous residue 298 
Skipped atom 1981 because residue number 247  < previous residue 298 
Skipped atom 1982 because residue number 248  < previous residue 298 
Skipped atom 1983 because residue number 248  < previous residue 298 
Skipped atom 1984 because residue number 248  < previous residue 298 
Skipped atom 1985 because residue number 248  < previous residue 298 
Skipped atom 1986 because residue number 248  < previous residue 298 
Skipped atom 1987 because residue number 249  < previous residue 298 
Skipped atom 1988 because residue number 249  < previous residue 298 
Skipped atom 1989 because residue number 249  < previous residue 298 
Skipped atom 1990 because residue number 249  < previous residue 298 
Skipped atom 1991 because residue number 249  < previous residue 298 
Skipped atom 1992 because residue number 249  < previous residue 298 
Skipped atom 1993 because residue number 249  < previous residue 298 
Skipped atom 1994 because residue number 249  < previous residue 298 
Skipped atom 1995 because residue number 249  < previous residue 298 
Skipped atom 1996 because residue number 249  < previous residue 298 
Skipped atom 1997 because residue number 249  < previous residue 298 
Skipped atom 1998 because residue number 250  < previous residue 298 
Skipped atom 1999 because residue number 250  < previous residue 298 
Skipped atom 2000 because residue number 250  < previous residue 298 
Skipped atom 2001 because residue number 250  < previous residue 298 
Skipped atom 2002 because residue number 250  < previous residue 298 
Skipped atom 2003 because residue number 250  < previous residue 298 
Skipped atom 2004 because residue number 250  < previous residue 298 
Skipped atom 2005 because residue number 251  < previous residue 298 
Skipped atom 2006 because residue number 251  < previous residue 298 
Skipped atom 2007 because residue number 251  < previous residue 298 
Skipped atom 2008 because residue number 251  < previous residue 298 
Skipped atom 2009 because residue number 251  < previous residue 298 
Skipped atom 2010 because residue number 251  < previous residue 298 
Skipped atom 2011 because residue number 251  < previous residue 298 
Skipped atom 2012 because residue number 251  < previous residue 298 
Skipped atom 2013 because residue number 251  < previous residue 298 
Skipped atom 2014 because residue number 251  < previous residue 298 
Skipped atom 2015 because residue number 251  < previous residue 298 
Skipped atom 2016 because residue number 251  < previous residue 298 
Skipped atom 2017 because residue number 252  < previous residue 298 
Skipped atom 2018 because residue number 252  < previous residue 298 
Skipped atom 2019 because residue number 252  < previous residue 298 
Skipped atom 2020 because residue number 252  < previous residue 298 
Skipped atom 2021 because residue number 252  < previous residue 298 
Skipped atom 2022 because residue number 252  < previous residue 298 
Skipped atom 2023 because residue number 252  < previous residue 298 
Skipped atom 2024 because residue number 253  < previous residue 298 
Skipped atom 2025 because residue number 253  < previous residue 298 
Skipped atom 2026 because residue number 253  < previous residue 298 
Skipped atom 2027 because residue number 253  < previous residue 298 
Skipped atom 2028 because residue number 253  < previous residue 298 
Skipped atom 2029 because residue number 253  < previous residue 298 
Skipped atom 2030 because residue number 253  < previous residue 298 
Skipped atom 2031 because residue number 253  < previous residue 298 
Skipped atom 2032 because residue number 253  < previous residue 298 
Skipped atom 2033 because residue number 253  < previous residue 298 
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1alq-orig.a2m
Writing a2m file: tmp/1alq-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27512


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27512/tmp -alignfile tmp/1alq-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1alq-orig.a2m (1 sequences, 266 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27512/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27512/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27512/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27512/tmp.a2m (1 sequences, 266 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27512/tmp.mod tmp/1alq-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27512 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1alq-align.mod
tmp/1alq-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27512/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1alq-orig.a2m tmp/1alq-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1alq-align.mod
Running w0.5 tmp/1alq-orig.a2m tmp/1alq-align.mod
Running align2model tmp/1alq-align -i tmp/1alq-align.mod -db tmp/1alq-orig.a2m -db tmp/1alq-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1alq.144.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1alq.145.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1alq.145.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1alq.145.0.a2m \
	-target T0124 -template 1alq \
	-out T0124-1alq.145.0 -outdir und
Skipped atom 298 because residue number 31  < previous residue 298 
Skipped atom 299 because residue number 31  < previous residue 298 
Skipped atom 300 because residue number 31  < previous residue 298 
Skipped atom 301 because residue number 31  < previous residue 298 
Skipped atom 302 because residue number 31  < previous residue 298 
Skipped atom 303 because residue number 31  < previous residue 298 
Skipped atom 304 because residue number 31  < previous residue 298 
Skipped atom 305 because residue number 31  < previous residue 298 
Skipped atom 306 because residue number 31  < previous residue 298 
Skipped atom 307 because residue number 32  < previous residue 298 
Skipped atom 308 because residue number 32  < previous residue 298 
Skipped atom 309 because residue number 32  < previous residue 298 
Skipped atom 310 because residue number 32  < previous residue 298 
Skipped atom 311 because residue number 32  < previous residue 298 
Skipped atom 312 because residue number 32  < previous residue 298 
Skipped atom 313 because residue number 32  < previous residue 298 
Skipped atom 314 because residue number 32  < previous residue 298 
Skipped atom 315 because residue number 32  < previous residue 298 
Skipped atom 316 because residue number 33  < previous residue 298 
Skipped atom 317 because residue number 33  < previous residue 298 
Skipped atom 318 because residue number 33  < previous residue 298 
Skipped atom 319 because residue number 33  < previous residue 298 
Skipped atom 320 because residue number 33  < previous residue 298 
Skipped atom 321 because residue number 33  < previous residue 298 
Skipped atom 322 because residue number 33  < previous residue 298 
Skipped atom 323 because residue number 33  < previous residue 298 
Skipped atom 324 because residue number 34  < previous residue 298 
Skipped atom 325 because residue number 34  < previous residue 298 
Skipped atom 326 because residue number 34  < previous residue 298 
Skipped atom 327 because residue number 34  < previous residue 298 
Skipped atom 328 because residue number 34  < previous residue 298 
Skipped atom 329 because residue number 34  < previous residue 298 
Skipped atom 330 because residue number 34  < previous residue 298 
Skipped atom 331 because residue number 34  < previous residue 298 
Skipped atom 332 because residue number 35  < previous residue 298 
Skipped atom 333 because residue number 35  < previous residue 298 
Skipped atom 334 because residue number 35  < previous residue 298 
Skipped atom 335 because residue number 35  < previous residue 298 
Skipped atom 336 because residue number 35  < previous residue 298 
Skipped atom 337 because residue number 35  < previous residue 298 
Skipped atom 338 because residue number 35  < previous residue 298 
Skipped atom 339 because residue number 35  < previous residue 298 
Skipped atom 340 because residue number 36  < previous residue 298 
Skipped atom 341 because residue number 36  < previous residue 298 
Skipped atom 342 because residue number 36  < previous residue 298 
Skipped atom 343 because residue number 36  < previous residue 298 
Skipped atom 344 because residue number 36  < previous residue 298 
Skipped atom 345 because residue number 36  < previous residue 298 
Skipped atom 346 because residue number 36  < previous residue 298 
Skipped atom 347 because residue number 36  < previous residue 298 
Skipped atom 348 because residue number 37  < previous residue 298 
Skipped atom 349 because residue number 37  < previous residue 298 
Skipped atom 350 because residue number 37  < previous residue 298 
Skipped atom 351 because residue number 37  < previous residue 298 
Skipped atom 352 because residue number 37  < previous residue 298 
Skipped atom 353 because residue number 37  < previous residue 298 
Skipped atom 354 because residue number 37  < previous residue 298 
Skipped atom 355 because residue number 37  < previous residue 298 
Skipped atom 356 because residue number 37  < previous residue 298 
Skipped atom 357 because residue number 38  < previous residue 298 
Skipped atom 358 because residue number 38  < previous residue 298 
Skipped atom 359 because residue number 38  < previous residue 298 
Skipped atom 360 because residue number 38  < previous residue 298 
Skipped atom 361 because residue number 38  < previous residue 298 
Skipped atom 362 because residue number 38  < previous residue 298 
Skipped atom 363 because residue number 38  < previous residue 298 
Skipped atom 364 because residue number 38  < previous residue 298 
Skipped atom 365 because residue number 38  < previous residue 298 
Skipped atom 366 because residue number 39  < previous residue 298 
Skipped atom 367 because residue number 39  < previous residue 298 
Skipped atom 368 because residue number 39  < previous residue 298 
Skipped atom 369 because residue number 39  < previous residue 298 
Skipped atom 370 because residue number 39  < previous residue 298 
Skipped atom 371 because residue number 39  < previous residue 298 
Skipped atom 372 because residue number 39  < previous residue 298 
Skipped atom 373 because residue number 39  < previous residue 298 
Skipped atom 374 because residue number 39  < previous residue 298 
Skipped atom 375 because residue number 40  < previous residue 298 
Skipped atom 376 because residue number 40  < previous residue 298 
Skipped atom 377 because residue number 40  < previous residue 298 
Skipped atom 378 because residue number 40  < previous residue 298 
Skipped atom 379 because residue number 40  < previous residue 298 
Skipped atom 380 because residue number 40  < previous residue 298 
Skipped atom 381 because residue number 40  < previous residue 298 
Skipped atom 382 because residue number 40  < previous residue 298 
Skipped atom 383 because residue number 40  < previous residue 298 
Skipped atom 384 because residue number 40  < previous residue 298 
Skipped atom 385 because residue number 40  < previous residue 298 
Skipped atom 386 because residue number 40  < previous residue 298 
Skipped atom 387 because residue number 41  < previous residue 298 
Skipped atom 388 because residue number 41  < previous residue 298 
Skipped atom 389 because residue number 41  < previous residue 298 
Skipped atom 390 because residue number 41  < previous residue 298 
Skipped atom 391 because residue number 41  < previous residue 298 
Skipped atom 392 because residue number 41  < previous residue 298 
Skipped atom 393 because residue number 41  < previous residue 298 
Skipped atom 394 because residue number 41  < previous residue 298 
Skipped atom 395 because residue number 42  < previous residue 298 
Skipped atom 396 because residue number 42  < previous residue 298 
Skipped atom 397 because residue number 42  < previous residue 298 
Skipped atom 398 because residue number 42  < previous residue 298 
Skipped atom 399 because residue number 42  < previous residue 298 
Skipped atom 400 because residue number 43  < previous residue 298 
Skipped atom 401 because residue number 43  < previous residue 298 
Skipped atom 402 because residue number 43  < previous residue 298 
Skipped atom 403 because residue number 43  < previous residue 298 
Skipped atom 404 because residue number 43  < previous residue 298 
Skipped atom 405 because residue number 43  < previous residue 298 
Skipped atom 406 because residue number 43  < previous residue 298 
Skipped atom 407 because residue number 43  < previous residue 298 
Skipped atom 408 because residue number 43  < previous residue 298 
Skipped atom 409 because residue number 43  < previous residue 298 
Skipped atom 410 because residue number 44  < previous residue 298 
Skipped atom 411 because residue number 44  < previous residue 298 
Skipped atom 412 because residue number 44  < previous residue 298 
Skipped atom 413 because residue number 44  < previous residue 298 
Skipped atom 414 because residue number 44  < previous residue 298 
Skipped atom 415 because residue number 44  < previous residue 298 
Skipped atom 416 because residue number 44  < previous residue 298 
Skipped atom 417 because residue number 44  < previous residue 298 
Skipped atom 418 because residue number 45  < previous residue 298 
Skipped atom 419 because residue number 45  < previous residue 298 
Skipped atom 420 because residue number 45  < previous residue 298 
Skipped atom 421 because residue number 45  < previous residue 298 
Skipped atom 422 because residue number 46  < previous residue 298 
Skipped atom 423 because residue number 46  < previous residue 298 
Skipped atom 424 because residue number 46  < previous residue 298 
Skipped atom 425 because residue number 46  < previous residue 298 
Skipped atom 426 because residue number 46  < previous residue 298 
Skipped atom 427 because residue number 46  < previous residue 298 
Skipped atom 428 because residue number 46  < previous residue 298 
Skipped atom 429 because residue number 47  < previous residue 298 
Skipped atom 430 because residue number 47  < previous residue 298 
Skipped atom 431 because residue number 47  < previous residue 298 
Skipped atom 432 because residue number 47  < previous residue 298 
Skipped atom 433 because residue number 47  < previous residue 298 
Skipped atom 434 because residue number 47  < previous residue 298 
Skipped atom 435 because residue number 47  < previous residue 298 
Skipped atom 436 because residue number 47  < previous residue 298 
Skipped atom 437 because residue number 47  < previous residue 298 
Skipped atom 438 because residue number 47  < previous residue 298 
Skipped atom 439 because residue number 47  < previous residue 298 
Skipped atom 440 because residue number 47  < previous residue 298 
Skipped atom 441 because residue number 48  < previous residue 298 
Skipped atom 442 because residue number 48  < previous residue 298 
Skipped atom 443 because residue number 48  < previous residue 298 
Skipped atom 444 because residue number 48  < previous residue 298 
Skipped atom 445 because residue number 48  < previous residue 298 
Skipped atom 446 because residue number 49  < previous residue 298 
Skipped atom 447 because residue number 49  < previous residue 298 
Skipped atom 448 because residue number 49  < previous residue 298 
Skipped atom 449 because residue number 49  < previous residue 298 
Skipped atom 450 because residue number 49  < previous residue 298 
Skipped atom 451 because residue number 49  < previous residue 298 
Skipped atom 452 because residue number 49  < previous residue 298 
Skipped atom 453 because residue number 49  < previous residue 298 
Skipped atom 454 because residue number 50  < previous residue 298 
Skipped atom 455 because residue number 50  < previous residue 298 
Skipped atom 456 because residue number 50  < previous residue 298 
Skipped atom 457 because residue number 50  < previous residue 298 
Skipped atom 458 because residue number 50  < previous residue 298 
Skipped atom 459 because residue number 50  < previous residue 298 
Skipped atom 460 because residue number 50  < previous residue 298 
Skipped atom 461 because residue number 50  < previous residue 298 
Skipped atom 462 because residue number 51  < previous residue 298 
Skipped atom 463 because residue number 51  < previous residue 298 
Skipped atom 464 because residue number 51  < previous residue 298 
Skipped atom 465 because residue number 51  < previous residue 298 
Skipped atom 466 because residue number 51  < previous residue 298 
Skipped atom 467 because residue number 51  < previous residue 298 
Skipped atom 468 because residue number 51  < previous residue 298 
Skipped atom 469 because residue number 52  < previous residue 298 
Skipped atom 470 because residue number 52  < previous residue 298 
Skipped atom 471 because residue number 52  < previous residue 298 
Skipped atom 472 because residue number 52  < previous residue 298 
Skipped atom 473 because residue number 52  < previous residue 298 
Skipped atom 474 because residue number 52  < previous residue 298 
Skipped atom 475 because residue number 52  < previous residue 298 
Skipped atom 476 because residue number 52  < previous residue 298 
Skipped atom 477 because residue number 52  < previous residue 298 
Skipped atom 478 because residue number 53  < previous residue 298 
Skipped atom 479 because residue number 53  < previous residue 298 
Skipped atom 480 because residue number 53  < previous residue 298 
Skipped atom 481 because residue number 53  < previous residue 298 
Skipped atom 482 because residue number 53  < previous residue 298 
Skipped atom 483 because residue number 53  < previous residue 298 
Skipped atom 484 because residue number 54  < previous residue 298 
Skipped atom 485 because residue number 54  < previous residue 298 
Skipped atom 486 because residue number 54  < previous residue 298 
Skipped atom 487 because residue number 54  < previous residue 298 
Skipped atom 488 because residue number 55  < previous residue 298 
Skipped atom 489 because residue number 55  < previous residue 298 
Skipped atom 490 because residue number 55  < previous residue 298 
Skipped atom 491 because residue number 55  < previous residue 298 
Skipped atom 492 because residue number 55  < previous residue 298 
Skipped atom 493 because residue number 55  < previous residue 298 
Skipped atom 494 because residue number 55  < previous residue 298 
Skipped atom 495 because residue number 55  < previous residue 298 
Skipped atom 496 because residue number 55  < previous residue 298 
Skipped atom 497 because residue number 56  < previous residue 298 
Skipped atom 498 because residue number 56  < previous residue 298 
Skipped atom 499 because residue number 56  < previous residue 298 
Skipped atom 500 because residue number 56  < previous residue 298 
Skipped atom 501 because residue number 56  < previous residue 298 
Skipped atom 502 because residue number 56  < previous residue 298 
Skipped atom 503 because residue number 56  < previous residue 298 
Skipped atom 504 because residue number 56  < previous residue 298 
Skipped atom 505 because residue number 56  < previous residue 298 
Skipped atom 506 because residue number 57  < previous residue 298 
Skipped atom 507 because residue number 57  < previous residue 298 
Skipped atom 508 because residue number 57  < previous residue 298 
Skipped atom 509 because residue number 57  < previous residue 298 
Skipped atom 510 because residue number 57  < previous residue 298 
Skipped atom 511 because residue number 57  < previous residue 298 
Skipped atom 512 because residue number 57  < previous residue 298 
Skipped atom 513 because residue number 59  < previous residue 298 
Skipped atom 514 because residue number 59  < previous residue 298 
Skipped atom 515 because residue number 59  < previous residue 298 
Skipped atom 516 because residue number 59  < previous residue 298 
Skipped atom 517 because residue number 59  < previous residue 298 
Skipped atom 518 because residue number 59  < previous residue 298 
Skipped atom 519 because residue number 59  < previous residue 298 
Skipped atom 520 because residue number 59  < previous residue 298 
Skipped atom 521 because residue number 59  < previous residue 298 
Skipped atom 522 because residue number 60  < previous residue 298 
Skipped atom 523 because residue number 60  < previous residue 298 
Skipped atom 524 because residue number 60  < previous residue 298 
Skipped atom 525 because residue number 60  < previous residue 298 
Skipped atom 526 because residue number 60  < previous residue 298 
Skipped atom 527 because residue number 60  < previous residue 298 
Skipped atom 528 because residue number 60  < previous residue 298 
Skipped atom 529 because residue number 60  < previous residue 298 
Skipped atom 530 because residue number 60  < previous residue 298 
Skipped atom 531 because residue number 60  < previous residue 298 
Skipped atom 532 because residue number 60  < previous residue 298 
Skipped atom 533 because residue number 61  < previous residue 298 
Skipped atom 534 because residue number 61  < previous residue 298 
Skipped atom 535 because residue number 61  < previous residue 298 
Skipped atom 536 because residue number 61  < previous residue 298 
Skipped atom 537 because residue number 61  < previous residue 298 
Skipped atom 538 because residue number 61  < previous residue 298 
Skipped atom 539 because residue number 61  < previous residue 298 
Skipped atom 540 because residue number 61  < previous residue 298 
Skipped atom 541 because residue number 62  < previous residue 298 
Skipped atom 542 because residue number 62  < previous residue 298 
Skipped atom 543 because residue number 62  < previous residue 298 
Skipped atom 544 because residue number 62  < previous residue 298 
Skipped atom 545 because residue number 62  < previous residue 298 
Skipped atom 546 because residue number 62  < previous residue 298 
Skipped atom 547 because residue number 63  < previous residue 298 
Skipped atom 548 because residue number 63  < previous residue 298 
Skipped atom 549 because residue number 63  < previous residue 298 
Skipped atom 550 because residue number 63  < previous residue 298 
Skipped atom 551 because residue number 63  < previous residue 298 
Skipped atom 552 because residue number 63  < previous residue 298 
Skipped atom 553 because residue number 63  < previous residue 298 
Skipped atom 554 because residue number 63  < previous residue 298 
Skipped atom 555 because residue number 64  < previous residue 298 
Skipped atom 556 because residue number 64  < previous residue 298 
Skipped atom 557 because residue number 64  < previous residue 298 
Skipped atom 558 because residue number 64  < previous residue 298 
Skipped atom 559 because residue number 64  < previous residue 298 
Skipped atom 560 because residue number 64  < previous residue 298 
Skipped atom 561 because residue number 64  < previous residue 298 
Skipped atom 562 because residue number 64  < previous residue 298 
Skipped atom 563 because residue number 64  < previous residue 298 
Skipped atom 564 because residue number 65  < previous residue 298 
Skipped atom 565 because residue number 65  < previous residue 298 
Skipped atom 566 because residue number 65  < previous residue 298 
Skipped atom 567 because residue number 65  < previous residue 298 
Skipped atom 568 because residue number 65  < previous residue 298 
Skipped atom 569 because residue number 65  < previous residue 298 
Skipped atom 570 because residue number 65  < previous residue 298 
Skipped atom 571 because residue number 65  < previous residue 298 
Skipped atom 572 because residue number 65  < previous residue 298 
Skipped atom 573 because residue number 65  < previous residue 298 
Skipped atom 574 because residue number 65  < previous residue 298 
Skipped atom 575 because residue number 66  < previous residue 298 
Skipped atom 576 because residue number 66  < previous residue 298 
Skipped atom 577 because residue number 66  < previous residue 298 
Skipped atom 578 because residue number 66  < previous residue 298 
Skipped atom 579 because residue number 66  < previous residue 298 
Skipped atom 580 because residue number 66  < previous residue 298 
Skipped atom 581 because residue number 66  < previous residue 298 
Skipped atom 582 because residue number 66  < previous residue 298 
Skipped atom 583 because residue number 66  < previous residue 298 
Skipped atom 584 because residue number 66  < previous residue 298 
Skipped atom 585 because residue number 66  < previous residue 298 
Skipped atom 586 because residue number 67  < previous residue 298 
Skipped atom 587 because residue number 67  < previous residue 298 
Skipped atom 588 because residue number 67  < previous residue 298 
Skipped atom 589 because residue number 67  < previous residue 298 
Skipped atom 590 because residue number 67  < previous residue 298 
Skipped atom 591 because residue number 68  < previous residue 298 
Skipped atom 592 because residue number 68  < previous residue 298 
Skipped atom 593 because residue number 68  < previous residue 298 
Skipped atom 594 because residue number 68  < previous residue 298 
Skipped atom 595 because residue number 68  < previous residue 298 
Skipped atom 596 because residue number 68  < previous residue 298 
Skipped atom 597 because residue number 68  < previous residue 298 
Skipped atom 598 because residue number 68  < previous residue 298 
Skipped atom 599 because residue number 68  < previous residue 298 
Skipped atom 600 because residue number 68  < previous residue 298 
Skipped atom 601 because residue number 68  < previous residue 298 
Skipped atom 602 because residue number 68  < previous residue 298 
Skipped atom 603 because residue number 69  < previous residue 298 
Skipped atom 604 because residue number 69  < previous residue 298 
Skipped atom 605 because residue number 69  < previous residue 298 
Skipped atom 606 because residue number 69  < previous residue 298 
Skipped atom 607 because residue number 69  < previous residue 298 
Skipped atom 608 because residue number 70  < previous residue 298 
Skipped atom 609 because residue number 70  < previous residue 298 
Skipped atom 610 because residue number 70  < previous residue 298 
Skipped atom 611 because residue number 70  < previous residue 298 
Skipped atom 612 because residue number 70  < previous residue 298 
Skipped atom 613 because residue number 70  < previous residue 298 
Skipped atom 614 because residue number 71  < previous residue 298 
Skipped atom 615 because residue number 71  < previous residue 298 
Skipped atom 616 because residue number 71  < previous residue 298 
Skipped atom 617 because residue number 71  < previous residue 298 
Skipped atom 618 because residue number 71  < previous residue 298 
Skipped atom 619 because residue number 71  < previous residue 298 
Skipped atom 620 because residue number 71  < previous residue 298 
Skipped atom 621 because residue number 72  < previous residue 298 
Skipped atom 622 because residue number 72  < previous residue 298 
Skipped atom 623 because residue number 72  < previous residue 298 
Skipped atom 624 because residue number 72  < previous residue 298 
Skipped atom 625 because residue number 72  < previous residue 298 
Skipped atom 626 because residue number 72  < previous residue 298 
Skipped atom 627 because residue number 73  < previous residue 298 
Skipped atom 628 because residue number 73  < previous residue 298 
Skipped atom 629 because residue number 73  < previous residue 298 
Skipped atom 630 because residue number 73  < previous residue 298 
Skipped atom 631 because residue number 73  < previous residue 298 
Skipped atom 632 because residue number 73  < previous residue 298 
Skipped atom 633 because residue number 73  < previous residue 298 
Skipped atom 634 because residue number 73  < previous residue 298 
Skipped atom 635 because residue number 73  < previous residue 298 
Skipped atom 636 because residue number 74  < previous residue 298 
Skipped atom 637 because residue number 74  < previous residue 298 
Skipped atom 638 because residue number 74  < previous residue 298 
Skipped atom 639 because residue number 74  < previous residue 298 
Skipped atom 640 because residue number 74  < previous residue 298 
Skipped atom 641 because residue number 75  < previous residue 298 
Skipped atom 642 because residue number 75  < previous residue 298 
Skipped atom 643 because residue number 75  < previous residue 298 
Skipped atom 644 because residue number 75  < previous residue 298 
Skipped atom 645 because residue number 75  < previous residue 298 
Skipped atom 646 because residue number 75  < previous residue 298 
Skipped atom 647 because residue number 75  < previous residue 298 
Skipped atom 648 because residue number 75  < previous residue 298 
Skipped atom 649 because residue number 76  < previous residue 298 
Skipped atom 650 because residue number 76  < previous residue 298 
Skipped atom 651 because residue number 76  < previous residue 298 
Skipped atom 652 because residue number 76  < previous residue 298 
Skipped atom 653 because residue number 76  < previous residue 298 
Skipped atom 654 because residue number 76  < previous residue 298 
Skipped atom 655 because residue number 76  < previous residue 298 
Skipped atom 656 because residue number 76  < previous residue 298 
Skipped atom 657 because residue number 77  < previous residue 298 
Skipped atom 658 because residue number 77  < previous residue 298 
Skipped atom 659 because residue number 77  < previous residue 298 
Skipped atom 660 because residue number 77  < previous residue 298 
Skipped atom 661 because residue number 77  < previous residue 298 
Skipped atom 662 because residue number 77  < previous residue 298 
Skipped atom 663 because residue number 78  < previous residue 298 
Skipped atom 664 because residue number 78  < previous residue 298 
Skipped atom 665 because residue number 78  < previous residue 298 
Skipped atom 666 because residue number 78  < previous residue 298 
Skipped atom 667 because residue number 78  < previous residue 298 
Skipped atom 668 because residue number 79  < previous residue 298 
Skipped atom 669 because residue number 79  < previous residue 298 
Skipped atom 670 because residue number 79  < previous residue 298 
Skipped atom 671 because residue number 79  < previous residue 298 
Skipped atom 672 because residue number 79  < previous residue 298 
Skipped atom 673 because residue number 79  < previous residue 298 
Skipped atom 674 because residue number 79  < previous residue 298 
Skipped atom 675 because residue number 79  < previous residue 298 
Skipped atom 676 because residue number 80  < previous residue 298 
Skipped atom 677 because residue number 80  < previous residue 298 
Skipped atom 678 because residue number 80  < previous residue 298 
Skipped atom 679 because residue number 80  < previous residue 298 
Skipped atom 680 because residue number 80  < previous residue 298 
Skipped atom 681 because residue number 80  < previous residue 298 
Skipped atom 682 because residue number 80  < previous residue 298 
Skipped atom 683 because residue number 80  < previous residue 298 
Skipped atom 684 because residue number 81  < previous residue 298 
Skipped atom 685 because residue number 81  < previous residue 298 
Skipped atom 686 because residue number 81  < previous residue 298 
Skipped atom 687 because residue number 81  < previous residue 298 
Skipped atom 688 because residue number 81  < previous residue 298 
Skipped atom 689 because residue number 81  < previous residue 298 
Skipped atom 690 because residue number 81  < previous residue 298 
Skipped atom 691 because residue number 81  < previous residue 298 
Skipped atom 692 because residue number 82  < previous residue 298 
Skipped atom 693 because residue number 82  < previous residue 298 
Skipped atom 694 because residue number 82  < previous residue 298 
Skipped atom 695 because residue number 82  < previous residue 298 
Skipped atom 696 because residue number 82  < previous residue 298 
Skipped atom 697 because residue number 82  < previous residue 298 
Skipped atom 698 because residue number 82  < previous residue 298 
Skipped atom 699 because residue number 82  < previous residue 298 
Skipped atom 700 because residue number 82  < previous residue 298 
Skipped atom 701 because residue number 83  < previous residue 298 
Skipped atom 702 because residue number 83  < previous residue 298 
Skipped atom 703 because residue number 83  < previous residue 298 
Skipped atom 704 because residue number 83  < previous residue 298 
Skipped atom 705 because residue number 83  < previous residue 298 
Skipped atom 706 because residue number 83  < previous residue 298 
Skipped atom 707 because residue number 83  < previous residue 298 
Skipped atom 708 because residue number 83  < previous residue 298 
Skipped atom 709 because residue number 83  < previous residue 298 
Skipped atom 710 because residue number 84  < previous residue 298 
Skipped atom 711 because residue number 84  < previous residue 298 
Skipped atom 712 because residue number 84  < previous residue 298 
Skipped atom 713 because residue number 84  < previous residue 298 
Skipped atom 714 because residue number 84  < previous residue 298 
Skipped atom 715 because residue number 84  < previous residue 298 
Skipped atom 716 because residue number 84  < previous residue 298 
Skipped atom 717 because residue number 87  < previous residue 298 
Skipped atom 718 because residue number 87  < previous residue 298 
Skipped atom 719 because residue number 87  < previous residue 298 
Skipped atom 720 because residue number 87  < previous residue 298 
Skipped atom 721 because residue number 87  < previous residue 298 
Skipped atom 722 because residue number 87  < previous residue 298 
Skipped atom 723 because residue number 87  < previous residue 298 
Skipped atom 724 because residue number 88  < previous residue 298 
Skipped atom 725 because residue number 88  < previous residue 298 
Skipped atom 726 because residue number 88  < previous residue 298 
Skipped atom 727 because residue number 88  < previous residue 298 
Skipped atom 728 because residue number 88  < previous residue 298 
Skipped atom 729 because residue number 88  < previous residue 298 
Skipped atom 730 because residue number 88  < previous residue 298 
Skipped atom 731 because residue number 88  < previous residue 298 
Skipped atom 732 because residue number 88  < previous residue 298 
Skipped atom 733 because residue number 88  < previous residue 298 
Skipped atom 734 because residue number 88  < previous residue 298 
Skipped atom 735 because residue number 88  < previous residue 298 
Skipped atom 736 because residue number 89  < previous residue 298 
Skipped atom 737 because residue number 89  < previous residue 298 
Skipped atom 738 because residue number 89  < previous residue 298 
Skipped atom 739 because residue number 89  < previous residue 298 
Skipped atom 740 because residue number 89  < previous residue 298 
Skipped atom 741 because residue number 89  < previous residue 298 
Skipped atom 742 because residue number 89  < previous residue 298 
Skipped atom 743 because residue number 89  < previous residue 298 
Skipped atom 744 because residue number 90  < previous residue 298 
Skipped atom 745 because residue number 90  < previous residue 298 
Skipped atom 746 because residue number 90  < previous residue 298 
Skipped atom 747 because residue number 90  < previous residue 298 
Skipped atom 748 because residue number 90  < previous residue 298 
Skipped atom 749 because residue number 90  < previous residue 298 
Skipped atom 750 because residue number 90  < previous residue 298 
Skipped atom 751 because residue number 90  < previous residue 298 
Skipped atom 752 because residue number 90  < previous residue 298 
Skipped atom 753 because residue number 91  < previous residue 298 
Skipped atom 754 because residue number 91  < previous residue 298 
Skipped atom 755 because residue number 91  < previous residue 298 
Skipped atom 756 because residue number 91  < previous residue 298 
Skipped atom 757 because residue number 91  < previous residue 298 
Skipped atom 758 because residue number 91  < previous residue 298 
Skipped atom 759 because residue number 91  < previous residue 298 
Skipped atom 760 because residue number 91  < previous residue 298 
Skipped atom 761 because residue number 92  < previous residue 298 
Skipped atom 762 because residue number 92  < previous residue 298 
Skipped atom 763 because residue number 92  < previous residue 298 
Skipped atom 764 because residue number 92  < previous residue 298 
Skipped atom 765 because residue number 92  < previous residue 298 
Skipped atom 766 because residue number 92  < previous residue 298 
Skipped atom 767 because residue number 92  < previous residue 298 
Skipped atom 768 because residue number 92  < previous residue 298 
Skipped atom 769 because residue number 93  < previous residue 298 
Skipped atom 770 because residue number 93  < previous residue 298 
Skipped atom 771 because residue number 93  < previous residue 298 
Skipped atom 772 because residue number 93  < previous residue 298 
Skipped atom 773 because residue number 93  < previous residue 298 
Skipped atom 774 because residue number 93  < previous residue 298 
Skipped atom 775 because residue number 93  < previous residue 298 
Skipped atom 776 because residue number 93  < previous residue 298 
Skipped atom 777 because residue number 93  < previous residue 298 
Skipped atom 778 because residue number 94  < previous residue 298 
Skipped atom 779 because residue number 94  < previous residue 298 
Skipped atom 780 because residue number 94  < previous residue 298 
Skipped atom 781 because residue number 94  < previous residue 298 
Skipped atom 782 because residue number 94  < previous residue 298 
Skipped atom 783 because residue number 94  < previous residue 298 
Skipped atom 784 because residue number 94  < previous residue 298 
Skipped atom 785 because residue number 94  < previous residue 298 
Skipped atom 786 because residue number 94  < previous residue 298 
Skipped atom 787 because residue number 95  < previous residue 298 
Skipped atom 788 because residue number 95  < previous residue 298 
Skipped atom 789 because residue number 95  < previous residue 298 
Skipped atom 790 because residue number 95  < previous residue 298 
Skipped atom 791 because residue number 95  < previous residue 298 
Skipped atom 792 because residue number 95  < previous residue 298 
Skipped atom 793 because residue number 95  < previous residue 298 
Skipped atom 794 because residue number 96  < previous residue 298 
Skipped atom 795 because residue number 96  < previous residue 298 
Skipped atom 796 because residue number 96  < previous residue 298 
Skipped atom 797 because residue number 96  < previous residue 298 
Skipped atom 798 because residue number 96  < previous residue 298 
Skipped atom 799 because residue number 96  < previous residue 298 
Skipped atom 800 because residue number 96  < previous residue 298 
Skipped atom 801 because residue number 96  < previous residue 298 
Skipped atom 802 because residue number 96  < previous residue 298 
Skipped atom 803 because residue number 96  < previous residue 298 
Skipped atom 804 because residue number 97  < previous residue 298 
Skipped atom 805 because residue number 97  < previous residue 298 
Skipped atom 806 because residue number 97  < previous residue 298 
Skipped atom 807 because residue number 97  < previous residue 298 
Skipped atom 808 because residue number 97  < previous residue 298 
Skipped atom 809 because residue number 97  < previous residue 298 
Skipped atom 810 because residue number 97  < previous residue 298 
Skipped atom 811 because residue number 97  < previous residue 298 
Skipped atom 812 because residue number 98  < previous residue 298 
Skipped atom 813 because residue number 98  < previous residue 298 
Skipped atom 814 because residue number 98  < previous residue 298 
Skipped atom 815 because residue number 98  < previous residue 298 
Skipped atom 816 because residue number 98  < previous residue 298 
Skipped atom 817 because residue number 98  < previous residue 298 
Skipped atom 818 because residue number 98  < previous residue 298 
Skipped atom 819 because residue number 98  < previous residue 298 
Skipped atom 820 because residue number 99  < previous residue 298 
Skipped atom 821 because residue number 99  < previous residue 298 
Skipped atom 822 because residue number 99  < previous residue 298 
Skipped atom 823 because residue number 99  < previous residue 298 
Skipped atom 824 because residue number 99  < previous residue 298 
Skipped atom 825 because residue number 99  < previous residue 298 
Skipped atom 826 because residue number 99  < previous residue 298 
Skipped atom 827 because residue number 99  < previous residue 298 
Skipped atom 828 because residue number 99  < previous residue 298 
Skipped atom 829 because residue number 100  < previous residue 298 
Skipped atom 830 because residue number 100  < previous residue 298 
Skipped atom 831 because residue number 100  < previous residue 298 
Skipped atom 832 because residue number 100  < previous residue 298 
Skipped atom 833 because residue number 100  < previous residue 298 
Skipped atom 834 because residue number 100  < previous residue 298 
Skipped atom 835 because residue number 100  < previous residue 298 
Skipped atom 836 because residue number 100  < previous residue 298 
Skipped atom 837 because residue number 101  < previous residue 298 
Skipped atom 838 because residue number 101  < previous residue 298 
Skipped atom 839 because residue number 101  < previous residue 298 
Skipped atom 840 because residue number 101  < previous residue 298 
Skipped atom 841 because residue number 101  < previous residue 298 
Skipped atom 842 because residue number 101  < previous residue 298 
Skipped atom 843 because residue number 101  < previous residue 298 
Skipped atom 844 because residue number 101  < previous residue 298 
Skipped atom 845 because residue number 102  < previous residue 298 
Skipped atom 846 because residue number 102  < previous residue 298 
Skipped atom 847 because residue number 102  < previous residue 298 
Skipped atom 848 because residue number 102  < previous residue 298 
Skipped atom 849 because residue number 102  < previous residue 298 
Skipped atom 850 because residue number 102  < previous residue 298 
Skipped atom 851 because residue number 102  < previous residue 298 
Skipped atom 852 because residue number 102  < previous residue 298 
Skipped atom 853 because residue number 103  < previous residue 298 
Skipped atom 854 because residue number 103  < previous residue 298 
Skipped atom 855 because residue number 103  < previous residue 298 
Skipped atom 856 because residue number 103  < previous residue 298 
Skipped atom 857 because residue number 103  < previous residue 298 
Skipped atom 858 because residue number 103  < previous residue 298 
Skipped atom 859 because residue number 103  < previous residue 298 
Skipped atom 860 because residue number 104  < previous residue 298 
Skipped atom 861 because residue number 104  < previous residue 298 
Skipped atom 862 because residue number 104  < previous residue 298 
Skipped atom 863 because residue number 104  < previous residue 298 
Skipped atom 864 because residue number 104  < previous residue 298 
Skipped atom 865 because residue number 105  < previous residue 298 
Skipped atom 866 because residue number 105  < previous residue 298 
Skipped atom 867 because residue number 105  < previous residue 298 
Skipped atom 868 because residue number 105  < previous residue 298 
Skipped atom 869 because residue number 105  < previous residue 298 
Skipped atom 870 because residue number 105  < previous residue 298 
Skipped atom 871 because residue number 105  < previous residue 298 
Skipped atom 872 because residue number 105  < previous residue 298 
Skipped atom 873 because residue number 105  < previous residue 298 
Skipped atom 874 because residue number 105  < previous residue 298 
Skipped atom 875 because residue number 105  < previous residue 298 
Skipped atom 876 because residue number 105  < previous residue 298 
Skipped atom 877 because residue number 106  < previous residue 298 
Skipped atom 878 because residue number 106  < previous residue 298 
Skipped atom 879 because residue number 106  < previous residue 298 
Skipped atom 880 because residue number 106  < previous residue 298 
Skipped atom 881 because residue number 106  < previous residue 298 
Skipped atom 882 because residue number 106  < previous residue 298 
Skipped atom 883 because residue number 107  < previous residue 298 
Skipped atom 884 because residue number 107  < previous residue 298 
Skipped atom 885 because residue number 107  < previous residue 298 
Skipped atom 886 because residue number 107  < previous residue 298 
Skipped atom 887 because residue number 107  < previous residue 298 
Skipped atom 888 because residue number 107  < previous residue 298 
Skipped atom 889 because residue number 107  < previous residue 298 
Skipped atom 890 because residue number 108  < previous residue 298 
Skipped atom 891 because residue number 108  < previous residue 298 
Skipped atom 892 because residue number 108  < previous residue 298 
Skipped atom 893 because residue number 108  < previous residue 298 
Skipped atom 894 because residue number 108  < previous residue 298 
Skipped atom 895 because residue number 108  < previous residue 298 
Skipped atom 896 because residue number 108  < previous residue 298 
Skipped atom 897 because residue number 108  < previous residue 298 
Skipped atom 898 because residue number 109  < previous residue 298 
Skipped atom 899 because residue number 109  < previous residue 298 
Skipped atom 900 because residue number 109  < previous residue 298 
Skipped atom 901 because residue number 109  < previous residue 298 
Skipped atom 902 because residue number 109  < previous residue 298 
Skipped atom 903 because residue number 109  < previous residue 298 
Skipped atom 904 because residue number 109  < previous residue 298 
Skipped atom 905 because residue number 109  < previous residue 298 
Skipped atom 906 because residue number 110  < previous residue 298 
Skipped atom 907 because residue number 110  < previous residue 298 
Skipped atom 908 because residue number 110  < previous residue 298 
Skipped atom 909 because residue number 110  < previous residue 298 
Skipped atom 910 because residue number 110  < previous residue 298 
Skipped atom 911 because residue number 110  < previous residue 298 
Skipped atom 912 because residue number 110  < previous residue 298 
Skipped atom 913 because residue number 110  < previous residue 298 
Skipped atom 914 because residue number 110  < previous residue 298 
Skipped atom 915 because residue number 111  < previous residue 298 
Skipped atom 916 because residue number 111  < previous residue 298 
Skipped atom 917 because residue number 111  < previous residue 298 
Skipped atom 918 because residue number 111  < previous residue 298 
Skipped atom 919 because residue number 111  < previous residue 298 
Skipped atom 920 because residue number 111  < previous residue 298 
Skipped atom 921 because residue number 111  < previous residue 298 
Skipped atom 922 because residue number 111  < previous residue 298 
Skipped atom 923 because residue number 111  < previous residue 298 
Skipped atom 924 because residue number 112  < previous residue 298 
Skipped atom 925 because residue number 112  < previous residue 298 
Skipped atom 926 because residue number 112  < previous residue 298 
Skipped atom 927 because residue number 112  < previous residue 298 
Skipped atom 928 because residue number 112  < previous residue 298 
Skipped atom 929 because residue number 112  < previous residue 298 
Skipped atom 930 because residue number 112  < previous residue 298 
Skipped atom 931 because residue number 112  < previous residue 298 
Skipped atom 932 because residue number 112  < previous residue 298 
Skipped atom 933 because residue number 112  < previous residue 298 
Skipped atom 934 because residue number 112  < previous residue 298 
Skipped atom 935 because residue number 112  < previous residue 298 
Skipped atom 936 because residue number 113  < previous residue 298 
Skipped atom 937 because residue number 113  < previous residue 298 
Skipped atom 938 because residue number 113  < previous residue 298 
Skipped atom 939 because residue number 113  < previous residue 298 
Skipped atom 940 because residue number 113  < previous residue 298 
Skipped atom 941 because residue number 113  < previous residue 298 
Skipped atom 942 because residue number 113  < previous residue 298 
Skipped atom 943 because residue number 114  < previous residue 298 
Skipped atom 944 because residue number 114  < previous residue 298 
Skipped atom 945 because residue number 114  < previous residue 298 
Skipped atom 946 because residue number 114  < previous residue 298 
Skipped atom 947 because residue number 115  < previous residue 298 
Skipped atom 948 because residue number 115  < previous residue 298 
Skipped atom 949 because residue number 115  < previous residue 298 
Skipped atom 950 because residue number 115  < previous residue 298 
Skipped atom 951 because residue number 115  < previous residue 298 
Skipped atom 952 because residue number 115  < previous residue 298 
Skipped atom 953 because residue number 115  < previous residue 298 
Skipped atom 954 because residue number 115  < previous residue 298 
Skipped atom 955 because residue number 115  < previous residue 298 
Skipped atom 956 because residue number 116  < previous residue 298 
Skipped atom 957 because residue number 116  < previous residue 298 
Skipped atom 958 because residue number 116  < previous residue 298 
Skipped atom 959 because residue number 116  < previous residue 298 
Skipped atom 960 because residue number 116  < previous residue 298 
Skipped atom 961 because residue number 116  < previous residue 298 
Skipped atom 962 because residue number 116  < previous residue 298 
Skipped atom 963 because residue number 116  < previous residue 298 
Skipped atom 964 because residue number 117  < previous residue 298 
Skipped atom 965 because residue number 117  < previous residue 298 
Skipped atom 966 because residue number 117  < previous residue 298 
Skipped atom 967 because residue number 117  < previous residue 298 
Skipped atom 968 because residue number 117  < previous residue 298 
Skipped atom 969 because residue number 117  < previous residue 298 
Skipped atom 970 because residue number 117  < previous residue 298 
Skipped atom 971 because residue number 117  < previous residue 298 
Skipped atom 972 because residue number 118  < previous residue 298 
Skipped atom 973 because residue number 118  < previous residue 298 
Skipped atom 974 because residue number 118  < previous residue 298 
Skipped atom 975 because residue number 118  < previous residue 298 
Skipped atom 976 because residue number 118  < previous residue 298 
Skipped atom 977 because residue number 118  < previous residue 298 
Skipped atom 978 because residue number 118  < previous residue 298 
Skipped atom 979 because residue number 119  < previous residue 298 
Skipped atom 980 because residue number 119  < previous residue 298 
Skipped atom 981 because residue number 119  < previous residue 298 
Skipped atom 982 because residue number 119  < previous residue 298 
Skipped atom 983 because residue number 119  < previous residue 298 
Skipped atom 984 because residue number 119  < previous residue 298 
Skipped atom 985 because residue number 119  < previous residue 298 
Skipped atom 986 because residue number 119  < previous residue 298 
Skipped atom 987 because residue number 120  < previous residue 298 
Skipped atom 988 because residue number 120  < previous residue 298 
Skipped atom 989 because residue number 120  < previous residue 298 
Skipped atom 990 because residue number 120  < previous residue 298 
Skipped atom 991 because residue number 120  < previous residue 298 
Skipped atom 992 because residue number 120  < previous residue 298 
Skipped atom 993 because residue number 120  < previous residue 298 
Skipped atom 994 because residue number 120  < previous residue 298 
Skipped atom 995 because residue number 120  < previous residue 298 
Skipped atom 996 because residue number 121  < previous residue 298 
Skipped atom 997 because residue number 121  < previous residue 298 
Skipped atom 998 because residue number 121  < previous residue 298 
Skipped atom 999 because residue number 121  < previous residue 298 
Skipped atom 1000 because residue number 121  < previous residue 298 
Skipped atom 1001 because residue number 122  < previous residue 298 
Skipped atom 1002 because residue number 122  < previous residue 298 
Skipped atom 1003 because residue number 122  < previous residue 298 
Skipped atom 1004 because residue number 122  < previous residue 298 
Skipped atom 1005 because residue number 122  < previous residue 298 
Skipped atom 1006 because residue number 122  < previous residue 298 
Skipped atom 1007 because residue number 122  < previous residue 298 
Skipped atom 1008 because residue number 122  < previous residue 298 
Skipped atom 1009 because residue number 123  < previous residue 298 
Skipped atom 1010 because residue number 123  < previous residue 298 
Skipped atom 1011 because residue number 123  < previous residue 298 
Skipped atom 1012 because residue number 123  < previous residue 298 
Skipped atom 1013 because residue number 123  < previous residue 298 
Skipped atom 1014 because residue number 123  < previous residue 298 
Skipped atom 1015 because residue number 123  < previous residue 298 
Skipped atom 1016 because residue number 123  < previous residue 298 
Skipped atom 1017 because residue number 124  < previous residue 298 
Skipped atom 1018 because residue number 124  < previous residue 298 
Skipped atom 1019 because residue number 124  < previous residue 298 
Skipped atom 1020 because residue number 124  < previous residue 298 
Skipped atom 1021 because residue number 124  < previous residue 298 
Skipped atom 1022 because residue number 124  < previous residue 298 
Skipped atom 1023 because residue number 124  < previous residue 298 
Skipped atom 1024 because residue number 124  < previous residue 298 
Skipped atom 1025 because residue number 124  < previous residue 298 
Skipped atom 1026 because residue number 125  < previous residue 298 
Skipped atom 1027 because residue number 125  < previous residue 298 
Skipped atom 1028 because residue number 125  < previous residue 298 
Skipped atom 1029 because residue number 125  < previous residue 298 
Skipped atom 1030 because residue number 125  < previous residue 298 
Skipped atom 1031 because residue number 126  < previous residue 298 
Skipped atom 1032 because residue number 126  < previous residue 298 
Skipped atom 1033 because residue number 126  < previous residue 298 
Skipped atom 1034 because residue number 126  < previous residue 298 
Skipped atom 1035 because residue number 126  < previous residue 298 
Skipped atom 1036 because residue number 126  < previous residue 298 
Skipped atom 1037 because residue number 127  < previous residue 298 
Skipped atom 1038 because residue number 127  < previous residue 298 
Skipped atom 1039 because residue number 127  < previous residue 298 
Skipped atom 1040 because residue number 127  < previous residue 298 
Skipped atom 1041 because residue number 127  < previous residue 298 
Skipped atom 1042 because residue number 127  < previous residue 298 
Skipped atom 1043 because residue number 127  < previous residue 298 
Skipped atom 1044 because residue number 127  < previous residue 298 
Skipped atom 1045 because residue number 128  < previous residue 298 
Skipped atom 1046 because residue number 128  < previous residue 298 
Skipped atom 1047 because residue number 128  < previous residue 298 
Skipped atom 1048 because residue number 128  < previous residue 298 
Skipped atom 1049 because residue number 128  < previous residue 298 
Skipped atom 1050 because residue number 128  < previous residue 298 
Skipped atom 1051 because residue number 128  < previous residue 298 
Skipped atom 1052 because residue number 129  < previous residue 298 
Skipped atom 1053 because residue number 129  < previous residue 298 
Skipped atom 1054 because residue number 129  < previous residue 298 
Skipped atom 1055 because residue number 129  < previous residue 298 
Skipped atom 1056 because residue number 129  < previous residue 298 
Skipped atom 1057 because residue number 129  < previous residue 298 
Skipped atom 1058 because residue number 129  < previous residue 298 
Skipped atom 1059 because residue number 129  < previous residue 298 
Skipped atom 1060 because residue number 129  < previous residue 298 
Skipped atom 1061 because residue number 129  < previous residue 298 
Skipped atom 1062 because residue number 129  < previous residue 298 
Skipped atom 1063 because residue number 129  < previous residue 298 
Skipped atom 1064 because residue number 130  < previous residue 298 
Skipped atom 1065 because residue number 130  < previous residue 298 
Skipped atom 1066 because residue number 130  < previous residue 298 
Skipped atom 1067 because residue number 130  < previous residue 298 
Skipped atom 1068 because residue number 130  < previous residue 298 
Skipped atom 1069 because residue number 130  < previous residue 298 
Skipped atom 1070 because residue number 131  < previous residue 298 
Skipped atom 1071 because residue number 131  < previous residue 298 
Skipped atom 1072 because residue number 131  < previous residue 298 
Skipped atom 1073 because residue number 131  < previous residue 298 
Skipped atom 1074 because residue number 131  < previous residue 298 
Skipped atom 1075 because residue number 131  < previous residue 298 
Skipped atom 1076 because residue number 131  < previous residue 298 
Skipped atom 1077 because residue number 131  < previous residue 298 
Skipped atom 1078 because residue number 132  < previous residue 298 
Skipped atom 1079 because residue number 132  < previous residue 298 
Skipped atom 1080 because residue number 132  < previous residue 298 
Skipped atom 1081 because residue number 132  < previous residue 298 
Skipped atom 1082 because residue number 132  < previous residue 298 
Skipped atom 1083 because residue number 132  < previous residue 298 
Skipped atom 1084 because residue number 132  < previous residue 298 
Skipped atom 1085 because residue number 132  < previous residue 298 
Skipped atom 1086 because residue number 133  < previous residue 298 
Skipped atom 1087 because residue number 133  < previous residue 298 
Skipped atom 1088 because residue number 133  < previous residue 298 
Skipped atom 1089 because residue number 133  < previous residue 298 
Skipped atom 1090 because residue number 133  < previous residue 298 
Skipped atom 1091 because residue number 133  < previous residue 298 
Skipped atom 1092 because residue number 133  < previous residue 298 
Skipped atom 1093 because residue number 134  < previous residue 298 
Skipped atom 1094 because residue number 134  < previous residue 298 
Skipped atom 1095 because residue number 134  < previous residue 298 
Skipped atom 1096 because residue number 134  < previous residue 298 
Skipped atom 1097 because residue number 134  < previous residue 298 
Skipped atom 1098 because residue number 135  < previous residue 298 
Skipped atom 1099 because residue number 135  < previous residue 298 
Skipped atom 1100 because residue number 135  < previous residue 298 
Skipped atom 1101 because residue number 135  < previous residue 298 
Skipped atom 1102 because residue number 135  < previous residue 298 
Skipped atom 1103 because residue number 135  < previous residue 298 
Skipped atom 1104 because residue number 135  < previous residue 298 
Skipped atom 1105 because residue number 135  < previous residue 298 
Skipped atom 1106 because residue number 136  < previous residue 298 
Skipped atom 1107 because residue number 136  < previous residue 298 
Skipped atom 1108 because residue number 136  < previous residue 298 
Skipped atom 1109 because residue number 136  < previous residue 298 
Skipped atom 1110 because residue number 136  < previous residue 298 
Skipped atom 1111 because residue number 136  < previous residue 298 
Skipped atom 1112 because residue number 136  < previous residue 298 
Skipped atom 1113 because residue number 136  < previous residue 298 
Skipped atom 1114 because residue number 137  < previous residue 298 
Skipped atom 1115 because residue number 137  < previous residue 298 
Skipped atom 1116 because residue number 137  < previous residue 298 
Skipped atom 1117 because residue number 137  < previous residue 298 
Skipped atom 1118 because residue number 137  < previous residue 298 
Skipped atom 1119 because residue number 137  < previous residue 298 
Skipped atom 1120 because residue number 137  < previous residue 298 
Skipped atom 1121 because residue number 137  < previous residue 298 
Skipped atom 1122 because residue number 137  < previous residue 298 
Skipped atom 1123 because residue number 138  < previous residue 298 
Skipped atom 1124 because residue number 138  < previous residue 298 
Skipped atom 1125 because residue number 138  < previous residue 298 
Skipped atom 1126 because residue number 138  < previous residue 298 
Skipped atom 1127 because residue number 138  < previous residue 298 
Skipped atom 1128 because residue number 138  < previous residue 298 
Skipped atom 1129 because residue number 138  < previous residue 298 
Skipped atom 1130 because residue number 138  < previous residue 298 
Skipped atom 1131 because residue number 139  < previous residue 298 
Skipped atom 1132 because residue number 139  < previous residue 298 
Skipped atom 1133 because residue number 139  < previous residue 298 
Skipped atom 1134 because residue number 139  < previous residue 298 
Skipped atom 1135 because residue number 139  < previous residue 298 
Skipped atom 1136 because residue number 139  < previous residue 298 
Skipped atom 1137 because residue number 139  < previous residue 298 
Skipped atom 1138 because residue number 139  < previous residue 298 
Skipped atom 1139 because residue number 140  < previous residue 298 
Skipped atom 1140 because residue number 140  < previous residue 298 
Skipped atom 1141 because residue number 140  < previous residue 298 
Skipped atom 1142 because residue number 140  < previous residue 298 
Skipped atom 1143 because residue number 140  < previous residue 298 
Skipped atom 1144 because residue number 140  < previous residue 298 
Skipped atom 1145 because residue number 140  < previous residue 298 
Skipped atom 1146 because residue number 140  < previous residue 298 
Skipped atom 1147 because residue number 140  < previous residue 298 
Skipped atom 1148 because residue number 141  < previous residue 298 
Skipped atom 1149 because residue number 141  < previous residue 298 
Skipped atom 1150 because residue number 141  < previous residue 298 
Skipped atom 1151 because residue number 141  < previous residue 298 
Skipped atom 1152 because residue number 141  < previous residue 298 
Skipped atom 1153 because residue number 141  < previous residue 298 
Skipped atom 1154 because residue number 141  < previous residue 298 
Skipped atom 1155 because residue number 141  < previous residue 298 
Skipped atom 1156 because residue number 141  < previous residue 298 
Skipped atom 1157 because residue number 142  < previous residue 298 
Skipped atom 1158 because residue number 142  < previous residue 298 
Skipped atom 1159 because residue number 142  < previous residue 298 
Skipped atom 1160 because residue number 142  < previous residue 298 
Skipped atom 1161 because residue number 142  < previous residue 298 
Skipped atom 1162 because residue number 142  < previous residue 298 
Skipped atom 1163 because residue number 142  < previous residue 298 
Skipped atom 1164 because residue number 142  < previous residue 298 
Skipped atom 1165 because residue number 143  < previous residue 298 
Skipped atom 1166 because residue number 143  < previous residue 298 
Skipped atom 1167 because residue number 143  < previous residue 298 
Skipped atom 1168 because residue number 143  < previous residue 298 
Skipped atom 1169 because residue number 144  < previous residue 298 
Skipped atom 1170 because residue number 144  < previous residue 298 
Skipped atom 1171 because residue number 144  < previous residue 298 
Skipped atom 1172 because residue number 144  < previous residue 298 
Skipped atom 1173 because residue number 145  < previous residue 298 
Skipped atom 1174 because residue number 145  < previous residue 298 
Skipped atom 1175 because residue number 145  < previous residue 298 
Skipped atom 1176 because residue number 145  < previous residue 298 
Skipped atom 1177 because residue number 145  < previous residue 298 
Skipped atom 1178 because residue number 145  < previous residue 298 
Skipped atom 1179 because residue number 145  < previous residue 298 
Skipped atom 1180 because residue number 145  < previous residue 298 
Skipped atom 1181 because residue number 146  < previous residue 298 
Skipped atom 1182 because residue number 146  < previous residue 298 
Skipped atom 1183 because residue number 146  < previous residue 298 
Skipped atom 1184 because residue number 146  < previous residue 298 
Skipped atom 1185 because residue number 146  < previous residue 298 
Skipped atom 1186 because residue number 146  < previous residue 298 
Skipped atom 1187 because residue number 146  < previous residue 298 
Skipped atom 1188 because residue number 146  < previous residue 298 
Skipped atom 1189 because residue number 146  < previous residue 298 
Skipped atom 1190 because residue number 147  < previous residue 298 
Skipped atom 1191 because residue number 147  < previous residue 298 
Skipped atom 1192 because residue number 147  < previous residue 298 
Skipped atom 1193 because residue number 147  < previous residue 298 
Skipped atom 1194 because residue number 147  < previous residue 298 
Skipped atom 1195 because residue number 147  < previous residue 298 
Skipped atom 1196 because residue number 147  < previous residue 298 
Skipped atom 1197 because residue number 147  < previous residue 298 
Skipped atom 1198 because residue number 147  < previous residue 298 
Skipped atom 1199 because residue number 148  < previous residue 298 
Skipped atom 1200 because residue number 148  < previous residue 298 
Skipped atom 1201 because residue number 148  < previous residue 298 
Skipped atom 1202 because residue number 148  < previous residue 298 
Skipped atom 1203 because residue number 148  < previous residue 298 
Skipped atom 1204 because residue number 148  < previous residue 298 
Skipped atom 1205 because residue number 148  < previous residue 298 
Skipped atom 1206 because residue number 149  < previous residue 298 
Skipped atom 1207 because residue number 149  < previous residue 298 
Skipped atom 1208 because residue number 149  < previous residue 298 
Skipped atom 1209 because residue number 149  < previous residue 298 
Skipped atom 1210 because residue number 149  < previous residue 298 
Skipped atom 1211 because residue number 149  < previous residue 298 
Skipped atom 1212 because residue number 149  < previous residue 298 
Skipped atom 1213 because residue number 149  < previous residue 298 
Skipped atom 1214 because residue number 149  < previous residue 298 
Skipped atom 1215 because residue number 150  < previous residue 298 
Skipped atom 1216 because residue number 150  < previous residue 298 
Skipped atom 1217 because residue number 150  < previous residue 298 
Skipped atom 1218 because residue number 150  < previous residue 298 
Skipped atom 1219 because residue number 150  < previous residue 298 
Skipped atom 1220 because residue number 150  < previous residue 298 
Skipped atom 1221 because residue number 150  < previous residue 298 
Skipped atom 1222 because residue number 150  < previous residue 298 
Skipped atom 1223 because residue number 150  < previous residue 298 
Skipped atom 1224 because residue number 151  < previous residue 298 
Skipped atom 1225 because residue number 151  < previous residue 298 
Skipped atom 1226 because residue number 151  < previous residue 298 
Skipped atom 1227 because residue number 151  < previous residue 298 
Skipped atom 1228 because residue number 151  < previous residue 298 
Skipped atom 1229 because residue number 151  < previous residue 298 
Skipped atom 1230 because residue number 151  < previous residue 298 
Skipped atom 1231 because residue number 151  < previous residue 298 
Skipped atom 1232 because residue number 151  < previous residue 298 
Skipped atom 1233 because residue number 151  < previous residue 298 
Skipped atom 1234 because residue number 151  < previous residue 298 
Skipped atom 1235 because residue number 152  < previous residue 298 
Skipped atom 1236 because residue number 152  < previous residue 298 
Skipped atom 1237 because residue number 152  < previous residue 298 
Skipped atom 1238 because residue number 152  < previous residue 298 
Skipped atom 1239 because residue number 152  < previous residue 298 
Skipped atom 1240 because residue number 152  < previous residue 298 
Skipped atom 1241 because residue number 152  < previous residue 298 
Skipped atom 1242 because residue number 152  < previous residue 298 
Skipped atom 1243 because residue number 153  < previous residue 298 
Skipped atom 1244 because residue number 153  < previous residue 298 
Skipped atom 1245 because residue number 153  < previous residue 298 
Skipped atom 1246 because residue number 153  < previous residue 298 
Skipped atom 1247 because residue number 153  < previous residue 298 
Skipped atom 1248 because residue number 153  < previous residue 298 
Skipped atom 1249 because residue number 153  < previous residue 298 
Skipped atom 1250 because residue number 153  < previous residue 298 
Skipped atom 1251 because residue number 153  < previous residue 298 
Skipped atom 1252 because residue number 154  < previous residue 298 
Skipped atom 1253 because residue number 154  < previous residue 298 
Skipped atom 1254 because residue number 154  < previous residue 298 
Skipped atom 1255 because residue number 154  < previous residue 298 
Skipped atom 1256 because residue number 154  < previous residue 298 
Skipped atom 1257 because residue number 154  < previous residue 298 
Skipped atom 1258 because residue number 154  < previous residue 298 
Skipped atom 1259 because residue number 154  < previous residue 298 
Skipped atom 1260 because residue number 154  < previous residue 298 
Skipped atom 1261 because residue number 155  < previous residue 298 
Skipped atom 1262 because residue number 155  < previous residue 298 
Skipped atom 1263 because residue number 155  < previous residue 298 
Skipped atom 1264 because residue number 155  < previous residue 298 
Skipped atom 1265 because residue number 155  < previous residue 298 
Skipped atom 1266 because residue number 155  < previous residue 298 
Skipped atom 1267 because residue number 155  < previous residue 298 
Skipped atom 1268 because residue number 155  < previous residue 298 
Skipped atom 1269 because residue number 156  < previous residue 298 
Skipped atom 1270 because residue number 156  < previous residue 298 
Skipped atom 1271 because residue number 156  < previous residue 298 
Skipped atom 1272 because residue number 156  < previous residue 298 
Skipped atom 1273 because residue number 157  < previous residue 298 
Skipped atom 1274 because residue number 157  < previous residue 298 
Skipped atom 1275 because residue number 157  < previous residue 298 
Skipped atom 1276 because residue number 157  < previous residue 298 
Skipped atom 1277 because residue number 157  < previous residue 298 
Skipped atom 1278 because residue number 157  < previous residue 298 
Skipped atom 1279 because residue number 157  < previous residue 298 
Skipped atom 1280 because residue number 157  < previous residue 298 
Skipped atom 1281 because residue number 158  < previous residue 298 
Skipped atom 1282 because residue number 158  < previous residue 298 
Skipped atom 1283 because residue number 158  < previous residue 298 
Skipped atom 1284 because residue number 158  < previous residue 298 
Skipped atom 1285 because residue number 158  < previous residue 298 
Skipped atom 1286 because residue number 158  < previous residue 298 
Skipped atom 1287 because residue number 158  < previous residue 298 
Skipped atom 1288 because residue number 158  < previous residue 298 
Skipped atom 1289 because residue number 158  < previous residue 298 
Skipped atom 1290 because residue number 159  < previous residue 298 
Skipped atom 1291 because residue number 159  < previous residue 298 
Skipped atom 1292 because residue number 159  < previous residue 298 
Skipped atom 1293 because residue number 159  < previous residue 298 
Skipped atom 1294 because residue number 159  < previous residue 298 
Skipped atom 1295 because residue number 159  < previous residue 298 
Skipped atom 1296 because residue number 159  < previous residue 298 
Skipped atom 1297 because residue number 160  < previous residue 298 
Skipped atom 1298 because residue number 160  < previous residue 298 
Skipped atom 1299 because residue number 160  < previous residue 298 
Skipped atom 1300 because residue number 160  < previous residue 298 
Skipped atom 1301 because residue number 160  < previous residue 298 
Skipped atom 1302 because residue number 160  < previous residue 298 
Skipped atom 1303 because residue number 160  < previous residue 298 
Skipped atom 1304 because residue number 161  < previous residue 298 
Skipped atom 1305 because residue number 161  < previous residue 298 
Skipped atom 1306 because residue number 161  < previous residue 298 
Skipped atom 1307 because residue number 161  < previous residue 298 
Skipped atom 1308 because residue number 161  < previous residue 298 
Skipped atom 1309 because residue number 161  < previous residue 298 
Skipped atom 1310 because residue number 161  < previous residue 298 
Skipped atom 1311 because residue number 161  < previous residue 298 
Skipped atom 1312 because residue number 162  < previous residue 298 
Skipped atom 1313 because residue number 162  < previous residue 298 
Skipped atom 1314 because residue number 162  < previous residue 298 
Skipped atom 1315 because residue number 162  < previous residue 298 
Skipped atom 1316 because residue number 162  < previous residue 298 
Skipped atom 1317 because residue number 162  < previous residue 298 
Skipped atom 1318 because residue number 162  < previous residue 298 
Skipped atom 1319 because residue number 163  < previous residue 298 
Skipped atom 1320 because residue number 163  < previous residue 298 
Skipped atom 1321 because residue number 163  < previous residue 298 
Skipped atom 1322 because residue number 163  < previous residue 298 
Skipped atom 1323 because residue number 163  < previous residue 298 
Skipped atom 1324 because residue number 163  < previous residue 298 
Skipped atom 1325 because residue number 163  < previous residue 298 
Skipped atom 1326 because residue number 164  < previous residue 298 
Skipped atom 1327 because residue number 164  < previous residue 298 
Skipped atom 1328 because residue number 164  < previous residue 298 
Skipped atom 1329 because residue number 164  < previous residue 298 
Skipped atom 1330 because residue number 164  < previous residue 298 
Skipped atom 1331 because residue number 164  < previous residue 298 
Skipped atom 1332 because residue number 164  < previous residue 298 
Skipped atom 1333 because residue number 164  < previous residue 298 
Skipped atom 1334 because residue number 164  < previous residue 298 
Skipped atom 1335 because residue number 164  < previous residue 298 
Skipped atom 1336 because residue number 164  < previous residue 298 
Skipped atom 1337 because residue number 165  < previous residue 298 
Skipped atom 1338 because residue number 165  < previous residue 298 
Skipped atom 1339 because residue number 165  < previous residue 298 
Skipped atom 1340 because residue number 165  < previous residue 298 
Skipped atom 1341 because residue number 165  < previous residue 298 
Skipped atom 1342 because residue number 165  < previous residue 298 
Skipped atom 1343 because residue number 165  < previous residue 298 
Skipped atom 1344 because residue number 165  < previous residue 298 
Skipped atom 1345 because residue number 165  < previous residue 298 
Skipped atom 1346 because residue number 165  < previous residue 298 
Skipped atom 1347 because residue number 165  < previous residue 298 
Skipped atom 1348 because residue number 165  < previous residue 298 
Skipped atom 1349 because residue number 166  < previous residue 298 
Skipped atom 1350 because residue number 166  < previous residue 298 
Skipped atom 1351 because residue number 166  < previous residue 298 
Skipped atom 1352 because residue number 166  < previous residue 298 
Skipped atom 1353 because residue number 166  < previous residue 298 
Skipped atom 1354 because residue number 166  < previous residue 298 
Skipped atom 1355 because residue number 166  < previous residue 298 
Skipped atom 1356 because residue number 166  < previous residue 298 
Skipped atom 1357 because residue number 166  < previous residue 298 
Skipped atom 1358 because residue number 167  < previous residue 298 
Skipped atom 1359 because residue number 167  < previous residue 298 
Skipped atom 1360 because residue number 167  < previous residue 298 
Skipped atom 1361 because residue number 167  < previous residue 298 
Skipped atom 1362 because residue number 167  < previous residue 298 
Skipped atom 1363 because residue number 167  < previous residue 298 
Skipped atom 1364 because residue number 167  < previous residue 298 
Skipped atom 1365 because residue number 167  < previous residue 298 
Skipped atom 1366 because residue number 168  < previous residue 298 
Skipped atom 1367 because residue number 168  < previous residue 298 
Skipped atom 1368 because residue number 168  < previous residue 298 
Skipped atom 1369 because residue number 168  < previous residue 298 
Skipped atom 1370 because residue number 168  < previous residue 298 
Skipped atom 1371 because residue number 168  < previous residue 298 
Skipped atom 1372 because residue number 168  < previous residue 298 
Skipped atom 1373 because residue number 168  < previous residue 298 
Skipped atom 1374 because residue number 168  < previous residue 298 
Skipped atom 1375 because residue number 169  < previous residue 298 
Skipped atom 1376 because residue number 169  < previous residue 298 
Skipped atom 1377 because residue number 169  < previous residue 298 
Skipped atom 1378 because residue number 169  < previous residue 298 
Skipped atom 1379 because residue number 169  < previous residue 298 
Skipped atom 1380 because residue number 169  < previous residue 298 
Skipped atom 1381 because residue number 169  < previous residue 298 
Skipped atom 1382 because residue number 169  < previous residue 298 
Skipped atom 1383 because residue number 170  < previous residue 298 
Skipped atom 1384 because residue number 170  < previous residue 298 
Skipped atom 1385 because residue number 170  < previous residue 298 
Skipped atom 1386 because residue number 170  < previous residue 298 
Skipped atom 1387 because residue number 170  < previous residue 298 
Skipped atom 1388 because residue number 170  < previous residue 298 
Skipped atom 1389 because residue number 170  < previous residue 298 
Skipped atom 1390 because residue number 170  < previous residue 298 
Skipped atom 1391 because residue number 171  < previous residue 298 
Skipped atom 1392 because residue number 171  < previous residue 298 
Skipped atom 1393 because residue number 171  < previous residue 298 
Skipped atom 1394 because residue number 171  < previous residue 298 
Skipped atom 1395 because residue number 171  < previous residue 298 
Skipped atom 1396 because residue number 171  < previous residue 298 
Skipped atom 1397 because residue number 171  < previous residue 298 
Skipped atom 1398 because residue number 171  < previous residue 298 
Skipped atom 1399 because residue number 171  < previous residue 298 
Skipped atom 1400 because residue number 171  < previous residue 298 
Skipped atom 1401 because residue number 171  < previous residue 298 
Skipped atom 1402 because residue number 171  < previous residue 298 
Skipped atom 1403 because residue number 172  < previous residue 298 
Skipped atom 1404 because residue number 172  < previous residue 298 
Skipped atom 1405 because residue number 172  < previous residue 298 
Skipped atom 1406 because residue number 172  < previous residue 298 
Skipped atom 1407 because residue number 172  < previous residue 298 
Skipped atom 1408 because residue number 172  < previous residue 298 
Skipped atom 1409 because residue number 172  < previous residue 298 
Skipped atom 1410 because residue number 172  < previous residue 298 
Skipped atom 1411 because residue number 172  < previous residue 298 
Skipped atom 1412 because residue number 172  < previous residue 298 
Skipped atom 1413 because residue number 172  < previous residue 298 
Skipped atom 1414 because residue number 172  < previous residue 298 
Skipped atom 1415 because residue number 173  < previous residue 298 
Skipped atom 1416 because residue number 173  < previous residue 298 
Skipped atom 1417 because residue number 173  < previous residue 298 
Skipped atom 1418 because residue number 173  < previous residue 298 
Skipped atom 1419 because residue number 173  < previous residue 298 
Skipped atom 1420 because residue number 173  < previous residue 298 
Skipped atom 1421 because residue number 174  < previous residue 298 
Skipped atom 1422 because residue number 174  < previous residue 298 
Skipped atom 1423 because residue number 174  < previous residue 298 
Skipped atom 1424 because residue number 174  < previous residue 298 
Skipped atom 1425 because residue number 174  < previous residue 298 
Skipped atom 1426 because residue number 174  < previous residue 298 
Skipped atom 1427 because residue number 174  < previous residue 298 
Skipped atom 1428 because residue number 175  < previous residue 298 
Skipped atom 1429 because residue number 175  < previous residue 298 
Skipped atom 1430 because residue number 175  < previous residue 298 
Skipped atom 1431 because residue number 175  < previous residue 298 
Skipped atom 1432 because residue number 175  < previous residue 298 
Skipped atom 1433 because residue number 175  < previous residue 298 
Skipped atom 1434 because residue number 175  < previous residue 298 
Skipped atom 1435 because residue number 175  < previous residue 298 
Skipped atom 1436 because residue number 175  < previous residue 298 
Skipped atom 1437 because residue number 176  < previous residue 298 
Skipped atom 1438 because residue number 176  < previous residue 298 
Skipped atom 1439 because residue number 176  < previous residue 298 
Skipped atom 1440 because residue number 176  < previous residue 298 
Skipped atom 1441 because residue number 176  < previous residue 298 
Skipped atom 1442 because residue number 176  < previous residue 298 
Skipped atom 1443 because residue number 177  < previous residue 298 
Skipped atom 1444 because residue number 177  < previous residue 298 
Skipped atom 1445 because residue number 177  < previous residue 298 
Skipped atom 1446 because residue number 177  < previous residue 298 
Skipped atom 1447 because residue number 177  < previous residue 298 
Skipped atom 1448 because residue number 177  < previous residue 298 
Skipped atom 1449 because residue number 177  < previous residue 298 
Skipped atom 1450 because residue number 177  < previous residue 298 
Skipped atom 1451 because residue number 177  < previous residue 298 
Skipped atom 1452 because residue number 178  < previous residue 298 
Skipped atom 1453 because residue number 178  < previous residue 298 
Skipped atom 1454 because residue number 178  < previous residue 298 
Skipped atom 1455 because residue number 178  < previous residue 298 
Skipped atom 1456 because residue number 178  < previous residue 298 
Skipped atom 1457 because residue number 178  < previous residue 298 
Skipped atom 1458 because residue number 178  < previous residue 298 
Skipped atom 1459 because residue number 178  < previous residue 298 
Skipped atom 1460 because residue number 178  < previous residue 298 
Skipped atom 1461 because residue number 179  < previous residue 298 
Skipped atom 1462 because residue number 179  < previous residue 298 
Skipped atom 1463 because residue number 179  < previous residue 298 
Skipped atom 1464 because residue number 179  < previous residue 298 
Skipped atom 1465 because residue number 179  < previous residue 298 
Skipped atom 1466 because residue number 179  < previous residue 298 
Skipped atom 1467 because residue number 179  < previous residue 298 
Skipped atom 1468 because residue number 179  < previous residue 298 
Skipped atom 1469 because residue number 180  < previous residue 298 
Skipped atom 1470 because residue number 180  < previous residue 298 
Skipped atom 1471 because residue number 180  < previous residue 298 
Skipped atom 1472 because residue number 180  < previous residue 298 
Skipped atom 1473 because residue number 180  < previous residue 298 
Skipped atom 1474 because residue number 180  < previous residue 298 
Skipped atom 1475 because residue number 180  < previous residue 298 
Skipped atom 1476 because residue number 181  < previous residue 298 
Skipped atom 1477 because residue number 181  < previous residue 298 
Skipped atom 1478 because residue number 181  < previous residue 298 
Skipped atom 1479 because residue number 181  < previous residue 298 
Skipped atom 1480 because residue number 181  < previous residue 298 
Skipped atom 1481 because residue number 181  < previous residue 298 
Skipped atom 1482 because residue number 182  < previous residue 298 
Skipped atom 1483 because residue number 182  < previous residue 298 
Skipped atom 1484 because residue number 182  < previous residue 298 
Skipped atom 1485 because residue number 182  < previous residue 298 
Skipped atom 1486 because residue number 182  < previous residue 298 
Skipped atom 1487 because residue number 182  < previous residue 298 
Skipped atom 1488 because residue number 182  < previous residue 298 
Skipped atom 1489 because residue number 183  < previous residue 298 
Skipped atom 1490 because residue number 183  < previous residue 298 
Skipped atom 1491 because residue number 183  < previous residue 298 
Skipped atom 1492 because residue number 183  < previous residue 298 
Skipped atom 1493 because residue number 183  < previous residue 298 
Skipped atom 1494 because residue number 183  < previous residue 298 
Skipped atom 1495 because residue number 183  < previous residue 298 
Skipped atom 1496 because residue number 184  < previous residue 298 
Skipped atom 1497 because residue number 184  < previous residue 298 
Skipped atom 1498 because residue number 184  < previous residue 298 
Skipped atom 1499 because residue number 184  < previous residue 298 
Skipped atom 1500 because residue number 184  < previous residue 298 
Skipped atom 1501 because residue number 185  < previous residue 298 
Skipped atom 1502 because residue number 185  < previous residue 298 
Skipped atom 1503 because residue number 185  < previous residue 298 
Skipped atom 1504 because residue number 185  < previous residue 298 
Skipped atom 1505 because residue number 185  < previous residue 298 
Skipped atom 1506 because residue number 186  < previous residue 298 
Skipped atom 1507 because residue number 186  < previous residue 298 
Skipped atom 1508 because residue number 186  < previous residue 298 
Skipped atom 1509 because residue number 186  < previous residue 298 
Skipped atom 1510 because residue number 186  < previous residue 298 
Skipped atom 1511 because residue number 186  < previous residue 298 
Skipped atom 1512 because residue number 186  < previous residue 298 
Skipped atom 1513 because residue number 186  < previous residue 298 
Skipped atom 1514 because residue number 186  < previous residue 298 
Skipped atom 1515 because residue number 186  < previous residue 298 
Skipped atom 1516 because residue number 186  < previous residue 298 
Skipped atom 1517 because residue number 187  < previous residue 298 
Skipped atom 1518 because residue number 187  < previous residue 298 
Skipped atom 1519 because residue number 187  < previous residue 298 
Skipped atom 1520 because residue number 187  < previous residue 298 
Skipped atom 1521 because residue number 188  < previous residue 298 
Skipped atom 1522 because residue number 188  < previous residue 298 
Skipped atom 1523 because residue number 188  < previous residue 298 
Skipped atom 1524 because residue number 188  < previous residue 298 
Skipped atom 1525 because residue number 188  < previous residue 298 
Skipped atom 1526 because residue number 188  < previous residue 298 
Skipped atom 1527 because residue number 188  < previous residue 298 
Skipped atom 1528 because residue number 188  < previous residue 298 
Skipped atom 1529 because residue number 188  < previous residue 298 
Skipped atom 1530 because residue number 189  < previous residue 298 
Skipped atom 1531 because residue number 189  < previous residue 298 
Skipped atom 1532 because residue number 189  < previous residue 298 
Skipped atom 1533 because residue number 189  < previous residue 298 
Skipped atom 1534 because residue number 189  < previous residue 298 
Skipped atom 1535 because residue number 189  < previous residue 298 
Skipped atom 1536 because residue number 189  < previous residue 298 
Skipped atom 1537 because residue number 190  < previous residue 298 
Skipped atom 1538 because residue number 190  < previous residue 298 
Skipped atom 1539 because residue number 190  < previous residue 298 
Skipped atom 1540 because residue number 190  < previous residue 298 
Skipped atom 1541 because residue number 190  < previous residue 298 
Skipped atom 1542 because residue number 190  < previous residue 298 
Skipped atom 1543 because residue number 190  < previous residue 298 
Skipped atom 1544 because residue number 190  < previous residue 298 
Skipped atom 1545 because residue number 191  < previous residue 298 
Skipped atom 1546 because residue number 191  < previous residue 298 
Skipped atom 1547 because residue number 191  < previous residue 298 
Skipped atom 1548 because residue number 191  < previous residue 298 
Skipped atom 1549 because residue number 191  < previous residue 298 
Skipped atom 1550 because residue number 191  < previous residue 298 
Skipped atom 1551 because residue number 191  < previous residue 298 
Skipped atom 1552 because residue number 191  < previous residue 298 
Skipped atom 1553 because residue number 192  < previous residue 298 
Skipped atom 1554 because residue number 192  < previous residue 298 
Skipped atom 1555 because residue number 192  < previous residue 298 
Skipped atom 1556 because residue number 192  < previous residue 298 
Skipped atom 1557 because residue number 192  < previous residue 298 
Skipped atom 1558 because residue number 192  < previous residue 298 
Skipped atom 1559 because residue number 192  < previous residue 298 
Skipped atom 1560 because residue number 192  < previous residue 298 
Skipped atom 1561 because residue number 192  < previous residue 298 
Skipped atom 1562 because residue number 193  < previous residue 298 
Skipped atom 1563 because residue number 193  < previous residue 298 
Skipped atom 1564 because residue number 193  < previous residue 298 
Skipped atom 1565 because residue number 193  < previous residue 298 
Skipped atom 1566 because residue number 193  < previous residue 298 
Skipped atom 1567 because residue number 193  < previous residue 298 
Skipped atom 1568 because residue number 193  < previous residue 298 
Skipped atom 1569 because residue number 193  < previous residue 298 
Skipped atom 1570 because residue number 194  < previous residue 298 
Skipped atom 1571 because residue number 194  < previous residue 298 
Skipped atom 1572 because residue number 194  < previous residue 298 
Skipped atom 1573 because residue number 194  < previous residue 298 
Skipped atom 1574 because residue number 194  < previous residue 298 
Skipped atom 1575 because residue number 194  < previous residue 298 
Skipped atom 1576 because residue number 194  < previous residue 298 
Skipped atom 1577 because residue number 194  < previous residue 298 
Skipped atom 1578 because residue number 195  < previous residue 298 
Skipped atom 1579 because residue number 195  < previous residue 298 
Skipped atom 1580 because residue number 195  < previous residue 298 
Skipped atom 1581 because residue number 195  < previous residue 298 
Skipped atom 1582 because residue number 195  < previous residue 298 
Skipped atom 1583 because residue number 196  < previous residue 298 
Skipped atom 1584 because residue number 196  < previous residue 298 
Skipped atom 1585 because residue number 196  < previous residue 298 
Skipped atom 1586 because residue number 196  < previous residue 298 
Skipped atom 1587 because residue number 196  < previous residue 298 
Skipped atom 1588 because residue number 196  < previous residue 298 
Skipped atom 1589 because residue number 196  < previous residue 298 
Skipped atom 1590 because residue number 196  < previous residue 298 
Skipped atom 1591 because residue number 197  < previous residue 298 
Skipped atom 1592 because residue number 197  < previous residue 298 
Skipped atom 1593 because residue number 197  < previous residue 298 
Skipped atom 1594 because residue number 197  < previous residue 298 
Skipped atom 1595 because residue number 198  < previous residue 298 
Skipped atom 1596 because residue number 198  < previous residue 298 
Skipped atom 1597 because residue number 198  < previous residue 298 
Skipped atom 1598 because residue number 198  < previous residue 298 
Skipped atom 1599 because residue number 198  < previous residue 298 
Skipped atom 1600 because residue number 198  < previous residue 298 
Skipped atom 1601 because residue number 198  < previous residue 298 
Skipped atom 1602 because residue number 198  < previous residue 298 
Skipped atom 1603 because residue number 198  < previous residue 298 
Skipped atom 1604 because residue number 199  < previous residue 298 
Skipped atom 1605 because residue number 199  < previous residue 298 
Skipped atom 1606 because residue number 199  < previous residue 298 
Skipped atom 1607 because residue number 199  < previous residue 298 
Skipped atom 1608 because residue number 199  < previous residue 298 
Skipped atom 1609 because residue number 199  < previous residue 298 
Skipped atom 1610 because residue number 199  < previous residue 298 
Skipped atom 1611 because residue number 199  < previous residue 298 
Skipped atom 1612 because residue number 200  < previous residue 298 
Skipped atom 1613 because residue number 200  < previous residue 298 
Skipped atom 1614 because residue number 200  < previous residue 298 
Skipped atom 1615 because residue number 200  < previous residue 298 
Skipped atom 1616 because residue number 200  < previous residue 298 
Skipped atom 1617 because residue number 200  < previous residue 298 
Skipped atom 1618 because residue number 201  < previous residue 298 
Skipped atom 1619 because residue number 201  < previous residue 298 
Skipped atom 1620 because residue number 201  < previous residue 298 
Skipped atom 1621 because residue number 201  < previous residue 298 
Skipped atom 1622 because residue number 201  < previous residue 298 
Skipped atom 1623 because residue number 201  < previous residue 298 
Skipped atom 1624 because residue number 201  < previous residue 298 
Skipped atom 1625 because residue number 201  < previous residue 298 
Skipped atom 1626 because residue number 201  < previous residue 298 
Skipped atom 1627 because residue number 202  < previous residue 298 
Skipped atom 1628 because residue number 202  < previous residue 298 
Skipped atom 1629 because residue number 202  < previous residue 298 
Skipped atom 1630 because residue number 202  < previous residue 298 
Skipped atom 1631 because residue number 202  < previous residue 298 
Skipped atom 1632 because residue number 202  < previous residue 298 
Skipped atom 1633 because residue number 202  < previous residue 298 
Skipped atom 1634 because residue number 202  < previous residue 298 
Skipped atom 1635 because residue number 202  < previous residue 298 
Skipped atom 1636 because residue number 203  < previous residue 298 
Skipped atom 1637 because residue number 203  < previous residue 298 
Skipped atom 1638 because residue number 203  < previous residue 298 
Skipped atom 1639 because residue number 203  < previous residue 298 
Skipped atom 1640 because residue number 203  < previous residue 298 
Skipped atom 1641 because residue number 203  < previous residue 298 
Skipped atom 1642 because residue number 203  < previous residue 298 
Skipped atom 1643 because residue number 203  < previous residue 298 
Skipped atom 1644 because residue number 204  < previous residue 298 
Skipped atom 1645 because residue number 204  < previous residue 298 
Skipped atom 1646 because residue number 204  < previous residue 298 
Skipped atom 1647 because residue number 204  < previous residue 298 
Skipped atom 1648 because residue number 204  < previous residue 298 
Skipped atom 1649 because residue number 204  < previous residue 298 
Skipped atom 1650 because residue number 204  < previous residue 298 
Skipped atom 1651 because residue number 204  < previous residue 298 
Skipped atom 1652 because residue number 204  < previous residue 298 
Skipped atom 1653 because residue number 205  < previous residue 298 
Skipped atom 1654 because residue number 205  < previous residue 298 
Skipped atom 1655 because residue number 205  < previous residue 298 
Skipped atom 1656 because residue number 205  < previous residue 298 
Skipped atom 1657 because residue number 205  < previous residue 298 
Skipped atom 1658 because residue number 205  < previous residue 298 
Skipped atom 1659 because residue number 205  < previous residue 298 
Skipped atom 1660 because residue number 205  < previous residue 298 
Skipped atom 1661 because residue number 205  < previous residue 298 
Skipped atom 1662 because residue number 206  < previous residue 298 
Skipped atom 1663 because residue number 206  < previous residue 298 
Skipped atom 1664 because residue number 206  < previous residue 298 
Skipped atom 1665 because residue number 206  < previous residue 298 
Skipped atom 1666 because residue number 206  < previous residue 298 
Skipped atom 1667 because residue number 206  < previous residue 298 
Skipped atom 1668 because residue number 206  < previous residue 298 
Skipped atom 1669 because residue number 206  < previous residue 298 
Skipped atom 1670 because residue number 206  < previous residue 298 
Skipped atom 1671 because residue number 206  < previous residue 298 
Skipped atom 1672 because residue number 206  < previous residue 298 
Skipped atom 1673 because residue number 207  < previous residue 298 
Skipped atom 1674 because residue number 207  < previous residue 298 
Skipped atom 1675 because residue number 207  < previous residue 298 
Skipped atom 1676 because residue number 207  < previous residue 298 
Skipped atom 1677 because residue number 207  < previous residue 298 
Skipped atom 1678 because residue number 207  < previous residue 298 
Skipped atom 1679 because residue number 207  < previous residue 298 
Skipped atom 1680 because residue number 207  < previous residue 298 
Skipped atom 1681 because residue number 208  < previous residue 298 
Skipped atom 1682 because residue number 208  < previous residue 298 
Skipped atom 1683 because residue number 208  < previous residue 298 
Skipped atom 1684 because residue number 208  < previous residue 298 
Skipped atom 1685 because residue number 208  < previous residue 298 
Skipped atom 1686 because residue number 208  < previous residue 298 
Skipped atom 1687 because residue number 208  < previous residue 298 
Skipped atom 1688 because residue number 208  < previous residue 298 
Skipped atom 1689 because residue number 209  < previous residue 298 
Skipped atom 1690 because residue number 209  < previous residue 298 
Skipped atom 1691 because residue number 209  < previous residue 298 
Skipped atom 1692 because residue number 209  < previous residue 298 
Skipped atom 1693 because residue number 209  < previous residue 298 
Skipped atom 1694 because residue number 209  < previous residue 298 
Skipped atom 1695 because residue number 209  < previous residue 298 
Skipped atom 1696 because residue number 209  < previous residue 298 
Skipped atom 1697 because residue number 210  < previous residue 298 
Skipped atom 1698 because residue number 210  < previous residue 298 
Skipped atom 1699 because residue number 210  < previous residue 298 
Skipped atom 1700 because residue number 210  < previous residue 298 
Skipped atom 1701 because residue number 210  < previous residue 298 
Skipped atom 1702 because residue number 210  < previous residue 298 
Skipped atom 1703 because residue number 210  < previous residue 298 
Skipped atom 1704 because residue number 210  < previous residue 298 
Skipped atom 1705 because residue number 211  < previous residue 298 
Skipped atom 1706 because residue number 211  < previous residue 298 
Skipped atom 1707 because residue number 211  < previous residue 298 
Skipped atom 1708 because residue number 211  < previous residue 298 
Skipped atom 1709 because residue number 211  < previous residue 298 
Skipped atom 1710 because residue number 211  < previous residue 298 
Skipped atom 1711 because residue number 211  < previous residue 298 
Skipped atom 1712 because residue number 211  < previous residue 298 
Skipped atom 1713 because residue number 212  < previous residue 298 
Skipped atom 1714 because residue number 212  < previous residue 298 
Skipped atom 1715 because residue number 212  < previous residue 298 
Skipped atom 1716 because residue number 212  < previous residue 298 
Skipped atom 1717 because residue number 212  < previous residue 298 
Skipped atom 1718 because residue number 212  < previous residue 298 
Skipped atom 1719 because residue number 212  < previous residue 298 
Skipped atom 1720 because residue number 212  < previous residue 298 
Skipped atom 1721 because residue number 213  < previous residue 298 
Skipped atom 1722 because residue number 213  < previous residue 298 
Skipped atom 1723 because residue number 213  < previous residue 298 
Skipped atom 1724 because residue number 213  < previous residue 298 
Skipped atom 1725 because residue number 213  < previous residue 298 
Skipped atom 1726 because residue number 213  < previous residue 298 
Skipped atom 1727 because residue number 213  < previous residue 298 
Skipped atom 1728 because residue number 213  < previous residue 298 
Skipped atom 1729 because residue number 214  < previous residue 298 
Skipped atom 1730 because residue number 214  < previous residue 298 
Skipped atom 1731 because residue number 214  < previous residue 298 
Skipped atom 1732 because residue number 214  < previous residue 298 
Skipped atom 1733 because residue number 214  < previous residue 298 
Skipped atom 1734 because residue number 214  < previous residue 298 
Skipped atom 1735 because residue number 214  < previous residue 298 
Skipped atom 1736 because residue number 214  < previous residue 298 
Skipped atom 1737 because residue number 215  < previous residue 298 
Skipped atom 1738 because residue number 215  < previous residue 298 
Skipped atom 1739 because residue number 215  < previous residue 298 
Skipped atom 1740 because residue number 215  < previous residue 298 
Skipped atom 1741 because residue number 215  < previous residue 298 
Skipped atom 1742 because residue number 215  < previous residue 298 
Skipped atom 1743 because residue number 215  < previous residue 298 
Skipped atom 1744 because residue number 215  < previous residue 298 
Skipped atom 1745 because residue number 215  < previous residue 298 
Skipped atom 1746 because residue number 216  < previous residue 298 
Skipped atom 1747 because residue number 216  < previous residue 298 
Skipped atom 1748 because residue number 216  < previous residue 298 
Skipped atom 1749 because residue number 216  < previous residue 298 
Skipped atom 1750 because residue number 216  < previous residue 298 
Skipped atom 1751 because residue number 216  < previous residue 298 
Skipped atom 1752 because residue number 217  < previous residue 298 
Skipped atom 1753 because residue number 217  < previous residue 298 
Skipped atom 1754 because residue number 217  < previous residue 298 
Skipped atom 1755 because residue number 217  < previous residue 298 
Skipped atom 1756 because residue number 218  < previous residue 298 
Skipped atom 1757 because residue number 218  < previous residue 298 
Skipped atom 1758 because residue number 218  < previous residue 298 
Skipped atom 1759 because residue number 218  < previous residue 298 
Skipped atom 1760 because residue number 218  < previous residue 298 
Skipped atom 1761 because residue number 218  < previous residue 298 
Skipped atom 1762 because residue number 218  < previous residue 298 
Skipped atom 1763 because residue number 218  < previous residue 298 
Skipped atom 1764 because residue number 219  < previous residue 298 
Skipped atom 1765 because residue number 219  < previous residue 298 
Skipped atom 1766 because residue number 219  < previous residue 298 
Skipped atom 1767 because residue number 219  < previous residue 298 
Skipped atom 1768 because residue number 219  < previous residue 298 
Skipped atom 1769 because residue number 219  < previous residue 298 
Skipped atom 1770 because residue number 219  < previous residue 298 
Skipped atom 1771 because residue number 220  < previous residue 298 
Skipped atom 1772 because residue number 220  < previous residue 298 
Skipped atom 1773 because residue number 220  < previous residue 298 
Skipped atom 1774 because residue number 220  < previous residue 298 
Skipped atom 1775 because residue number 220  < previous residue 298 
Skipped atom 1776 because residue number 220  < previous residue 298 
Skipped atom 1777 because residue number 220  < previous residue 298 
Skipped atom 1778 because residue number 220  < previous residue 298 
Skipped atom 1779 because residue number 221  < previous residue 298 
Skipped atom 1780 because residue number 221  < previous residue 298 
Skipped atom 1781 because residue number 221  < previous residue 298 
Skipped atom 1782 because residue number 221  < previous residue 298 
Skipped atom 1783 because residue number 221  < previous residue 298 
Skipped atom 1784 because residue number 221  < previous residue 298 
Skipped atom 1785 because residue number 221  < previous residue 298 
Skipped atom 1786 because residue number 221  < previous residue 298 
Skipped atom 1787 because residue number 222  < previous residue 298 
Skipped atom 1788 because residue number 222  < previous residue 298 
Skipped atom 1789 because residue number 222  < previous residue 298 
Skipped atom 1790 because residue number 222  < previous residue 298 
Skipped atom 1791 because residue number 222  < previous residue 298 
Skipped atom 1792 because residue number 222  < previous residue 298 
Skipped atom 1793 because residue number 222  < previous residue 298 
Skipped atom 1794 because residue number 222  < previous residue 298 
Skipped atom 1795 because residue number 222  < previous residue 298 
Skipped atom 1796 because residue number 223  < previous residue 298 
Skipped atom 1797 because residue number 223  < previous residue 298 
Skipped atom 1798 because residue number 223  < previous residue 298 
Skipped atom 1799 because residue number 223  < previous residue 298 
Skipped atom 1800 because residue number 223  < previous residue 298 
Skipped atom 1801 because residue number 223  < previous residue 298 
Skipped atom 1802 because residue number 223  < previous residue 298 
Skipped atom 1803 because residue number 223  < previous residue 298 
Skipped atom 1804 because residue number 224  < previous residue 298 
Skipped atom 1805 because residue number 224  < previous residue 298 
Skipped atom 1806 because residue number 224  < previous residue 298 
Skipped atom 1807 because residue number 224  < previous residue 298 
Skipped atom 1808 because residue number 225  < previous residue 298 
Skipped atom 1809 because residue number 225  < previous residue 298 
Skipped atom 1810 because residue number 225  < previous residue 298 
Skipped atom 1811 because residue number 225  < previous residue 298 
Skipped atom 1812 because residue number 225  < previous residue 298 
Skipped atom 1813 because residue number 225  < previous residue 298 
Skipped atom 1814 because residue number 225  < previous residue 298 
Skipped atom 1815 because residue number 226  < previous residue 298 
Skipped atom 1816 because residue number 226  < previous residue 298 
Skipped atom 1817 because residue number 226  < previous residue 298 
Skipped atom 1818 because residue number 226  < previous residue 298 
Skipped atom 1819 because residue number 226  < previous residue 298 
Skipped atom 1820 because residue number 226  < previous residue 298 
Skipped atom 1821 because residue number 226  < previous residue 298 
Skipped atom 1822 because residue number 227  < previous residue 298 
Skipped atom 1823 because residue number 227  < previous residue 298 
Skipped atom 1824 because residue number 227  < previous residue 298 
Skipped atom 1825 because residue number 227  < previous residue 298 
Skipped atom 1826 because residue number 227  < previous residue 298 
Skipped atom 1827 because residue number 227  < previous residue 298 
Skipped atom 1828 because residue number 228  < previous residue 298 
Skipped atom 1829 because residue number 228  < previous residue 298 
Skipped atom 1830 because residue number 228  < previous residue 298 
Skipped atom 1831 because residue number 228  < previous residue 298 
Skipped atom 1832 because residue number 228  < previous residue 298 
Skipped atom 1833 because residue number 228  < previous residue 298 
Skipped atom 1834 because residue number 228  < previous residue 298 
Skipped atom 1835 because residue number 228  < previous residue 298 
Skipped atom 1836 because residue number 229  < previous residue 298 
Skipped atom 1837 because residue number 229  < previous residue 298 
Skipped atom 1838 because residue number 229  < previous residue 298 
Skipped atom 1839 because residue number 229  < previous residue 298 
Skipped atom 1840 because residue number 229  < previous residue 298 
Skipped atom 1841 because residue number 229  < previous residue 298 
Skipped atom 1842 because residue number 229  < previous residue 298 
Skipped atom 1843 because residue number 229  < previous residue 298 
Skipped atom 1844 because residue number 229  < previous residue 298 
Skipped atom 1845 because residue number 229  < previous residue 298 
Skipped atom 1846 because residue number 229  < previous residue 298 
Skipped atom 1847 because residue number 229  < previous residue 298 
Skipped atom 1848 because residue number 230  < previous residue 298 
Skipped atom 1849 because residue number 230  < previous residue 298 
Skipped atom 1850 because residue number 230  < previous residue 298 
Skipped atom 1851 because residue number 230  < previous residue 298 
Skipped atom 1852 because residue number 230  < previous residue 298 
Skipped atom 1853 because residue number 230  < previous residue 298 
Skipped atom 1854 because residue number 230  < previous residue 298 
Skipped atom 1855 because residue number 230  < previous residue 298 
Skipped atom 1856 because residue number 230  < previous residue 298 
Skipped atom 1857 because residue number 231  < previous residue 298 
Skipped atom 1858 because residue number 231  < previous residue 298 
Skipped atom 1859 because residue number 231  < previous residue 298 
Skipped atom 1860 because residue number 231  < previous residue 298 
Skipped atom 1861 because residue number 231  < previous residue 298 
Skipped atom 1862 because residue number 231  < previous residue 298 
Skipped atom 1863 because residue number 231  < previous residue 298 
Skipped atom 1864 because residue number 232  < previous residue 298 
Skipped atom 1865 because residue number 232  < previous residue 298 
Skipped atom 1866 because residue number 232  < previous residue 298 
Skipped atom 1867 because residue number 232  < previous residue 298 
Skipped atom 1868 because residue number 232  < previous residue 298 
Skipped atom 1869 because residue number 233  < previous residue 298 
Skipped atom 1870 because residue number 233  < previous residue 298 
Skipped atom 1871 because residue number 233  < previous residue 298 
Skipped atom 1872 because residue number 233  < previous residue 298 
Skipped atom 1873 because residue number 233  < previous residue 298 
Skipped atom 1874 because residue number 233  < previous residue 298 
Skipped atom 1875 because residue number 233  < previous residue 298 
Skipped atom 1876 because residue number 233  < previous residue 298 
Skipped atom 1877 because residue number 234  < previous residue 298 
Skipped atom 1878 because residue number 234  < previous residue 298 
Skipped atom 1879 because residue number 234  < previous residue 298 
Skipped atom 1880 because residue number 234  < previous residue 298 
Skipped atom 1881 because residue number 234  < previous residue 298 
Skipped atom 1882 because residue number 234  < previous residue 298 
Skipped atom 1883 because residue number 234  < previous residue 298 
Skipped atom 1884 because residue number 234  < previous residue 298 
Skipped atom 1885 because residue number 234  < previous residue 298 
Skipped atom 1886 because residue number 235  < previous residue 298 
Skipped atom 1887 because residue number 235  < previous residue 298 
Skipped atom 1888 because residue number 235  < previous residue 298 
Skipped atom 1889 because residue number 235  < previous residue 298 
Skipped atom 1890 because residue number 235  < previous residue 298 
Skipped atom 1891 because residue number 235  < previous residue 298 
Skipped atom 1892 because residue number 236  < previous residue 298 
Skipped atom 1893 because residue number 236  < previous residue 298 
Skipped atom 1894 because residue number 236  < previous residue 298 
Skipped atom 1895 because residue number 236  < previous residue 298 
Skipped atom 1896 because residue number 237  < previous residue 298 
Skipped atom 1897 because residue number 237  < previous residue 298 
Skipped atom 1898 because residue number 237  < previous residue 298 
Skipped atom 1899 because residue number 237  < previous residue 298 
Skipped atom 1900 because residue number 237  < previous residue 298 
Skipped atom 1901 because residue number 237  < previous residue 298 
Skipped atom 1902 because residue number 237  < previous residue 298 
Skipped atom 1903 because residue number 237  < previous residue 298 
Skipped atom 1904 because residue number 237  < previous residue 298 
Skipped atom 1905 because residue number 238  < previous residue 298 
Skipped atom 1906 because residue number 238  < previous residue 298 
Skipped atom 1907 because residue number 238  < previous residue 298 
Skipped atom 1908 because residue number 238  < previous residue 298 
Skipped atom 1909 because residue number 238  < previous residue 298 
Skipped atom 1910 because residue number 239  < previous residue 298 
Skipped atom 1911 because residue number 239  < previous residue 298 
Skipped atom 1912 because residue number 239  < previous residue 298 
Skipped atom 1913 because residue number 239  < previous residue 298 
Skipped atom 1914 because residue number 239  < previous residue 298 
Skipped atom 1915 because residue number 239  < previous residue 298 
Skipped atom 1916 because residue number 239  < previous residue 298 
Skipped atom 1917 because residue number 239  < previous residue 298 
Skipped atom 1918 because residue number 240  < previous residue 298 
Skipped atom 1919 because residue number 240  < previous residue 298 
Skipped atom 1920 because residue number 240  < previous residue 298 
Skipped atom 1921 because residue number 240  < previous residue 298 
Skipped atom 1922 because residue number 240  < previous residue 298 
Skipped atom 1923 because residue number 240  < previous residue 298 
Skipped atom 1924 because residue number 240  < previous residue 298 
Skipped atom 1925 because residue number 241  < previous residue 298 
Skipped atom 1926 because residue number 241  < previous residue 298 
Skipped atom 1927 because residue number 241  < previous residue 298 
Skipped atom 1928 because residue number 241  < previous residue 298 
Skipped atom 1929 because residue number 241  < previous residue 298 
Skipped atom 1930 because residue number 241  < previous residue 298 
Skipped atom 1931 because residue number 241  < previous residue 298 
Skipped atom 1932 because residue number 241  < previous residue 298 
Skipped atom 1933 because residue number 241  < previous residue 298 
Skipped atom 1934 because residue number 241  < previous residue 298 
Skipped atom 1935 because residue number 241  < previous residue 298 
Skipped atom 1936 because residue number 241  < previous residue 298 
Skipped atom 1937 because residue number 242  < previous residue 298 
Skipped atom 1938 because residue number 242  < previous residue 298 
Skipped atom 1939 because residue number 242  < previous residue 298 
Skipped atom 1940 because residue number 242  < previous residue 298 
Skipped atom 1941 because residue number 242  < previous residue 298 
Skipped atom 1942 because residue number 243  < previous residue 298 
Skipped atom 1943 because residue number 243  < previous residue 298 
Skipped atom 1944 because residue number 243  < previous residue 298 
Skipped atom 1945 because residue number 243  < previous residue 298 
Skipped atom 1946 because residue number 243  < previous residue 298 
Skipped atom 1947 because residue number 243  < previous residue 298 
Skipped atom 1948 because residue number 244  < previous residue 298 
Skipped atom 1949 because residue number 244  < previous residue 298 
Skipped atom 1950 because residue number 244  < previous residue 298 
Skipped atom 1951 because residue number 244  < previous residue 298 
Skipped atom 1952 because residue number 244  < previous residue 298 
Skipped atom 1953 because residue number 244  < previous residue 298 
Skipped atom 1954 because residue number 244  < previous residue 298 
Skipped atom 1955 because residue number 244  < previous residue 298 
Skipped atom 1956 because residue number 244  < previous residue 298 
Skipped atom 1957 because residue number 244  < previous residue 298 
Skipped atom 1958 because residue number 244  < previous residue 298 
Skipped atom 1959 because residue number 245  < previous residue 298 
Skipped atom 1960 because residue number 245  < previous residue 298 
Skipped atom 1961 because residue number 245  < previous residue 298 
Skipped atom 1962 because residue number 245  < previous residue 298 
Skipped atom 1963 because residue number 245  < previous residue 298 
Skipped atom 1964 because residue number 245  < previous residue 298 
Skipped atom 1965 because residue number 245  < previous residue 298 
Skipped atom 1966 because residue number 245  < previous residue 298 
Skipped atom 1967 because residue number 246  < previous residue 298 
Skipped atom 1968 because residue number 246  < previous residue 298 
Skipped atom 1969 because residue number 246  < previous residue 298 
Skipped atom 1970 because residue number 246  < previous residue 298 
Skipped atom 1971 because residue number 246  < previous residue 298 
Skipped atom 1972 because residue number 246  < previous residue 298 
Skipped atom 1973 because residue number 246  < previous residue 298 
Skipped atom 1974 because residue number 246  < previous residue 298 
Skipped atom 1975 because residue number 247  < previous residue 298 
Skipped atom 1976 because residue number 247  < previous residue 298 
Skipped atom 1977 because residue number 247  < previous residue 298 
Skipped atom 1978 because residue number 247  < previous residue 298 
Skipped atom 1979 because residue number 247  < previous residue 298 
Skipped atom 1980 because residue number 247  < previous residue 298 
Skipped atom 1981 because residue number 247  < previous residue 298 
Skipped atom 1982 because residue number 248  < previous residue 298 
Skipped atom 1983 because residue number 248  < previous residue 298 
Skipped atom 1984 because residue number 248  < previous residue 298 
Skipped atom 1985 because residue number 248  < previous residue 298 
Skipped atom 1986 because residue number 248  < previous residue 298 
Skipped atom 1987 because residue number 249  < previous residue 298 
Skipped atom 1988 because residue number 249  < previous residue 298 
Skipped atom 1989 because residue number 249  < previous residue 298 
Skipped atom 1990 because residue number 249  < previous residue 298 
Skipped atom 1991 because residue number 249  < previous residue 298 
Skipped atom 1992 because residue number 249  < previous residue 298 
Skipped atom 1993 because residue number 249  < previous residue 298 
Skipped atom 1994 because residue number 249  < previous residue 298 
Skipped atom 1995 because residue number 249  < previous residue 298 
Skipped atom 1996 because residue number 249  < previous residue 298 
Skipped atom 1997 because residue number 249  < previous residue 298 
Skipped atom 1998 because residue number 250  < previous residue 298 
Skipped atom 1999 because residue number 250  < previous residue 298 
Skipped atom 2000 because residue number 250  < previous residue 298 
Skipped atom 2001 because residue number 250  < previous residue 298 
Skipped atom 2002 because residue number 250  < previous residue 298 
Skipped atom 2003 because residue number 250  < previous residue 298 
Skipped atom 2004 because residue number 250  < previous residue 298 
Skipped atom 2005 because residue number 251  < previous residue 298 
Skipped atom 2006 because residue number 251  < previous residue 298 
Skipped atom 2007 because residue number 251  < previous residue 298 
Skipped atom 2008 because residue number 251  < previous residue 298 
Skipped atom 2009 because residue number 251  < previous residue 298 
Skipped atom 2010 because residue number 251  < previous residue 298 
Skipped atom 2011 because residue number 251  < previous residue 298 
Skipped atom 2012 because residue number 251  < previous residue 298 
Skipped atom 2013 because residue number 251  < previous residue 298 
Skipped atom 2014 because residue number 251  < previous residue 298 
Skipped atom 2015 because residue number 251  < previous residue 298 
Skipped atom 2016 because residue number 251  < previous residue 298 
Skipped atom 2017 because residue number 252  < previous residue 298 
Skipped atom 2018 because residue number 252  < previous residue 298 
Skipped atom 2019 because residue number 252  < previous residue 298 
Skipped atom 2020 because residue number 252  < previous residue 298 
Skipped atom 2021 because residue number 252  < previous residue 298 
Skipped atom 2022 because residue number 252  < previous residue 298 
Skipped atom 2023 because residue number 252  < previous residue 298 
Skipped atom 2024 because residue number 253  < previous residue 298 
Skipped atom 2025 because residue number 253  < previous residue 298 
Skipped atom 2026 because residue number 253  < previous residue 298 
Skipped atom 2027 because residue number 253  < previous residue 298 
Skipped atom 2028 because residue number 253  < previous residue 298 
Skipped atom 2029 because residue number 253  < previous residue 298 
Skipped atom 2030 because residue number 253  < previous residue 298 
Skipped atom 2031 because residue number 253  < previous residue 298 
Skipped atom 2032 because residue number 253  < previous residue 298 
Skipped atom 2033 because residue number 253  < previous residue 298 
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1alq-orig.a2m
Writing a2m file: tmp/1alq-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25033


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25033/tmp -alignfile tmp/1alq-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1alq-orig.a2m (1 sequences, 266 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25033/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25033/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25033/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25033/tmp.a2m (1 sequences, 266 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25033/tmp.mod tmp/1alq-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25033 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1alq-align.mod
tmp/1alq-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25033/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1alq-orig.a2m tmp/1alq-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1alq-align.mod
Running w0.5 tmp/1alq-orig.a2m tmp/1alq-align.mod
Running align2model tmp/1alq-align -i tmp/1alq-align.mod -db tmp/1alq-orig.a2m -db tmp/1alq-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1alq.145.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1alq.146.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1alq.146.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1alq.146.1.a2m \
	-target T0124 -template 1alq \
	-out T0124-1alq.146.1 -outdir und
Skipped atom 298 because residue number 31  < previous residue 298 
Skipped atom 299 because residue number 31  < previous residue 298 
Skipped atom 300 because residue number 31  < previous residue 298 
Skipped atom 301 because residue number 31  < previous residue 298 
Skipped atom 302 because residue number 31  < previous residue 298 
Skipped atom 303 because residue number 31  < previous residue 298 
Skipped atom 304 because residue number 31  < previous residue 298 
Skipped atom 305 because residue number 31  < previous residue 298 
Skipped atom 306 because residue number 31  < previous residue 298 
Skipped atom 307 because residue number 32  < previous residue 298 
Skipped atom 308 because residue number 32  < previous residue 298 
Skipped atom 309 because residue number 32  < previous residue 298 
Skipped atom 310 because residue number 32  < previous residue 298 
Skipped atom 311 because residue number 32  < previous residue 298 
Skipped atom 312 because residue number 32  < previous residue 298 
Skipped atom 313 because residue number 32  < previous residue 298 
Skipped atom 314 because residue number 32  < previous residue 298 
Skipped atom 315 because residue number 32  < previous residue 298 
Skipped atom 316 because residue number 33  < previous residue 298 
Skipped atom 317 because residue number 33  < previous residue 298 
Skipped atom 318 because residue number 33  < previous residue 298 
Skipped atom 319 because residue number 33  < previous residue 298 
Skipped atom 320 because residue number 33  < previous residue 298 
Skipped atom 321 because residue number 33  < previous residue 298 
Skipped atom 322 because residue number 33  < previous residue 298 
Skipped atom 323 because residue number 33  < previous residue 298 
Skipped atom 324 because residue number 34  < previous residue 298 
Skipped atom 325 because residue number 34  < previous residue 298 
Skipped atom 326 because residue number 34  < previous residue 298 
Skipped atom 327 because residue number 34  < previous residue 298 
Skipped atom 328 because residue number 34  < previous residue 298 
Skipped atom 329 because residue number 34  < previous residue 298 
Skipped atom 330 because residue number 34  < previous residue 298 
Skipped atom 331 because residue number 34  < previous residue 298 
Skipped atom 332 because residue number 35  < previous residue 298 
Skipped atom 333 because residue number 35  < previous residue 298 
Skipped atom 334 because residue number 35  < previous residue 298 
Skipped atom 335 because residue number 35  < previous residue 298 
Skipped atom 336 because residue number 35  < previous residue 298 
Skipped atom 337 because residue number 35  < previous residue 298 
Skipped atom 338 because residue number 35  < previous residue 298 
Skipped atom 339 because residue number 35  < previous residue 298 
Skipped atom 340 because residue number 36  < previous residue 298 
Skipped atom 341 because residue number 36  < previous residue 298 
Skipped atom 342 because residue number 36  < previous residue 298 
Skipped atom 343 because residue number 36  < previous residue 298 
Skipped atom 344 because residue number 36  < previous residue 298 
Skipped atom 345 because residue number 36  < previous residue 298 
Skipped atom 346 because residue number 36  < previous residue 298 
Skipped atom 347 because residue number 36  < previous residue 298 
Skipped atom 348 because residue number 37  < previous residue 298 
Skipped atom 349 because residue number 37  < previous residue 298 
Skipped atom 350 because residue number 37  < previous residue 298 
Skipped atom 351 because residue number 37  < previous residue 298 
Skipped atom 352 because residue number 37  < previous residue 298 
Skipped atom 353 because residue number 37  < previous residue 298 
Skipped atom 354 because residue number 37  < previous residue 298 
Skipped atom 355 because residue number 37  < previous residue 298 
Skipped atom 356 because residue number 37  < previous residue 298 
Skipped atom 357 because residue number 38  < previous residue 298 
Skipped atom 358 because residue number 38  < previous residue 298 
Skipped atom 359 because residue number 38  < previous residue 298 
Skipped atom 360 because residue number 38  < previous residue 298 
Skipped atom 361 because residue number 38  < previous residue 298 
Skipped atom 362 because residue number 38  < previous residue 298 
Skipped atom 363 because residue number 38  < previous residue 298 
Skipped atom 364 because residue number 38  < previous residue 298 
Skipped atom 365 because residue number 38  < previous residue 298 
Skipped atom 366 because residue number 39  < previous residue 298 
Skipped atom 367 because residue number 39  < previous residue 298 
Skipped atom 368 because residue number 39  < previous residue 298 
Skipped atom 369 because residue number 39  < previous residue 298 
Skipped atom 370 because residue number 39  < previous residue 298 
Skipped atom 371 because residue number 39  < previous residue 298 
Skipped atom 372 because residue number 39  < previous residue 298 
Skipped atom 373 because residue number 39  < previous residue 298 
Skipped atom 374 because residue number 39  < previous residue 298 
Skipped atom 375 because residue number 40  < previous residue 298 
Skipped atom 376 because residue number 40  < previous residue 298 
Skipped atom 377 because residue number 40  < previous residue 298 
Skipped atom 378 because residue number 40  < previous residue 298 
Skipped atom 379 because residue number 40  < previous residue 298 
Skipped atom 380 because residue number 40  < previous residue 298 
Skipped atom 381 because residue number 40  < previous residue 298 
Skipped atom 382 because residue number 40  < previous residue 298 
Skipped atom 383 because residue number 40  < previous residue 298 
Skipped atom 384 because residue number 40  < previous residue 298 
Skipped atom 385 because residue number 40  < previous residue 298 
Skipped atom 386 because residue number 40  < previous residue 298 
Skipped atom 387 because residue number 41  < previous residue 298 
Skipped atom 388 because residue number 41  < previous residue 298 
Skipped atom 389 because residue number 41  < previous residue 298 
Skipped atom 390 because residue number 41  < previous residue 298 
Skipped atom 391 because residue number 41  < previous residue 298 
Skipped atom 392 because residue number 41  < previous residue 298 
Skipped atom 393 because residue number 41  < previous residue 298 
Skipped atom 394 because residue number 41  < previous residue 298 
Skipped atom 395 because residue number 42  < previous residue 298 
Skipped atom 396 because residue number 42  < previous residue 298 
Skipped atom 397 because residue number 42  < previous residue 298 
Skipped atom 398 because residue number 42  < previous residue 298 
Skipped atom 399 because residue number 42  < previous residue 298 
Skipped atom 400 because residue number 43  < previous residue 298 
Skipped atom 401 because residue number 43  < previous residue 298 
Skipped atom 402 because residue number 43  < previous residue 298 
Skipped atom 403 because residue number 43  < previous residue 298 
Skipped atom 404 because residue number 43  < previous residue 298 
Skipped atom 405 because residue number 43  < previous residue 298 
Skipped atom 406 because residue number 43  < previous residue 298 
Skipped atom 407 because residue number 43  < previous residue 298 
Skipped atom 408 because residue number 43  < previous residue 298 
Skipped atom 409 because residue number 43  < previous residue 298 
Skipped atom 410 because residue number 44  < previous residue 298 
Skipped atom 411 because residue number 44  < previous residue 298 
Skipped atom 412 because residue number 44  < previous residue 298 
Skipped atom 413 because residue number 44  < previous residue 298 
Skipped atom 414 because residue number 44  < previous residue 298 
Skipped atom 415 because residue number 44  < previous residue 298 
Skipped atom 416 because residue number 44  < previous residue 298 
Skipped atom 417 because residue number 44  < previous residue 298 
Skipped atom 418 because residue number 45  < previous residue 298 
Skipped atom 419 because residue number 45  < previous residue 298 
Skipped atom 420 because residue number 45  < previous residue 298 
Skipped atom 421 because residue number 45  < previous residue 298 
Skipped atom 422 because residue number 46  < previous residue 298 
Skipped atom 423 because residue number 46  < previous residue 298 
Skipped atom 424 because residue number 46  < previous residue 298 
Skipped atom 425 because residue number 46  < previous residue 298 
Skipped atom 426 because residue number 46  < previous residue 298 
Skipped atom 427 because residue number 46  < previous residue 298 
Skipped atom 428 because residue number 46  < previous residue 298 
Skipped atom 429 because residue number 47  < previous residue 298 
Skipped atom 430 because residue number 47  < previous residue 298 
Skipped atom 431 because residue number 47  < previous residue 298 
Skipped atom 432 because residue number 47  < previous residue 298 
Skipped atom 433 because residue number 47  < previous residue 298 
Skipped atom 434 because residue number 47  < previous residue 298 
Skipped atom 435 because residue number 47  < previous residue 298 
Skipped atom 436 because residue number 47  < previous residue 298 
Skipped atom 437 because residue number 47  < previous residue 298 
Skipped atom 438 because residue number 47  < previous residue 298 
Skipped atom 439 because residue number 47  < previous residue 298 
Skipped atom 440 because residue number 47  < previous residue 298 
Skipped atom 441 because residue number 48  < previous residue 298 
Skipped atom 442 because residue number 48  < previous residue 298 
Skipped atom 443 because residue number 48  < previous residue 298 
Skipped atom 444 because residue number 48  < previous residue 298 
Skipped atom 445 because residue number 48  < previous residue 298 
Skipped atom 446 because residue number 49  < previous residue 298 
Skipped atom 447 because residue number 49  < previous residue 298 
Skipped atom 448 because residue number 49  < previous residue 298 
Skipped atom 449 because residue number 49  < previous residue 298 
Skipped atom 450 because residue number 49  < previous residue 298 
Skipped atom 451 because residue number 49  < previous residue 298 
Skipped atom 452 because residue number 49  < previous residue 298 
Skipped atom 453 because residue number 49  < previous residue 298 
Skipped atom 454 because residue number 50  < previous residue 298 
Skipped atom 455 because residue number 50  < previous residue 298 
Skipped atom 456 because residue number 50  < previous residue 298 
Skipped atom 457 because residue number 50  < previous residue 298 
Skipped atom 458 because residue number 50  < previous residue 298 
Skipped atom 459 because residue number 50  < previous residue 298 
Skipped atom 460 because residue number 50  < previous residue 298 
Skipped atom 461 because residue number 50  < previous residue 298 
Skipped atom 462 because residue number 51  < previous residue 298 
Skipped atom 463 because residue number 51  < previous residue 298 
Skipped atom 464 because residue number 51  < previous residue 298 
Skipped atom 465 because residue number 51  < previous residue 298 
Skipped atom 466 because residue number 51  < previous residue 298 
Skipped atom 467 because residue number 51  < previous residue 298 
Skipped atom 468 because residue number 51  < previous residue 298 
Skipped atom 469 because residue number 52  < previous residue 298 
Skipped atom 470 because residue number 52  < previous residue 298 
Skipped atom 471 because residue number 52  < previous residue 298 
Skipped atom 472 because residue number 52  < previous residue 298 
Skipped atom 473 because residue number 52  < previous residue 298 
Skipped atom 474 because residue number 52  < previous residue 298 
Skipped atom 475 because residue number 52  < previous residue 298 
Skipped atom 476 because residue number 52  < previous residue 298 
Skipped atom 477 because residue number 52  < previous residue 298 
Skipped atom 478 because residue number 53  < previous residue 298 
Skipped atom 479 because residue number 53  < previous residue 298 
Skipped atom 480 because residue number 53  < previous residue 298 
Skipped atom 481 because residue number 53  < previous residue 298 
Skipped atom 482 because residue number 53  < previous residue 298 
Skipped atom 483 because residue number 53  < previous residue 298 
Skipped atom 484 because residue number 54  < previous residue 298 
Skipped atom 485 because residue number 54  < previous residue 298 
Skipped atom 486 because residue number 54  < previous residue 298 
Skipped atom 487 because residue number 54  < previous residue 298 
Skipped atom 488 because residue number 55  < previous residue 298 
Skipped atom 489 because residue number 55  < previous residue 298 
Skipped atom 490 because residue number 55  < previous residue 298 
Skipped atom 491 because residue number 55  < previous residue 298 
Skipped atom 492 because residue number 55  < previous residue 298 
Skipped atom 493 because residue number 55  < previous residue 298 
Skipped atom 494 because residue number 55  < previous residue 298 
Skipped atom 495 because residue number 55  < previous residue 298 
Skipped atom 496 because residue number 55  < previous residue 298 
Skipped atom 497 because residue number 56  < previous residue 298 
Skipped atom 498 because residue number 56  < previous residue 298 
Skipped atom 499 because residue number 56  < previous residue 298 
Skipped atom 500 because residue number 56  < previous residue 298 
Skipped atom 501 because residue number 56  < previous residue 298 
Skipped atom 502 because residue number 56  < previous residue 298 
Skipped atom 503 because residue number 56  < previous residue 298 
Skipped atom 504 because residue number 56  < previous residue 298 
Skipped atom 505 because residue number 56  < previous residue 298 
Skipped atom 506 because residue number 57  < previous residue 298 
Skipped atom 507 because residue number 57  < previous residue 298 
Skipped atom 508 because residue number 57  < previous residue 298 
Skipped atom 509 because residue number 57  < previous residue 298 
Skipped atom 510 because residue number 57  < previous residue 298 
Skipped atom 511 because residue number 57  < previous residue 298 
Skipped atom 512 because residue number 57  < previous residue 298 
Skipped atom 513 because residue number 59  < previous residue 298 
Skipped atom 514 because residue number 59  < previous residue 298 
Skipped atom 515 because residue number 59  < previous residue 298 
Skipped atom 516 because residue number 59  < previous residue 298 
Skipped atom 517 because residue number 59  < previous residue 298 
Skipped atom 518 because residue number 59  < previous residue 298 
Skipped atom 519 because residue number 59  < previous residue 298 
Skipped atom 520 because residue number 59  < previous residue 298 
Skipped atom 521 because residue number 59  < previous residue 298 
Skipped atom 522 because residue number 60  < previous residue 298 
Skipped atom 523 because residue number 60  < previous residue 298 
Skipped atom 524 because residue number 60  < previous residue 298 
Skipped atom 525 because residue number 60  < previous residue 298 
Skipped atom 526 because residue number 60  < previous residue 298 
Skipped atom 527 because residue number 60  < previous residue 298 
Skipped atom 528 because residue number 60  < previous residue 298 
Skipped atom 529 because residue number 60  < previous residue 298 
Skipped atom 530 because residue number 60  < previous residue 298 
Skipped atom 531 because residue number 60  < previous residue 298 
Skipped atom 532 because residue number 60  < previous residue 298 
Skipped atom 533 because residue number 61  < previous residue 298 
Skipped atom 534 because residue number 61  < previous residue 298 
Skipped atom 535 because residue number 61  < previous residue 298 
Skipped atom 536 because residue number 61  < previous residue 298 
Skipped atom 537 because residue number 61  < previous residue 298 
Skipped atom 538 because residue number 61  < previous residue 298 
Skipped atom 539 because residue number 61  < previous residue 298 
Skipped atom 540 because residue number 61  < previous residue 298 
Skipped atom 541 because residue number 62  < previous residue 298 
Skipped atom 542 because residue number 62  < previous residue 298 
Skipped atom 543 because residue number 62  < previous residue 298 
Skipped atom 544 because residue number 62  < previous residue 298 
Skipped atom 545 because residue number 62  < previous residue 298 
Skipped atom 546 because residue number 62  < previous residue 298 
Skipped atom 547 because residue number 63  < previous residue 298 
Skipped atom 548 because residue number 63  < previous residue 298 
Skipped atom 549 because residue number 63  < previous residue 298 
Skipped atom 550 because residue number 63  < previous residue 298 
Skipped atom 551 because residue number 63  < previous residue 298 
Skipped atom 552 because residue number 63  < previous residue 298 
Skipped atom 553 because residue number 63  < previous residue 298 
Skipped atom 554 because residue number 63  < previous residue 298 
Skipped atom 555 because residue number 64  < previous residue 298 
Skipped atom 556 because residue number 64  < previous residue 298 
Skipped atom 557 because residue number 64  < previous residue 298 
Skipped atom 558 because residue number 64  < previous residue 298 
Skipped atom 559 because residue number 64  < previous residue 298 
Skipped atom 560 because residue number 64  < previous residue 298 
Skipped atom 561 because residue number 64  < previous residue 298 
Skipped atom 562 because residue number 64  < previous residue 298 
Skipped atom 563 because residue number 64  < previous residue 298 
Skipped atom 564 because residue number 65  < previous residue 298 
Skipped atom 565 because residue number 65  < previous residue 298 
Skipped atom 566 because residue number 65  < previous residue 298 
Skipped atom 567 because residue number 65  < previous residue 298 
Skipped atom 568 because residue number 65  < previous residue 298 
Skipped atom 569 because residue number 65  < previous residue 298 
Skipped atom 570 because residue number 65  < previous residue 298 
Skipped atom 571 because residue number 65  < previous residue 298 
Skipped atom 572 because residue number 65  < previous residue 298 
Skipped atom 573 because residue number 65  < previous residue 298 
Skipped atom 574 because residue number 65  < previous residue 298 
Skipped atom 575 because residue number 66  < previous residue 298 
Skipped atom 576 because residue number 66  < previous residue 298 
Skipped atom 577 because residue number 66  < previous residue 298 
Skipped atom 578 because residue number 66  < previous residue 298 
Skipped atom 579 because residue number 66  < previous residue 298 
Skipped atom 580 because residue number 66  < previous residue 298 
Skipped atom 581 because residue number 66  < previous residue 298 
Skipped atom 582 because residue number 66  < previous residue 298 
Skipped atom 583 because residue number 66  < previous residue 298 
Skipped atom 584 because residue number 66  < previous residue 298 
Skipped atom 585 because residue number 66  < previous residue 298 
Skipped atom 586 because residue number 67  < previous residue 298 
Skipped atom 587 because residue number 67  < previous residue 298 
Skipped atom 588 because residue number 67  < previous residue 298 
Skipped atom 589 because residue number 67  < previous residue 298 
Skipped atom 590 because residue number 67  < previous residue 298 
Skipped atom 591 because residue number 68  < previous residue 298 
Skipped atom 592 because residue number 68  < previous residue 298 
Skipped atom 593 because residue number 68  < previous residue 298 
Skipped atom 594 because residue number 68  < previous residue 298 
Skipped atom 595 because residue number 68  < previous residue 298 
Skipped atom 596 because residue number 68  < previous residue 298 
Skipped atom 597 because residue number 68  < previous residue 298 
Skipped atom 598 because residue number 68  < previous residue 298 
Skipped atom 599 because residue number 68  < previous residue 298 
Skipped atom 600 because residue number 68  < previous residue 298 
Skipped atom 601 because residue number 68  < previous residue 298 
Skipped atom 602 because residue number 68  < previous residue 298 
Skipped atom 603 because residue number 69  < previous residue 298 
Skipped atom 604 because residue number 69  < previous residue 298 
Skipped atom 605 because residue number 69  < previous residue 298 
Skipped atom 606 because residue number 69  < previous residue 298 
Skipped atom 607 because residue number 69  < previous residue 298 
Skipped atom 608 because residue number 70  < previous residue 298 
Skipped atom 609 because residue number 70  < previous residue 298 
Skipped atom 610 because residue number 70  < previous residue 298 
Skipped atom 611 because residue number 70  < previous residue 298 
Skipped atom 612 because residue number 70  < previous residue 298 
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Skipped atom 614 because residue number 71  < previous residue 298 
Skipped atom 615 because residue number 71  < previous residue 298 
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Skipped atom 617 because residue number 71  < previous residue 298 
Skipped atom 618 because residue number 71  < previous residue 298 
Skipped atom 619 because residue number 71  < previous residue 298 
Skipped atom 620 because residue number 71  < previous residue 298 
Skipped atom 621 because residue number 72  < previous residue 298 
Skipped atom 622 because residue number 72  < previous residue 298 
Skipped atom 623 because residue number 72  < previous residue 298 
Skipped atom 624 because residue number 72  < previous residue 298 
Skipped atom 625 because residue number 72  < previous residue 298 
Skipped atom 626 because residue number 72  < previous residue 298 
Skipped atom 627 because residue number 73  < previous residue 298 
Skipped atom 628 because residue number 73  < previous residue 298 
Skipped atom 629 because residue number 73  < previous residue 298 
Skipped atom 630 because residue number 73  < previous residue 298 
Skipped atom 631 because residue number 73  < previous residue 298 
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Skipped atom 633 because residue number 73  < previous residue 298 
Skipped atom 634 because residue number 73  < previous residue 298 
Skipped atom 635 because residue number 73  < previous residue 298 
Skipped atom 636 because residue number 74  < previous residue 298 
Skipped atom 637 because residue number 74  < previous residue 298 
Skipped atom 638 because residue number 74  < previous residue 298 
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Skipped atom 640 because residue number 74  < previous residue 298 
Skipped atom 641 because residue number 75  < previous residue 298 
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Skipped atom 643 because residue number 75  < previous residue 298 
Skipped atom 644 because residue number 75  < previous residue 298 
Skipped atom 645 because residue number 75  < previous residue 298 
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Skipped atom 649 because residue number 76  < previous residue 298 
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Skipped atom 651 because residue number 76  < previous residue 298 
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Skipped atom 676 because residue number 80  < previous residue 298 
Skipped atom 677 because residue number 80  < previous residue 298 
Skipped atom 678 because residue number 80  < previous residue 298 
Skipped atom 679 because residue number 80  < previous residue 298 
Skipped atom 680 because residue number 80  < previous residue 298 
Skipped atom 681 because residue number 80  < previous residue 298 
Skipped atom 682 because residue number 80  < previous residue 298 
Skipped atom 683 because residue number 80  < previous residue 298 
Skipped atom 684 because residue number 81  < previous residue 298 
Skipped atom 685 because residue number 81  < previous residue 298 
Skipped atom 686 because residue number 81  < previous residue 298 
Skipped atom 687 because residue number 81  < previous residue 298 
Skipped atom 688 because residue number 81  < previous residue 298 
Skipped atom 689 because residue number 81  < previous residue 298 
Skipped atom 690 because residue number 81  < previous residue 298 
Skipped atom 691 because residue number 81  < previous residue 298 
Skipped atom 692 because residue number 82  < previous residue 298 
Skipped atom 693 because residue number 82  < previous residue 298 
Skipped atom 694 because residue number 82  < previous residue 298 
Skipped atom 695 because residue number 82  < previous residue 298 
Skipped atom 696 because residue number 82  < previous residue 298 
Skipped atom 697 because residue number 82  < previous residue 298 
Skipped atom 698 because residue number 82  < previous residue 298 
Skipped atom 699 because residue number 82  < previous residue 298 
Skipped atom 700 because residue number 82  < previous residue 298 
Skipped atom 701 because residue number 83  < previous residue 298 
Skipped atom 702 because residue number 83  < previous residue 298 
Skipped atom 703 because residue number 83  < previous residue 298 
Skipped atom 704 because residue number 83  < previous residue 298 
Skipped atom 705 because residue number 83  < previous residue 298 
Skipped atom 706 because residue number 83  < previous residue 298 
Skipped atom 707 because residue number 83  < previous residue 298 
Skipped atom 708 because residue number 83  < previous residue 298 
Skipped atom 709 because residue number 83  < previous residue 298 
Skipped atom 710 because residue number 84  < previous residue 298 
Skipped atom 711 because residue number 84  < previous residue 298 
Skipped atom 712 because residue number 84  < previous residue 298 
Skipped atom 713 because residue number 84  < previous residue 298 
Skipped atom 714 because residue number 84  < previous residue 298 
Skipped atom 715 because residue number 84  < previous residue 298 
Skipped atom 716 because residue number 84  < previous residue 298 
Skipped atom 717 because residue number 87  < previous residue 298 
Skipped atom 718 because residue number 87  < previous residue 298 
Skipped atom 719 because residue number 87  < previous residue 298 
Skipped atom 720 because residue number 87  < previous residue 298 
Skipped atom 721 because residue number 87  < previous residue 298 
Skipped atom 722 because residue number 87  < previous residue 298 
Skipped atom 723 because residue number 87  < previous residue 298 
Skipped atom 724 because residue number 88  < previous residue 298 
Skipped atom 725 because residue number 88  < previous residue 298 
Skipped atom 726 because residue number 88  < previous residue 298 
Skipped atom 727 because residue number 88  < previous residue 298 
Skipped atom 728 because residue number 88  < previous residue 298 
Skipped atom 729 because residue number 88  < previous residue 298 
Skipped atom 730 because residue number 88  < previous residue 298 
Skipped atom 731 because residue number 88  < previous residue 298 
Skipped atom 732 because residue number 88  < previous residue 298 
Skipped atom 733 because residue number 88  < previous residue 298 
Skipped atom 734 because residue number 88  < previous residue 298 
Skipped atom 735 because residue number 88  < previous residue 298 
Skipped atom 736 because residue number 89  < previous residue 298 
Skipped atom 737 because residue number 89  < previous residue 298 
Skipped atom 738 because residue number 89  < previous residue 298 
Skipped atom 739 because residue number 89  < previous residue 298 
Skipped atom 740 because residue number 89  < previous residue 298 
Skipped atom 741 because residue number 89  < previous residue 298 
Skipped atom 742 because residue number 89  < previous residue 298 
Skipped atom 743 because residue number 89  < previous residue 298 
Skipped atom 744 because residue number 90  < previous residue 298 
Skipped atom 745 because residue number 90  < previous residue 298 
Skipped atom 746 because residue number 90  < previous residue 298 
Skipped atom 747 because residue number 90  < previous residue 298 
Skipped atom 748 because residue number 90  < previous residue 298 
Skipped atom 749 because residue number 90  < previous residue 298 
Skipped atom 750 because residue number 90  < previous residue 298 
Skipped atom 751 because residue number 90  < previous residue 298 
Skipped atom 752 because residue number 90  < previous residue 298 
Skipped atom 753 because residue number 91  < previous residue 298 
Skipped atom 754 because residue number 91  < previous residue 298 
Skipped atom 755 because residue number 91  < previous residue 298 
Skipped atom 756 because residue number 91  < previous residue 298 
Skipped atom 757 because residue number 91  < previous residue 298 
Skipped atom 758 because residue number 91  < previous residue 298 
Skipped atom 759 because residue number 91  < previous residue 298 
Skipped atom 760 because residue number 91  < previous residue 298 
Skipped atom 761 because residue number 92  < previous residue 298 
Skipped atom 762 because residue number 92  < previous residue 298 
Skipped atom 763 because residue number 92  < previous residue 298 
Skipped atom 764 because residue number 92  < previous residue 298 
Skipped atom 765 because residue number 92  < previous residue 298 
Skipped atom 766 because residue number 92  < previous residue 298 
Skipped atom 767 because residue number 92  < previous residue 298 
Skipped atom 768 because residue number 92  < previous residue 298 
Skipped atom 769 because residue number 93  < previous residue 298 
Skipped atom 770 because residue number 93  < previous residue 298 
Skipped atom 771 because residue number 93  < previous residue 298 
Skipped atom 772 because residue number 93  < previous residue 298 
Skipped atom 773 because residue number 93  < previous residue 298 
Skipped atom 774 because residue number 93  < previous residue 298 
Skipped atom 775 because residue number 93  < previous residue 298 
Skipped atom 776 because residue number 93  < previous residue 298 
Skipped atom 777 because residue number 93  < previous residue 298 
Skipped atom 778 because residue number 94  < previous residue 298 
Skipped atom 779 because residue number 94  < previous residue 298 
Skipped atom 780 because residue number 94  < previous residue 298 
Skipped atom 781 because residue number 94  < previous residue 298 
Skipped atom 782 because residue number 94  < previous residue 298 
Skipped atom 783 because residue number 94  < previous residue 298 
Skipped atom 784 because residue number 94  < previous residue 298 
Skipped atom 785 because residue number 94  < previous residue 298 
Skipped atom 786 because residue number 94  < previous residue 298 
Skipped atom 787 because residue number 95  < previous residue 298 
Skipped atom 788 because residue number 95  < previous residue 298 
Skipped atom 789 because residue number 95  < previous residue 298 
Skipped atom 790 because residue number 95  < previous residue 298 
Skipped atom 791 because residue number 95  < previous residue 298 
Skipped atom 792 because residue number 95  < previous residue 298 
Skipped atom 793 because residue number 95  < previous residue 298 
Skipped atom 794 because residue number 96  < previous residue 298 
Skipped atom 795 because residue number 96  < previous residue 298 
Skipped atom 796 because residue number 96  < previous residue 298 
Skipped atom 797 because residue number 96  < previous residue 298 
Skipped atom 798 because residue number 96  < previous residue 298 
Skipped atom 799 because residue number 96  < previous residue 298 
Skipped atom 800 because residue number 96  < previous residue 298 
Skipped atom 801 because residue number 96  < previous residue 298 
Skipped atom 802 because residue number 96  < previous residue 298 
Skipped atom 803 because residue number 96  < previous residue 298 
Skipped atom 804 because residue number 97  < previous residue 298 
Skipped atom 805 because residue number 97  < previous residue 298 
Skipped atom 806 because residue number 97  < previous residue 298 
Skipped atom 807 because residue number 97  < previous residue 298 
Skipped atom 808 because residue number 97  < previous residue 298 
Skipped atom 809 because residue number 97  < previous residue 298 
Skipped atom 810 because residue number 97  < previous residue 298 
Skipped atom 811 because residue number 97  < previous residue 298 
Skipped atom 812 because residue number 98  < previous residue 298 
Skipped atom 813 because residue number 98  < previous residue 298 
Skipped atom 814 because residue number 98  < previous residue 298 
Skipped atom 815 because residue number 98  < previous residue 298 
Skipped atom 816 because residue number 98  < previous residue 298 
Skipped atom 817 because residue number 98  < previous residue 298 
Skipped atom 818 because residue number 98  < previous residue 298 
Skipped atom 819 because residue number 98  < previous residue 298 
Skipped atom 820 because residue number 99  < previous residue 298 
Skipped atom 821 because residue number 99  < previous residue 298 
Skipped atom 822 because residue number 99  < previous residue 298 
Skipped atom 823 because residue number 99  < previous residue 298 
Skipped atom 824 because residue number 99  < previous residue 298 
Skipped atom 825 because residue number 99  < previous residue 298 
Skipped atom 826 because residue number 99  < previous residue 298 
Skipped atom 827 because residue number 99  < previous residue 298 
Skipped atom 828 because residue number 99  < previous residue 298 
Skipped atom 829 because residue number 100  < previous residue 298 
Skipped atom 830 because residue number 100  < previous residue 298 
Skipped atom 831 because residue number 100  < previous residue 298 
Skipped atom 832 because residue number 100  < previous residue 298 
Skipped atom 833 because residue number 100  < previous residue 298 
Skipped atom 834 because residue number 100  < previous residue 298 
Skipped atom 835 because residue number 100  < previous residue 298 
Skipped atom 836 because residue number 100  < previous residue 298 
Skipped atom 837 because residue number 101  < previous residue 298 
Skipped atom 838 because residue number 101  < previous residue 298 
Skipped atom 839 because residue number 101  < previous residue 298 
Skipped atom 840 because residue number 101  < previous residue 298 
Skipped atom 841 because residue number 101  < previous residue 298 
Skipped atom 842 because residue number 101  < previous residue 298 
Skipped atom 843 because residue number 101  < previous residue 298 
Skipped atom 844 because residue number 101  < previous residue 298 
Skipped atom 845 because residue number 102  < previous residue 298 
Skipped atom 846 because residue number 102  < previous residue 298 
Skipped atom 847 because residue number 102  < previous residue 298 
Skipped atom 848 because residue number 102  < previous residue 298 
Skipped atom 849 because residue number 102  < previous residue 298 
Skipped atom 850 because residue number 102  < previous residue 298 
Skipped atom 851 because residue number 102  < previous residue 298 
Skipped atom 852 because residue number 102  < previous residue 298 
Skipped atom 853 because residue number 103  < previous residue 298 
Skipped atom 854 because residue number 103  < previous residue 298 
Skipped atom 855 because residue number 103  < previous residue 298 
Skipped atom 856 because residue number 103  < previous residue 298 
Skipped atom 857 because residue number 103  < previous residue 298 
Skipped atom 858 because residue number 103  < previous residue 298 
Skipped atom 859 because residue number 103  < previous residue 298 
Skipped atom 860 because residue number 104  < previous residue 298 
Skipped atom 861 because residue number 104  < previous residue 298 
Skipped atom 862 because residue number 104  < previous residue 298 
Skipped atom 863 because residue number 104  < previous residue 298 
Skipped atom 864 because residue number 104  < previous residue 298 
Skipped atom 865 because residue number 105  < previous residue 298 
Skipped atom 866 because residue number 105  < previous residue 298 
Skipped atom 867 because residue number 105  < previous residue 298 
Skipped atom 868 because residue number 105  < previous residue 298 
Skipped atom 869 because residue number 105  < previous residue 298 
Skipped atom 870 because residue number 105  < previous residue 298 
Skipped atom 871 because residue number 105  < previous residue 298 
Skipped atom 872 because residue number 105  < previous residue 298 
Skipped atom 873 because residue number 105  < previous residue 298 
Skipped atom 874 because residue number 105  < previous residue 298 
Skipped atom 875 because residue number 105  < previous residue 298 
Skipped atom 876 because residue number 105  < previous residue 298 
Skipped atom 877 because residue number 106  < previous residue 298 
Skipped atom 878 because residue number 106  < previous residue 298 
Skipped atom 879 because residue number 106  < previous residue 298 
Skipped atom 880 because residue number 106  < previous residue 298 
Skipped atom 881 because residue number 106  < previous residue 298 
Skipped atom 882 because residue number 106  < previous residue 298 
Skipped atom 883 because residue number 107  < previous residue 298 
Skipped atom 884 because residue number 107  < previous residue 298 
Skipped atom 885 because residue number 107  < previous residue 298 
Skipped atom 886 because residue number 107  < previous residue 298 
Skipped atom 887 because residue number 107  < previous residue 298 
Skipped atom 888 because residue number 107  < previous residue 298 
Skipped atom 889 because residue number 107  < previous residue 298 
Skipped atom 890 because residue number 108  < previous residue 298 
Skipped atom 891 because residue number 108  < previous residue 298 
Skipped atom 892 because residue number 108  < previous residue 298 
Skipped atom 893 because residue number 108  < previous residue 298 
Skipped atom 894 because residue number 108  < previous residue 298 
Skipped atom 895 because residue number 108  < previous residue 298 
Skipped atom 896 because residue number 108  < previous residue 298 
Skipped atom 897 because residue number 108  < previous residue 298 
Skipped atom 898 because residue number 109  < previous residue 298 
Skipped atom 899 because residue number 109  < previous residue 298 
Skipped atom 900 because residue number 109  < previous residue 298 
Skipped atom 901 because residue number 109  < previous residue 298 
Skipped atom 902 because residue number 109  < previous residue 298 
Skipped atom 903 because residue number 109  < previous residue 298 
Skipped atom 904 because residue number 109  < previous residue 298 
Skipped atom 905 because residue number 109  < previous residue 298 
Skipped atom 906 because residue number 110  < previous residue 298 
Skipped atom 907 because residue number 110  < previous residue 298 
Skipped atom 908 because residue number 110  < previous residue 298 
Skipped atom 909 because residue number 110  < previous residue 298 
Skipped atom 910 because residue number 110  < previous residue 298 
Skipped atom 911 because residue number 110  < previous residue 298 
Skipped atom 912 because residue number 110  < previous residue 298 
Skipped atom 913 because residue number 110  < previous residue 298 
Skipped atom 914 because residue number 110  < previous residue 298 
Skipped atom 915 because residue number 111  < previous residue 298 
Skipped atom 916 because residue number 111  < previous residue 298 
Skipped atom 917 because residue number 111  < previous residue 298 
Skipped atom 918 because residue number 111  < previous residue 298 
Skipped atom 919 because residue number 111  < previous residue 298 
Skipped atom 920 because residue number 111  < previous residue 298 
Skipped atom 921 because residue number 111  < previous residue 298 
Skipped atom 922 because residue number 111  < previous residue 298 
Skipped atom 923 because residue number 111  < previous residue 298 
Skipped atom 924 because residue number 112  < previous residue 298 
Skipped atom 925 because residue number 112  < previous residue 298 
Skipped atom 926 because residue number 112  < previous residue 298 
Skipped atom 927 because residue number 112  < previous residue 298 
Skipped atom 928 because residue number 112  < previous residue 298 
Skipped atom 929 because residue number 112  < previous residue 298 
Skipped atom 930 because residue number 112  < previous residue 298 
Skipped atom 931 because residue number 112  < previous residue 298 
Skipped atom 932 because residue number 112  < previous residue 298 
Skipped atom 933 because residue number 112  < previous residue 298 
Skipped atom 934 because residue number 112  < previous residue 298 
Skipped atom 935 because residue number 112  < previous residue 298 
Skipped atom 936 because residue number 113  < previous residue 298 
Skipped atom 937 because residue number 113  < previous residue 298 
Skipped atom 938 because residue number 113  < previous residue 298 
Skipped atom 939 because residue number 113  < previous residue 298 
Skipped atom 940 because residue number 113  < previous residue 298 
Skipped atom 941 because residue number 113  < previous residue 298 
Skipped atom 942 because residue number 113  < previous residue 298 
Skipped atom 943 because residue number 114  < previous residue 298 
Skipped atom 944 because residue number 114  < previous residue 298 
Skipped atom 945 because residue number 114  < previous residue 298 
Skipped atom 946 because residue number 114  < previous residue 298 
Skipped atom 947 because residue number 115  < previous residue 298 
Skipped atom 948 because residue number 115  < previous residue 298 
Skipped atom 949 because residue number 115  < previous residue 298 
Skipped atom 950 because residue number 115  < previous residue 298 
Skipped atom 951 because residue number 115  < previous residue 298 
Skipped atom 952 because residue number 115  < previous residue 298 
Skipped atom 953 because residue number 115  < previous residue 298 
Skipped atom 954 because residue number 115  < previous residue 298 
Skipped atom 955 because residue number 115  < previous residue 298 
Skipped atom 956 because residue number 116  < previous residue 298 
Skipped atom 957 because residue number 116  < previous residue 298 
Skipped atom 958 because residue number 116  < previous residue 298 
Skipped atom 959 because residue number 116  < previous residue 298 
Skipped atom 960 because residue number 116  < previous residue 298 
Skipped atom 961 because residue number 116  < previous residue 298 
Skipped atom 962 because residue number 116  < previous residue 298 
Skipped atom 963 because residue number 116  < previous residue 298 
Skipped atom 964 because residue number 117  < previous residue 298 
Skipped atom 965 because residue number 117  < previous residue 298 
Skipped atom 966 because residue number 117  < previous residue 298 
Skipped atom 967 because residue number 117  < previous residue 298 
Skipped atom 968 because residue number 117  < previous residue 298 
Skipped atom 969 because residue number 117  < previous residue 298 
Skipped atom 970 because residue number 117  < previous residue 298 
Skipped atom 971 because residue number 117  < previous residue 298 
Skipped atom 972 because residue number 118  < previous residue 298 
Skipped atom 973 because residue number 118  < previous residue 298 
Skipped atom 974 because residue number 118  < previous residue 298 
Skipped atom 975 because residue number 118  < previous residue 298 
Skipped atom 976 because residue number 118  < previous residue 298 
Skipped atom 977 because residue number 118  < previous residue 298 
Skipped atom 978 because residue number 118  < previous residue 298 
Skipped atom 979 because residue number 119  < previous residue 298 
Skipped atom 980 because residue number 119  < previous residue 298 
Skipped atom 981 because residue number 119  < previous residue 298 
Skipped atom 982 because residue number 119  < previous residue 298 
Skipped atom 983 because residue number 119  < previous residue 298 
Skipped atom 984 because residue number 119  < previous residue 298 
Skipped atom 985 because residue number 119  < previous residue 298 
Skipped atom 986 because residue number 119  < previous residue 298 
Skipped atom 987 because residue number 120  < previous residue 298 
Skipped atom 988 because residue number 120  < previous residue 298 
Skipped atom 989 because residue number 120  < previous residue 298 
Skipped atom 990 because residue number 120  < previous residue 298 
Skipped atom 991 because residue number 120  < previous residue 298 
Skipped atom 992 because residue number 120  < previous residue 298 
Skipped atom 993 because residue number 120  < previous residue 298 
Skipped atom 994 because residue number 120  < previous residue 298 
Skipped atom 995 because residue number 120  < previous residue 298 
Skipped atom 996 because residue number 121  < previous residue 298 
Skipped atom 997 because residue number 121  < previous residue 298 
Skipped atom 998 because residue number 121  < previous residue 298 
Skipped atom 999 because residue number 121  < previous residue 298 
Skipped atom 1000 because residue number 121  < previous residue 298 
Skipped atom 1001 because residue number 122  < previous residue 298 
Skipped atom 1002 because residue number 122  < previous residue 298 
Skipped atom 1003 because residue number 122  < previous residue 298 
Skipped atom 1004 because residue number 122  < previous residue 298 
Skipped atom 1005 because residue number 122  < previous residue 298 
Skipped atom 1006 because residue number 122  < previous residue 298 
Skipped atom 1007 because residue number 122  < previous residue 298 
Skipped atom 1008 because residue number 122  < previous residue 298 
Skipped atom 1009 because residue number 123  < previous residue 298 
Skipped atom 1010 because residue number 123  < previous residue 298 
Skipped atom 1011 because residue number 123  < previous residue 298 
Skipped atom 1012 because residue number 123  < previous residue 298 
Skipped atom 1013 because residue number 123  < previous residue 298 
Skipped atom 1014 because residue number 123  < previous residue 298 
Skipped atom 1015 because residue number 123  < previous residue 298 
Skipped atom 1016 because residue number 123  < previous residue 298 
Skipped atom 1017 because residue number 124  < previous residue 298 
Skipped atom 1018 because residue number 124  < previous residue 298 
Skipped atom 1019 because residue number 124  < previous residue 298 
Skipped atom 1020 because residue number 124  < previous residue 298 
Skipped atom 1021 because residue number 124  < previous residue 298 
Skipped atom 1022 because residue number 124  < previous residue 298 
Skipped atom 1023 because residue number 124  < previous residue 298 
Skipped atom 1024 because residue number 124  < previous residue 298 
Skipped atom 1025 because residue number 124  < previous residue 298 
Skipped atom 1026 because residue number 125  < previous residue 298 
Skipped atom 1027 because residue number 125  < previous residue 298 
Skipped atom 1028 because residue number 125  < previous residue 298 
Skipped atom 1029 because residue number 125  < previous residue 298 
Skipped atom 1030 because residue number 125  < previous residue 298 
Skipped atom 1031 because residue number 126  < previous residue 298 
Skipped atom 1032 because residue number 126  < previous residue 298 
Skipped atom 1033 because residue number 126  < previous residue 298 
Skipped atom 1034 because residue number 126  < previous residue 298 
Skipped atom 1035 because residue number 126  < previous residue 298 
Skipped atom 1036 because residue number 126  < previous residue 298 
Skipped atom 1037 because residue number 127  < previous residue 298 
Skipped atom 1038 because residue number 127  < previous residue 298 
Skipped atom 1039 because residue number 127  < previous residue 298 
Skipped atom 1040 because residue number 127  < previous residue 298 
Skipped atom 1041 because residue number 127  < previous residue 298 
Skipped atom 1042 because residue number 127  < previous residue 298 
Skipped atom 1043 because residue number 127  < previous residue 298 
Skipped atom 1044 because residue number 127  < previous residue 298 
Skipped atom 1045 because residue number 128  < previous residue 298 
Skipped atom 1046 because residue number 128  < previous residue 298 
Skipped atom 1047 because residue number 128  < previous residue 298 
Skipped atom 1048 because residue number 128  < previous residue 298 
Skipped atom 1049 because residue number 128  < previous residue 298 
Skipped atom 1050 because residue number 128  < previous residue 298 
Skipped atom 1051 because residue number 128  < previous residue 298 
Skipped atom 1052 because residue number 129  < previous residue 298 
Skipped atom 1053 because residue number 129  < previous residue 298 
Skipped atom 1054 because residue number 129  < previous residue 298 
Skipped atom 1055 because residue number 129  < previous residue 298 
Skipped atom 1056 because residue number 129  < previous residue 298 
Skipped atom 1057 because residue number 129  < previous residue 298 
Skipped atom 1058 because residue number 129  < previous residue 298 
Skipped atom 1059 because residue number 129  < previous residue 298 
Skipped atom 1060 because residue number 129  < previous residue 298 
Skipped atom 1061 because residue number 129  < previous residue 298 
Skipped atom 1062 because residue number 129  < previous residue 298 
Skipped atom 1063 because residue number 129  < previous residue 298 
Skipped atom 1064 because residue number 130  < previous residue 298 
Skipped atom 1065 because residue number 130  < previous residue 298 
Skipped atom 1066 because residue number 130  < previous residue 298 
Skipped atom 1067 because residue number 130  < previous residue 298 
Skipped atom 1068 because residue number 130  < previous residue 298 
Skipped atom 1069 because residue number 130  < previous residue 298 
Skipped atom 1070 because residue number 131  < previous residue 298 
Skipped atom 1071 because residue number 131  < previous residue 298 
Skipped atom 1072 because residue number 131  < previous residue 298 
Skipped atom 1073 because residue number 131  < previous residue 298 
Skipped atom 1074 because residue number 131  < previous residue 298 
Skipped atom 1075 because residue number 131  < previous residue 298 
Skipped atom 1076 because residue number 131  < previous residue 298 
Skipped atom 1077 because residue number 131  < previous residue 298 
Skipped atom 1078 because residue number 132  < previous residue 298 
Skipped atom 1079 because residue number 132  < previous residue 298 
Skipped atom 1080 because residue number 132  < previous residue 298 
Skipped atom 1081 because residue number 132  < previous residue 298 
Skipped atom 1082 because residue number 132  < previous residue 298 
Skipped atom 1083 because residue number 132  < previous residue 298 
Skipped atom 1084 because residue number 132  < previous residue 298 
Skipped atom 1085 because residue number 132  < previous residue 298 
Skipped atom 1086 because residue number 133  < previous residue 298 
Skipped atom 1087 because residue number 133  < previous residue 298 
Skipped atom 1088 because residue number 133  < previous residue 298 
Skipped atom 1089 because residue number 133  < previous residue 298 
Skipped atom 1090 because residue number 133  < previous residue 298 
Skipped atom 1091 because residue number 133  < previous residue 298 
Skipped atom 1092 because residue number 133  < previous residue 298 
Skipped atom 1093 because residue number 134  < previous residue 298 
Skipped atom 1094 because residue number 134  < previous residue 298 
Skipped atom 1095 because residue number 134  < previous residue 298 
Skipped atom 1096 because residue number 134  < previous residue 298 
Skipped atom 1097 because residue number 134  < previous residue 298 
Skipped atom 1098 because residue number 135  < previous residue 298 
Skipped atom 1099 because residue number 135  < previous residue 298 
Skipped atom 1100 because residue number 135  < previous residue 298 
Skipped atom 1101 because residue number 135  < previous residue 298 
Skipped atom 1102 because residue number 135  < previous residue 298 
Skipped atom 1103 because residue number 135  < previous residue 298 
Skipped atom 1104 because residue number 135  < previous residue 298 
Skipped atom 1105 because residue number 135  < previous residue 298 
Skipped atom 1106 because residue number 136  < previous residue 298 
Skipped atom 1107 because residue number 136  < previous residue 298 
Skipped atom 1108 because residue number 136  < previous residue 298 
Skipped atom 1109 because residue number 136  < previous residue 298 
Skipped atom 1110 because residue number 136  < previous residue 298 
Skipped atom 1111 because residue number 136  < previous residue 298 
Skipped atom 1112 because residue number 136  < previous residue 298 
Skipped atom 1113 because residue number 136  < previous residue 298 
Skipped atom 1114 because residue number 137  < previous residue 298 
Skipped atom 1115 because residue number 137  < previous residue 298 
Skipped atom 1116 because residue number 137  < previous residue 298 
Skipped atom 1117 because residue number 137  < previous residue 298 
Skipped atom 1118 because residue number 137  < previous residue 298 
Skipped atom 1119 because residue number 137  < previous residue 298 
Skipped atom 1120 because residue number 137  < previous residue 298 
Skipped atom 1121 because residue number 137  < previous residue 298 
Skipped atom 1122 because residue number 137  < previous residue 298 
Skipped atom 1123 because residue number 138  < previous residue 298 
Skipped atom 1124 because residue number 138  < previous residue 298 
Skipped atom 1125 because residue number 138  < previous residue 298 
Skipped atom 1126 because residue number 138  < previous residue 298 
Skipped atom 1127 because residue number 138  < previous residue 298 
Skipped atom 1128 because residue number 138  < previous residue 298 
Skipped atom 1129 because residue number 138  < previous residue 298 
Skipped atom 1130 because residue number 138  < previous residue 298 
Skipped atom 1131 because residue number 139  < previous residue 298 
Skipped atom 1132 because residue number 139  < previous residue 298 
Skipped atom 1133 because residue number 139  < previous residue 298 
Skipped atom 1134 because residue number 139  < previous residue 298 
Skipped atom 1135 because residue number 139  < previous residue 298 
Skipped atom 1136 because residue number 139  < previous residue 298 
Skipped atom 1137 because residue number 139  < previous residue 298 
Skipped atom 1138 because residue number 139  < previous residue 298 
Skipped atom 1139 because residue number 140  < previous residue 298 
Skipped atom 1140 because residue number 140  < previous residue 298 
Skipped atom 1141 because residue number 140  < previous residue 298 
Skipped atom 1142 because residue number 140  < previous residue 298 
Skipped atom 1143 because residue number 140  < previous residue 298 
Skipped atom 1144 because residue number 140  < previous residue 298 
Skipped atom 1145 because residue number 140  < previous residue 298 
Skipped atom 1146 because residue number 140  < previous residue 298 
Skipped atom 1147 because residue number 140  < previous residue 298 
Skipped atom 1148 because residue number 141  < previous residue 298 
Skipped atom 1149 because residue number 141  < previous residue 298 
Skipped atom 1150 because residue number 141  < previous residue 298 
Skipped atom 1151 because residue number 141  < previous residue 298 
Skipped atom 1152 because residue number 141  < previous residue 298 
Skipped atom 1153 because residue number 141  < previous residue 298 
Skipped atom 1154 because residue number 141  < previous residue 298 
Skipped atom 1155 because residue number 141  < previous residue 298 
Skipped atom 1156 because residue number 141  < previous residue 298 
Skipped atom 1157 because residue number 142  < previous residue 298 
Skipped atom 1158 because residue number 142  < previous residue 298 
Skipped atom 1159 because residue number 142  < previous residue 298 
Skipped atom 1160 because residue number 142  < previous residue 298 
Skipped atom 1161 because residue number 142  < previous residue 298 
Skipped atom 1162 because residue number 142  < previous residue 298 
Skipped atom 1163 because residue number 142  < previous residue 298 
Skipped atom 1164 because residue number 142  < previous residue 298 
Skipped atom 1165 because residue number 143  < previous residue 298 
Skipped atom 1166 because residue number 143  < previous residue 298 
Skipped atom 1167 because residue number 143  < previous residue 298 
Skipped atom 1168 because residue number 143  < previous residue 298 
Skipped atom 1169 because residue number 144  < previous residue 298 
Skipped atom 1170 because residue number 144  < previous residue 298 
Skipped atom 1171 because residue number 144  < previous residue 298 
Skipped atom 1172 because residue number 144  < previous residue 298 
Skipped atom 1173 because residue number 145  < previous residue 298 
Skipped atom 1174 because residue number 145  < previous residue 298 
Skipped atom 1175 because residue number 145  < previous residue 298 
Skipped atom 1176 because residue number 145  < previous residue 298 
Skipped atom 1177 because residue number 145  < previous residue 298 
Skipped atom 1178 because residue number 145  < previous residue 298 
Skipped atom 1179 because residue number 145  < previous residue 298 
Skipped atom 1180 because residue number 145  < previous residue 298 
Skipped atom 1181 because residue number 146  < previous residue 298 
Skipped atom 1182 because residue number 146  < previous residue 298 
Skipped atom 1183 because residue number 146  < previous residue 298 
Skipped atom 1184 because residue number 146  < previous residue 298 
Skipped atom 1185 because residue number 146  < previous residue 298 
Skipped atom 1186 because residue number 146  < previous residue 298 
Skipped atom 1187 because residue number 146  < previous residue 298 
Skipped atom 1188 because residue number 146  < previous residue 298 
Skipped atom 1189 because residue number 146  < previous residue 298 
Skipped atom 1190 because residue number 147  < previous residue 298 
Skipped atom 1191 because residue number 147  < previous residue 298 
Skipped atom 1192 because residue number 147  < previous residue 298 
Skipped atom 1193 because residue number 147  < previous residue 298 
Skipped atom 1194 because residue number 147  < previous residue 298 
Skipped atom 1195 because residue number 147  < previous residue 298 
Skipped atom 1196 because residue number 147  < previous residue 298 
Skipped atom 1197 because residue number 147  < previous residue 298 
Skipped atom 1198 because residue number 147  < previous residue 298 
Skipped atom 1199 because residue number 148  < previous residue 298 
Skipped atom 1200 because residue number 148  < previous residue 298 
Skipped atom 1201 because residue number 148  < previous residue 298 
Skipped atom 1202 because residue number 148  < previous residue 298 
Skipped atom 1203 because residue number 148  < previous residue 298 
Skipped atom 1204 because residue number 148  < previous residue 298 
Skipped atom 1205 because residue number 148  < previous residue 298 
Skipped atom 1206 because residue number 149  < previous residue 298 
Skipped atom 1207 because residue number 149  < previous residue 298 
Skipped atom 1208 because residue number 149  < previous residue 298 
Skipped atom 1209 because residue number 149  < previous residue 298 
Skipped atom 1210 because residue number 149  < previous residue 298 
Skipped atom 1211 because residue number 149  < previous residue 298 
Skipped atom 1212 because residue number 149  < previous residue 298 
Skipped atom 1213 because residue number 149  < previous residue 298 
Skipped atom 1214 because residue number 149  < previous residue 298 
Skipped atom 1215 because residue number 150  < previous residue 298 
Skipped atom 1216 because residue number 150  < previous residue 298 
Skipped atom 1217 because residue number 150  < previous residue 298 
Skipped atom 1218 because residue number 150  < previous residue 298 
Skipped atom 1219 because residue number 150  < previous residue 298 
Skipped atom 1220 because residue number 150  < previous residue 298 
Skipped atom 1221 because residue number 150  < previous residue 298 
Skipped atom 1222 because residue number 150  < previous residue 298 
Skipped atom 1223 because residue number 150  < previous residue 298 
Skipped atom 1224 because residue number 151  < previous residue 298 
Skipped atom 1225 because residue number 151  < previous residue 298 
Skipped atom 1226 because residue number 151  < previous residue 298 
Skipped atom 1227 because residue number 151  < previous residue 298 
Skipped atom 1228 because residue number 151  < previous residue 298 
Skipped atom 1229 because residue number 151  < previous residue 298 
Skipped atom 1230 because residue number 151  < previous residue 298 
Skipped atom 1231 because residue number 151  < previous residue 298 
Skipped atom 1232 because residue number 151  < previous residue 298 
Skipped atom 1233 because residue number 151  < previous residue 298 
Skipped atom 1234 because residue number 151  < previous residue 298 
Skipped atom 1235 because residue number 152  < previous residue 298 
Skipped atom 1236 because residue number 152  < previous residue 298 
Skipped atom 1237 because residue number 152  < previous residue 298 
Skipped atom 1238 because residue number 152  < previous residue 298 
Skipped atom 1239 because residue number 152  < previous residue 298 
Skipped atom 1240 because residue number 152  < previous residue 298 
Skipped atom 1241 because residue number 152  < previous residue 298 
Skipped atom 1242 because residue number 152  < previous residue 298 
Skipped atom 1243 because residue number 153  < previous residue 298 
Skipped atom 1244 because residue number 153  < previous residue 298 
Skipped atom 1245 because residue number 153  < previous residue 298 
Skipped atom 1246 because residue number 153  < previous residue 298 
Skipped atom 1247 because residue number 153  < previous residue 298 
Skipped atom 1248 because residue number 153  < previous residue 298 
Skipped atom 1249 because residue number 153  < previous residue 298 
Skipped atom 1250 because residue number 153  < previous residue 298 
Skipped atom 1251 because residue number 153  < previous residue 298 
Skipped atom 1252 because residue number 154  < previous residue 298 
Skipped atom 1253 because residue number 154  < previous residue 298 
Skipped atom 1254 because residue number 154  < previous residue 298 
Skipped atom 1255 because residue number 154  < previous residue 298 
Skipped atom 1256 because residue number 154  < previous residue 298 
Skipped atom 1257 because residue number 154  < previous residue 298 
Skipped atom 1258 because residue number 154  < previous residue 298 
Skipped atom 1259 because residue number 154  < previous residue 298 
Skipped atom 1260 because residue number 154  < previous residue 298 
Skipped atom 1261 because residue number 155  < previous residue 298 
Skipped atom 1262 because residue number 155  < previous residue 298 
Skipped atom 1263 because residue number 155  < previous residue 298 
Skipped atom 1264 because residue number 155  < previous residue 298 
Skipped atom 1265 because residue number 155  < previous residue 298 
Skipped atom 1266 because residue number 155  < previous residue 298 
Skipped atom 1267 because residue number 155  < previous residue 298 
Skipped atom 1268 because residue number 155  < previous residue 298 
Skipped atom 1269 because residue number 156  < previous residue 298 
Skipped atom 1270 because residue number 156  < previous residue 298 
Skipped atom 1271 because residue number 156  < previous residue 298 
Skipped atom 1272 because residue number 156  < previous residue 298 
Skipped atom 1273 because residue number 157  < previous residue 298 
Skipped atom 1274 because residue number 157  < previous residue 298 
Skipped atom 1275 because residue number 157  < previous residue 298 
Skipped atom 1276 because residue number 157  < previous residue 298 
Skipped atom 1277 because residue number 157  < previous residue 298 
Skipped atom 1278 because residue number 157  < previous residue 298 
Skipped atom 1279 because residue number 157  < previous residue 298 
Skipped atom 1280 because residue number 157  < previous residue 298 
Skipped atom 1281 because residue number 158  < previous residue 298 
Skipped atom 1282 because residue number 158  < previous residue 298 
Skipped atom 1283 because residue number 158  < previous residue 298 
Skipped atom 1284 because residue number 158  < previous residue 298 
Skipped atom 1285 because residue number 158  < previous residue 298 
Skipped atom 1286 because residue number 158  < previous residue 298 
Skipped atom 1287 because residue number 158  < previous residue 298 
Skipped atom 1288 because residue number 158  < previous residue 298 
Skipped atom 1289 because residue number 158  < previous residue 298 
Skipped atom 1290 because residue number 159  < previous residue 298 
Skipped atom 1291 because residue number 159  < previous residue 298 
Skipped atom 1292 because residue number 159  < previous residue 298 
Skipped atom 1293 because residue number 159  < previous residue 298 
Skipped atom 1294 because residue number 159  < previous residue 298 
Skipped atom 1295 because residue number 159  < previous residue 298 
Skipped atom 1296 because residue number 159  < previous residue 298 
Skipped atom 1297 because residue number 160  < previous residue 298 
Skipped atom 1298 because residue number 160  < previous residue 298 
Skipped atom 1299 because residue number 160  < previous residue 298 
Skipped atom 1300 because residue number 160  < previous residue 298 
Skipped atom 1301 because residue number 160  < previous residue 298 
Skipped atom 1302 because residue number 160  < previous residue 298 
Skipped atom 1303 because residue number 160  < previous residue 298 
Skipped atom 1304 because residue number 161  < previous residue 298 
Skipped atom 1305 because residue number 161  < previous residue 298 
Skipped atom 1306 because residue number 161  < previous residue 298 
Skipped atom 1307 because residue number 161  < previous residue 298 
Skipped atom 1308 because residue number 161  < previous residue 298 
Skipped atom 1309 because residue number 161  < previous residue 298 
Skipped atom 1310 because residue number 161  < previous residue 298 
Skipped atom 1311 because residue number 161  < previous residue 298 
Skipped atom 1312 because residue number 162  < previous residue 298 
Skipped atom 1313 because residue number 162  < previous residue 298 
Skipped atom 1314 because residue number 162  < previous residue 298 
Skipped atom 1315 because residue number 162  < previous residue 298 
Skipped atom 1316 because residue number 162  < previous residue 298 
Skipped atom 1317 because residue number 162  < previous residue 298 
Skipped atom 1318 because residue number 162  < previous residue 298 
Skipped atom 1319 because residue number 163  < previous residue 298 
Skipped atom 1320 because residue number 163  < previous residue 298 
Skipped atom 1321 because residue number 163  < previous residue 298 
Skipped atom 1322 because residue number 163  < previous residue 298 
Skipped atom 1323 because residue number 163  < previous residue 298 
Skipped atom 1324 because residue number 163  < previous residue 298 
Skipped atom 1325 because residue number 163  < previous residue 298 
Skipped atom 1326 because residue number 164  < previous residue 298 
Skipped atom 1327 because residue number 164  < previous residue 298 
Skipped atom 1328 because residue number 164  < previous residue 298 
Skipped atom 1329 because residue number 164  < previous residue 298 
Skipped atom 1330 because residue number 164  < previous residue 298 
Skipped atom 1331 because residue number 164  < previous residue 298 
Skipped atom 1332 because residue number 164  < previous residue 298 
Skipped atom 1333 because residue number 164  < previous residue 298 
Skipped atom 1334 because residue number 164  < previous residue 298 
Skipped atom 1335 because residue number 164  < previous residue 298 
Skipped atom 1336 because residue number 164  < previous residue 298 
Skipped atom 1337 because residue number 165  < previous residue 298 
Skipped atom 1338 because residue number 165  < previous residue 298 
Skipped atom 1339 because residue number 165  < previous residue 298 
Skipped atom 1340 because residue number 165  < previous residue 298 
Skipped atom 1341 because residue number 165  < previous residue 298 
Skipped atom 1342 because residue number 165  < previous residue 298 
Skipped atom 1343 because residue number 165  < previous residue 298 
Skipped atom 1344 because residue number 165  < previous residue 298 
Skipped atom 1345 because residue number 165  < previous residue 298 
Skipped atom 1346 because residue number 165  < previous residue 298 
Skipped atom 1347 because residue number 165  < previous residue 298 
Skipped atom 1348 because residue number 165  < previous residue 298 
Skipped atom 1349 because residue number 166  < previous residue 298 
Skipped atom 1350 because residue number 166  < previous residue 298 
Skipped atom 1351 because residue number 166  < previous residue 298 
Skipped atom 1352 because residue number 166  < previous residue 298 
Skipped atom 1353 because residue number 166  < previous residue 298 
Skipped atom 1354 because residue number 166  < previous residue 298 
Skipped atom 1355 because residue number 166  < previous residue 298 
Skipped atom 1356 because residue number 166  < previous residue 298 
Skipped atom 1357 because residue number 166  < previous residue 298 
Skipped atom 1358 because residue number 167  < previous residue 298 
Skipped atom 1359 because residue number 167  < previous residue 298 
Skipped atom 1360 because residue number 167  < previous residue 298 
Skipped atom 1361 because residue number 167  < previous residue 298 
Skipped atom 1362 because residue number 167  < previous residue 298 
Skipped atom 1363 because residue number 167  < previous residue 298 
Skipped atom 1364 because residue number 167  < previous residue 298 
Skipped atom 1365 because residue number 167  < previous residue 298 
Skipped atom 1366 because residue number 168  < previous residue 298 
Skipped atom 1367 because residue number 168  < previous residue 298 
Skipped atom 1368 because residue number 168  < previous residue 298 
Skipped atom 1369 because residue number 168  < previous residue 298 
Skipped atom 1370 because residue number 168  < previous residue 298 
Skipped atom 1371 because residue number 168  < previous residue 298 
Skipped atom 1372 because residue number 168  < previous residue 298 
Skipped atom 1373 because residue number 168  < previous residue 298 
Skipped atom 1374 because residue number 168  < previous residue 298 
Skipped atom 1375 because residue number 169  < previous residue 298 
Skipped atom 1376 because residue number 169  < previous residue 298 
Skipped atom 1377 because residue number 169  < previous residue 298 
Skipped atom 1378 because residue number 169  < previous residue 298 
Skipped atom 1379 because residue number 169  < previous residue 298 
Skipped atom 1380 because residue number 169  < previous residue 298 
Skipped atom 1381 because residue number 169  < previous residue 298 
Skipped atom 1382 because residue number 169  < previous residue 298 
Skipped atom 1383 because residue number 170  < previous residue 298 
Skipped atom 1384 because residue number 170  < previous residue 298 
Skipped atom 1385 because residue number 170  < previous residue 298 
Skipped atom 1386 because residue number 170  < previous residue 298 
Skipped atom 1387 because residue number 170  < previous residue 298 
Skipped atom 1388 because residue number 170  < previous residue 298 
Skipped atom 1389 because residue number 170  < previous residue 298 
Skipped atom 1390 because residue number 170  < previous residue 298 
Skipped atom 1391 because residue number 171  < previous residue 298 
Skipped atom 1392 because residue number 171  < previous residue 298 
Skipped atom 1393 because residue number 171  < previous residue 298 
Skipped atom 1394 because residue number 171  < previous residue 298 
Skipped atom 1395 because residue number 171  < previous residue 298 
Skipped atom 1396 because residue number 171  < previous residue 298 
Skipped atom 1397 because residue number 171  < previous residue 298 
Skipped atom 1398 because residue number 171  < previous residue 298 
Skipped atom 1399 because residue number 171  < previous residue 298 
Skipped atom 1400 because residue number 171  < previous residue 298 
Skipped atom 1401 because residue number 171  < previous residue 298 
Skipped atom 1402 because residue number 171  < previous residue 298 
Skipped atom 1403 because residue number 172  < previous residue 298 
Skipped atom 1404 because residue number 172  < previous residue 298 
Skipped atom 1405 because residue number 172  < previous residue 298 
Skipped atom 1406 because residue number 172  < previous residue 298 
Skipped atom 1407 because residue number 172  < previous residue 298 
Skipped atom 1408 because residue number 172  < previous residue 298 
Skipped atom 1409 because residue number 172  < previous residue 298 
Skipped atom 1410 because residue number 172  < previous residue 298 
Skipped atom 1411 because residue number 172  < previous residue 298 
Skipped atom 1412 because residue number 172  < previous residue 298 
Skipped atom 1413 because residue number 172  < previous residue 298 
Skipped atom 1414 because residue number 172  < previous residue 298 
Skipped atom 1415 because residue number 173  < previous residue 298 
Skipped atom 1416 because residue number 173  < previous residue 298 
Skipped atom 1417 because residue number 173  < previous residue 298 
Skipped atom 1418 because residue number 173  < previous residue 298 
Skipped atom 1419 because residue number 173  < previous residue 298 
Skipped atom 1420 because residue number 173  < previous residue 298 
Skipped atom 1421 because residue number 174  < previous residue 298 
Skipped atom 1422 because residue number 174  < previous residue 298 
Skipped atom 1423 because residue number 174  < previous residue 298 
Skipped atom 1424 because residue number 174  < previous residue 298 
Skipped atom 1425 because residue number 174  < previous residue 298 
Skipped atom 1426 because residue number 174  < previous residue 298 
Skipped atom 1427 because residue number 174  < previous residue 298 
Skipped atom 1428 because residue number 175  < previous residue 298 
Skipped atom 1429 because residue number 175  < previous residue 298 
Skipped atom 1430 because residue number 175  < previous residue 298 
Skipped atom 1431 because residue number 175  < previous residue 298 
Skipped atom 1432 because residue number 175  < previous residue 298 
Skipped atom 1433 because residue number 175  < previous residue 298 
Skipped atom 1434 because residue number 175  < previous residue 298 
Skipped atom 1435 because residue number 175  < previous residue 298 
Skipped atom 1436 because residue number 175  < previous residue 298 
Skipped atom 1437 because residue number 176  < previous residue 298 
Skipped atom 1438 because residue number 176  < previous residue 298 
Skipped atom 1439 because residue number 176  < previous residue 298 
Skipped atom 1440 because residue number 176  < previous residue 298 
Skipped atom 1441 because residue number 176  < previous residue 298 
Skipped atom 1442 because residue number 176  < previous residue 298 
Skipped atom 1443 because residue number 177  < previous residue 298 
Skipped atom 1444 because residue number 177  < previous residue 298 
Skipped atom 1445 because residue number 177  < previous residue 298 
Skipped atom 1446 because residue number 177  < previous residue 298 
Skipped atom 1447 because residue number 177  < previous residue 298 
Skipped atom 1448 because residue number 177  < previous residue 298 
Skipped atom 1449 because residue number 177  < previous residue 298 
Skipped atom 1450 because residue number 177  < previous residue 298 
Skipped atom 1451 because residue number 177  < previous residue 298 
Skipped atom 1452 because residue number 178  < previous residue 298 
Skipped atom 1453 because residue number 178  < previous residue 298 
Skipped atom 1454 because residue number 178  < previous residue 298 
Skipped atom 1455 because residue number 178  < previous residue 298 
Skipped atom 1456 because residue number 178  < previous residue 298 
Skipped atom 1457 because residue number 178  < previous residue 298 
Skipped atom 1458 because residue number 178  < previous residue 298 
Skipped atom 1459 because residue number 178  < previous residue 298 
Skipped atom 1460 because residue number 178  < previous residue 298 
Skipped atom 1461 because residue number 179  < previous residue 298 
Skipped atom 1462 because residue number 179  < previous residue 298 
Skipped atom 1463 because residue number 179  < previous residue 298 
Skipped atom 1464 because residue number 179  < previous residue 298 
Skipped atom 1465 because residue number 179  < previous residue 298 
Skipped atom 1466 because residue number 179  < previous residue 298 
Skipped atom 1467 because residue number 179  < previous residue 298 
Skipped atom 1468 because residue number 179  < previous residue 298 
Skipped atom 1469 because residue number 180  < previous residue 298 
Skipped atom 1470 because residue number 180  < previous residue 298 
Skipped atom 1471 because residue number 180  < previous residue 298 
Skipped atom 1472 because residue number 180  < previous residue 298 
Skipped atom 1473 because residue number 180  < previous residue 298 
Skipped atom 1474 because residue number 180  < previous residue 298 
Skipped atom 1475 because residue number 180  < previous residue 298 
Skipped atom 1476 because residue number 181  < previous residue 298 
Skipped atom 1477 because residue number 181  < previous residue 298 
Skipped atom 1478 because residue number 181  < previous residue 298 
Skipped atom 1479 because residue number 181  < previous residue 298 
Skipped atom 1480 because residue number 181  < previous residue 298 
Skipped atom 1481 because residue number 181  < previous residue 298 
Skipped atom 1482 because residue number 182  < previous residue 298 
Skipped atom 1483 because residue number 182  < previous residue 298 
Skipped atom 1484 because residue number 182  < previous residue 298 
Skipped atom 1485 because residue number 182  < previous residue 298 
Skipped atom 1486 because residue number 182  < previous residue 298 
Skipped atom 1487 because residue number 182  < previous residue 298 
Skipped atom 1488 because residue number 182  < previous residue 298 
Skipped atom 1489 because residue number 183  < previous residue 298 
Skipped atom 1490 because residue number 183  < previous residue 298 
Skipped atom 1491 because residue number 183  < previous residue 298 
Skipped atom 1492 because residue number 183  < previous residue 298 
Skipped atom 1493 because residue number 183  < previous residue 298 
Skipped atom 1494 because residue number 183  < previous residue 298 
Skipped atom 1495 because residue number 183  < previous residue 298 
Skipped atom 1496 because residue number 184  < previous residue 298 
Skipped atom 1497 because residue number 184  < previous residue 298 
Skipped atom 1498 because residue number 184  < previous residue 298 
Skipped atom 1499 because residue number 184  < previous residue 298 
Skipped atom 1500 because residue number 184  < previous residue 298 
Skipped atom 1501 because residue number 185  < previous residue 298 
Skipped atom 1502 because residue number 185  < previous residue 298 
Skipped atom 1503 because residue number 185  < previous residue 298 
Skipped atom 1504 because residue number 185  < previous residue 298 
Skipped atom 1505 because residue number 185  < previous residue 298 
Skipped atom 1506 because residue number 186  < previous residue 298 
Skipped atom 1507 because residue number 186  < previous residue 298 
Skipped atom 1508 because residue number 186  < previous residue 298 
Skipped atom 1509 because residue number 186  < previous residue 298 
Skipped atom 1510 because residue number 186  < previous residue 298 
Skipped atom 1511 because residue number 186  < previous residue 298 
Skipped atom 1512 because residue number 186  < previous residue 298 
Skipped atom 1513 because residue number 186  < previous residue 298 
Skipped atom 1514 because residue number 186  < previous residue 298 
Skipped atom 1515 because residue number 186  < previous residue 298 
Skipped atom 1516 because residue number 186  < previous residue 298 
Skipped atom 1517 because residue number 187  < previous residue 298 
Skipped atom 1518 because residue number 187  < previous residue 298 
Skipped atom 1519 because residue number 187  < previous residue 298 
Skipped atom 1520 because residue number 187  < previous residue 298 
Skipped atom 1521 because residue number 188  < previous residue 298 
Skipped atom 1522 because residue number 188  < previous residue 298 
Skipped atom 1523 because residue number 188  < previous residue 298 
Skipped atom 1524 because residue number 188  < previous residue 298 
Skipped atom 1525 because residue number 188  < previous residue 298 
Skipped atom 1526 because residue number 188  < previous residue 298 
Skipped atom 1527 because residue number 188  < previous residue 298 
Skipped atom 1528 because residue number 188  < previous residue 298 
Skipped atom 1529 because residue number 188  < previous residue 298 
Skipped atom 1530 because residue number 189  < previous residue 298 
Skipped atom 1531 because residue number 189  < previous residue 298 
Skipped atom 1532 because residue number 189  < previous residue 298 
Skipped atom 1533 because residue number 189  < previous residue 298 
Skipped atom 1534 because residue number 189  < previous residue 298 
Skipped atom 1535 because residue number 189  < previous residue 298 
Skipped atom 1536 because residue number 189  < previous residue 298 
Skipped atom 1537 because residue number 190  < previous residue 298 
Skipped atom 1538 because residue number 190  < previous residue 298 
Skipped atom 1539 because residue number 190  < previous residue 298 
Skipped atom 1540 because residue number 190  < previous residue 298 
Skipped atom 1541 because residue number 190  < previous residue 298 
Skipped atom 1542 because residue number 190  < previous residue 298 
Skipped atom 1543 because residue number 190  < previous residue 298 
Skipped atom 1544 because residue number 190  < previous residue 298 
Skipped atom 1545 because residue number 191  < previous residue 298 
Skipped atom 1546 because residue number 191  < previous residue 298 
Skipped atom 1547 because residue number 191  < previous residue 298 
Skipped atom 1548 because residue number 191  < previous residue 298 
Skipped atom 1549 because residue number 191  < previous residue 298 
Skipped atom 1550 because residue number 191  < previous residue 298 
Skipped atom 1551 because residue number 191  < previous residue 298 
Skipped atom 1552 because residue number 191  < previous residue 298 
Skipped atom 1553 because residue number 192  < previous residue 298 
Skipped atom 1554 because residue number 192  < previous residue 298 
Skipped atom 1555 because residue number 192  < previous residue 298 
Skipped atom 1556 because residue number 192  < previous residue 298 
Skipped atom 1557 because residue number 192  < previous residue 298 
Skipped atom 1558 because residue number 192  < previous residue 298 
Skipped atom 1559 because residue number 192  < previous residue 298 
Skipped atom 1560 because residue number 192  < previous residue 298 
Skipped atom 1561 because residue number 192  < previous residue 298 
Skipped atom 1562 because residue number 193  < previous residue 298 
Skipped atom 1563 because residue number 193  < previous residue 298 
Skipped atom 1564 because residue number 193  < previous residue 298 
Skipped atom 1565 because residue number 193  < previous residue 298 
Skipped atom 1566 because residue number 193  < previous residue 298 
Skipped atom 1567 because residue number 193  < previous residue 298 
Skipped atom 1568 because residue number 193  < previous residue 298 
Skipped atom 1569 because residue number 193  < previous residue 298 
Skipped atom 1570 because residue number 194  < previous residue 298 
Skipped atom 1571 because residue number 194  < previous residue 298 
Skipped atom 1572 because residue number 194  < previous residue 298 
Skipped atom 1573 because residue number 194  < previous residue 298 
Skipped atom 1574 because residue number 194  < previous residue 298 
Skipped atom 1575 because residue number 194  < previous residue 298 
Skipped atom 1576 because residue number 194  < previous residue 298 
Skipped atom 1577 because residue number 194  < previous residue 298 
Skipped atom 1578 because residue number 195  < previous residue 298 
Skipped atom 1579 because residue number 195  < previous residue 298 
Skipped atom 1580 because residue number 195  < previous residue 298 
Skipped atom 1581 because residue number 195  < previous residue 298 
Skipped atom 1582 because residue number 195  < previous residue 298 
Skipped atom 1583 because residue number 196  < previous residue 298 
Skipped atom 1584 because residue number 196  < previous residue 298 
Skipped atom 1585 because residue number 196  < previous residue 298 
Skipped atom 1586 because residue number 196  < previous residue 298 
Skipped atom 1587 because residue number 196  < previous residue 298 
Skipped atom 1588 because residue number 196  < previous residue 298 
Skipped atom 1589 because residue number 196  < previous residue 298 
Skipped atom 1590 because residue number 196  < previous residue 298 
Skipped atom 1591 because residue number 197  < previous residue 298 
Skipped atom 1592 because residue number 197  < previous residue 298 
Skipped atom 1593 because residue number 197  < previous residue 298 
Skipped atom 1594 because residue number 197  < previous residue 298 
Skipped atom 1595 because residue number 198  < previous residue 298 
Skipped atom 1596 because residue number 198  < previous residue 298 
Skipped atom 1597 because residue number 198  < previous residue 298 
Skipped atom 1598 because residue number 198  < previous residue 298 
Skipped atom 1599 because residue number 198  < previous residue 298 
Skipped atom 1600 because residue number 198  < previous residue 298 
Skipped atom 1601 because residue number 198  < previous residue 298 
Skipped atom 1602 because residue number 198  < previous residue 298 
Skipped atom 1603 because residue number 198  < previous residue 298 
Skipped atom 1604 because residue number 199  < previous residue 298 
Skipped atom 1605 because residue number 199  < previous residue 298 
Skipped atom 1606 because residue number 199  < previous residue 298 
Skipped atom 1607 because residue number 199  < previous residue 298 
Skipped atom 1608 because residue number 199  < previous residue 298 
Skipped atom 1609 because residue number 199  < previous residue 298 
Skipped atom 1610 because residue number 199  < previous residue 298 
Skipped atom 1611 because residue number 199  < previous residue 298 
Skipped atom 1612 because residue number 200  < previous residue 298 
Skipped atom 1613 because residue number 200  < previous residue 298 
Skipped atom 1614 because residue number 200  < previous residue 298 
Skipped atom 1615 because residue number 200  < previous residue 298 
Skipped atom 1616 because residue number 200  < previous residue 298 
Skipped atom 1617 because residue number 200  < previous residue 298 
Skipped atom 1618 because residue number 201  < previous residue 298 
Skipped atom 1619 because residue number 201  < previous residue 298 
Skipped atom 1620 because residue number 201  < previous residue 298 
Skipped atom 1621 because residue number 201  < previous residue 298 
Skipped atom 1622 because residue number 201  < previous residue 298 
Skipped atom 1623 because residue number 201  < previous residue 298 
Skipped atom 1624 because residue number 201  < previous residue 298 
Skipped atom 1625 because residue number 201  < previous residue 298 
Skipped atom 1626 because residue number 201  < previous residue 298 
Skipped atom 1627 because residue number 202  < previous residue 298 
Skipped atom 1628 because residue number 202  < previous residue 298 
Skipped atom 1629 because residue number 202  < previous residue 298 
Skipped atom 1630 because residue number 202  < previous residue 298 
Skipped atom 1631 because residue number 202  < previous residue 298 
Skipped atom 1632 because residue number 202  < previous residue 298 
Skipped atom 1633 because residue number 202  < previous residue 298 
Skipped atom 1634 because residue number 202  < previous residue 298 
Skipped atom 1635 because residue number 202  < previous residue 298 
Skipped atom 1636 because residue number 203  < previous residue 298 
Skipped atom 1637 because residue number 203  < previous residue 298 
Skipped atom 1638 because residue number 203  < previous residue 298 
Skipped atom 1639 because residue number 203  < previous residue 298 
Skipped atom 1640 because residue number 203  < previous residue 298 
Skipped atom 1641 because residue number 203  < previous residue 298 
Skipped atom 1642 because residue number 203  < previous residue 298 
Skipped atom 1643 because residue number 203  < previous residue 298 
Skipped atom 1644 because residue number 204  < previous residue 298 
Skipped atom 1645 because residue number 204  < previous residue 298 
Skipped atom 1646 because residue number 204  < previous residue 298 
Skipped atom 1647 because residue number 204  < previous residue 298 
Skipped atom 1648 because residue number 204  < previous residue 298 
Skipped atom 1649 because residue number 204  < previous residue 298 
Skipped atom 1650 because residue number 204  < previous residue 298 
Skipped atom 1651 because residue number 204  < previous residue 298 
Skipped atom 1652 because residue number 204  < previous residue 298 
Skipped atom 1653 because residue number 205  < previous residue 298 
Skipped atom 1654 because residue number 205  < previous residue 298 
Skipped atom 1655 because residue number 205  < previous residue 298 
Skipped atom 1656 because residue number 205  < previous residue 298 
Skipped atom 1657 because residue number 205  < previous residue 298 
Skipped atom 1658 because residue number 205  < previous residue 298 
Skipped atom 1659 because residue number 205  < previous residue 298 
Skipped atom 1660 because residue number 205  < previous residue 298 
Skipped atom 1661 because residue number 205  < previous residue 298 
Skipped atom 1662 because residue number 206  < previous residue 298 
Skipped atom 1663 because residue number 206  < previous residue 298 
Skipped atom 1664 because residue number 206  < previous residue 298 
Skipped atom 1665 because residue number 206  < previous residue 298 
Skipped atom 1666 because residue number 206  < previous residue 298 
Skipped atom 1667 because residue number 206  < previous residue 298 
Skipped atom 1668 because residue number 206  < previous residue 298 
Skipped atom 1669 because residue number 206  < previous residue 298 
Skipped atom 1670 because residue number 206  < previous residue 298 
Skipped atom 1671 because residue number 206  < previous residue 298 
Skipped atom 1672 because residue number 206  < previous residue 298 
Skipped atom 1673 because residue number 207  < previous residue 298 
Skipped atom 1674 because residue number 207  < previous residue 298 
Skipped atom 1675 because residue number 207  < previous residue 298 
Skipped atom 1676 because residue number 207  < previous residue 298 
Skipped atom 1677 because residue number 207  < previous residue 298 
Skipped atom 1678 because residue number 207  < previous residue 298 
Skipped atom 1679 because residue number 207  < previous residue 298 
Skipped atom 1680 because residue number 207  < previous residue 298 
Skipped atom 1681 because residue number 208  < previous residue 298 
Skipped atom 1682 because residue number 208  < previous residue 298 
Skipped atom 1683 because residue number 208  < previous residue 298 
Skipped atom 1684 because residue number 208  < previous residue 298 
Skipped atom 1685 because residue number 208  < previous residue 298 
Skipped atom 1686 because residue number 208  < previous residue 298 
Skipped atom 1687 because residue number 208  < previous residue 298 
Skipped atom 1688 because residue number 208  < previous residue 298 
Skipped atom 1689 because residue number 209  < previous residue 298 
Skipped atom 1690 because residue number 209  < previous residue 298 
Skipped atom 1691 because residue number 209  < previous residue 298 
Skipped atom 1692 because residue number 209  < previous residue 298 
Skipped atom 1693 because residue number 209  < previous residue 298 
Skipped atom 1694 because residue number 209  < previous residue 298 
Skipped atom 1695 because residue number 209  < previous residue 298 
Skipped atom 1696 because residue number 209  < previous residue 298 
Skipped atom 1697 because residue number 210  < previous residue 298 
Skipped atom 1698 because residue number 210  < previous residue 298 
Skipped atom 1699 because residue number 210  < previous residue 298 
Skipped atom 1700 because residue number 210  < previous residue 298 
Skipped atom 1701 because residue number 210  < previous residue 298 
Skipped atom 1702 because residue number 210  < previous residue 298 
Skipped atom 1703 because residue number 210  < previous residue 298 
Skipped atom 1704 because residue number 210  < previous residue 298 
Skipped atom 1705 because residue number 211  < previous residue 298 
Skipped atom 1706 because residue number 211  < previous residue 298 
Skipped atom 1707 because residue number 211  < previous residue 298 
Skipped atom 1708 because residue number 211  < previous residue 298 
Skipped atom 1709 because residue number 211  < previous residue 298 
Skipped atom 1710 because residue number 211  < previous residue 298 
Skipped atom 1711 because residue number 211  < previous residue 298 
Skipped atom 1712 because residue number 211  < previous residue 298 
Skipped atom 1713 because residue number 212  < previous residue 298 
Skipped atom 1714 because residue number 212  < previous residue 298 
Skipped atom 1715 because residue number 212  < previous residue 298 
Skipped atom 1716 because residue number 212  < previous residue 298 
Skipped atom 1717 because residue number 212  < previous residue 298 
Skipped atom 1718 because residue number 212  < previous residue 298 
Skipped atom 1719 because residue number 212  < previous residue 298 
Skipped atom 1720 because residue number 212  < previous residue 298 
Skipped atom 1721 because residue number 213  < previous residue 298 
Skipped atom 1722 because residue number 213  < previous residue 298 
Skipped atom 1723 because residue number 213  < previous residue 298 
Skipped atom 1724 because residue number 213  < previous residue 298 
Skipped atom 1725 because residue number 213  < previous residue 298 
Skipped atom 1726 because residue number 213  < previous residue 298 
Skipped atom 1727 because residue number 213  < previous residue 298 
Skipped atom 1728 because residue number 213  < previous residue 298 
Skipped atom 1729 because residue number 214  < previous residue 298 
Skipped atom 1730 because residue number 214  < previous residue 298 
Skipped atom 1731 because residue number 214  < previous residue 298 
Skipped atom 1732 because residue number 214  < previous residue 298 
Skipped atom 1733 because residue number 214  < previous residue 298 
Skipped atom 1734 because residue number 214  < previous residue 298 
Skipped atom 1735 because residue number 214  < previous residue 298 
Skipped atom 1736 because residue number 214  < previous residue 298 
Skipped atom 1737 because residue number 215  < previous residue 298 
Skipped atom 1738 because residue number 215  < previous residue 298 
Skipped atom 1739 because residue number 215  < previous residue 298 
Skipped atom 1740 because residue number 215  < previous residue 298 
Skipped atom 1741 because residue number 215  < previous residue 298 
Skipped atom 1742 because residue number 215  < previous residue 298 
Skipped atom 1743 because residue number 215  < previous residue 298 
Skipped atom 1744 because residue number 215  < previous residue 298 
Skipped atom 1745 because residue number 215  < previous residue 298 
Skipped atom 1746 because residue number 216  < previous residue 298 
Skipped atom 1747 because residue number 216  < previous residue 298 
Skipped atom 1748 because residue number 216  < previous residue 298 
Skipped atom 1749 because residue number 216  < previous residue 298 
Skipped atom 1750 because residue number 216  < previous residue 298 
Skipped atom 1751 because residue number 216  < previous residue 298 
Skipped atom 1752 because residue number 217  < previous residue 298 
Skipped atom 1753 because residue number 217  < previous residue 298 
Skipped atom 1754 because residue number 217  < previous residue 298 
Skipped atom 1755 because residue number 217  < previous residue 298 
Skipped atom 1756 because residue number 218  < previous residue 298 
Skipped atom 1757 because residue number 218  < previous residue 298 
Skipped atom 1758 because residue number 218  < previous residue 298 
Skipped atom 1759 because residue number 218  < previous residue 298 
Skipped atom 1760 because residue number 218  < previous residue 298 
Skipped atom 1761 because residue number 218  < previous residue 298 
Skipped atom 1762 because residue number 218  < previous residue 298 
Skipped atom 1763 because residue number 218  < previous residue 298 
Skipped atom 1764 because residue number 219  < previous residue 298 
Skipped atom 1765 because residue number 219  < previous residue 298 
Skipped atom 1766 because residue number 219  < previous residue 298 
Skipped atom 1767 because residue number 219  < previous residue 298 
Skipped atom 1768 because residue number 219  < previous residue 298 
Skipped atom 1769 because residue number 219  < previous residue 298 
Skipped atom 1770 because residue number 219  < previous residue 298 
Skipped atom 1771 because residue number 220  < previous residue 298 
Skipped atom 1772 because residue number 220  < previous residue 298 
Skipped atom 1773 because residue number 220  < previous residue 298 
Skipped atom 1774 because residue number 220  < previous residue 298 
Skipped atom 1775 because residue number 220  < previous residue 298 
Skipped atom 1776 because residue number 220  < previous residue 298 
Skipped atom 1777 because residue number 220  < previous residue 298 
Skipped atom 1778 because residue number 220  < previous residue 298 
Skipped atom 1779 because residue number 221  < previous residue 298 
Skipped atom 1780 because residue number 221  < previous residue 298 
Skipped atom 1781 because residue number 221  < previous residue 298 
Skipped atom 1782 because residue number 221  < previous residue 298 
Skipped atom 1783 because residue number 221  < previous residue 298 
Skipped atom 1784 because residue number 221  < previous residue 298 
Skipped atom 1785 because residue number 221  < previous residue 298 
Skipped atom 1786 because residue number 221  < previous residue 298 
Skipped atom 1787 because residue number 222  < previous residue 298 
Skipped atom 1788 because residue number 222  < previous residue 298 
Skipped atom 1789 because residue number 222  < previous residue 298 
Skipped atom 1790 because residue number 222  < previous residue 298 
Skipped atom 1791 because residue number 222  < previous residue 298 
Skipped atom 1792 because residue number 222  < previous residue 298 
Skipped atom 1793 because residue number 222  < previous residue 298 
Skipped atom 1794 because residue number 222  < previous residue 298 
Skipped atom 1795 because residue number 222  < previous residue 298 
Skipped atom 1796 because residue number 223  < previous residue 298 
Skipped atom 1797 because residue number 223  < previous residue 298 
Skipped atom 1798 because residue number 223  < previous residue 298 
Skipped atom 1799 because residue number 223  < previous residue 298 
Skipped atom 1800 because residue number 223  < previous residue 298 
Skipped atom 1801 because residue number 223  < previous residue 298 
Skipped atom 1802 because residue number 223  < previous residue 298 
Skipped atom 1803 because residue number 223  < previous residue 298 
Skipped atom 1804 because residue number 224  < previous residue 298 
Skipped atom 1805 because residue number 224  < previous residue 298 
Skipped atom 1806 because residue number 224  < previous residue 298 
Skipped atom 1807 because residue number 224  < previous residue 298 
Skipped atom 1808 because residue number 225  < previous residue 298 
Skipped atom 1809 because residue number 225  < previous residue 298 
Skipped atom 1810 because residue number 225  < previous residue 298 
Skipped atom 1811 because residue number 225  < previous residue 298 
Skipped atom 1812 because residue number 225  < previous residue 298 
Skipped atom 1813 because residue number 225  < previous residue 298 
Skipped atom 1814 because residue number 225  < previous residue 298 
Skipped atom 1815 because residue number 226  < previous residue 298 
Skipped atom 1816 because residue number 226  < previous residue 298 
Skipped atom 1817 because residue number 226  < previous residue 298 
Skipped atom 1818 because residue number 226  < previous residue 298 
Skipped atom 1819 because residue number 226  < previous residue 298 
Skipped atom 1820 because residue number 226  < previous residue 298 
Skipped atom 1821 because residue number 226  < previous residue 298 
Skipped atom 1822 because residue number 227  < previous residue 298 
Skipped atom 1823 because residue number 227  < previous residue 298 
Skipped atom 1824 because residue number 227  < previous residue 298 
Skipped atom 1825 because residue number 227  < previous residue 298 
Skipped atom 1826 because residue number 227  < previous residue 298 
Skipped atom 1827 because residue number 227  < previous residue 298 
Skipped atom 1828 because residue number 228  < previous residue 298 
Skipped atom 1829 because residue number 228  < previous residue 298 
Skipped atom 1830 because residue number 228  < previous residue 298 
Skipped atom 1831 because residue number 228  < previous residue 298 
Skipped atom 1832 because residue number 228  < previous residue 298 
Skipped atom 1833 because residue number 228  < previous residue 298 
Skipped atom 1834 because residue number 228  < previous residue 298 
Skipped atom 1835 because residue number 228  < previous residue 298 
Skipped atom 1836 because residue number 229  < previous residue 298 
Skipped atom 1837 because residue number 229  < previous residue 298 
Skipped atom 1838 because residue number 229  < previous residue 298 
Skipped atom 1839 because residue number 229  < previous residue 298 
Skipped atom 1840 because residue number 229  < previous residue 298 
Skipped atom 1841 because residue number 229  < previous residue 298 
Skipped atom 1842 because residue number 229  < previous residue 298 
Skipped atom 1843 because residue number 229  < previous residue 298 
Skipped atom 1844 because residue number 229  < previous residue 298 
Skipped atom 1845 because residue number 229  < previous residue 298 
Skipped atom 1846 because residue number 229  < previous residue 298 
Skipped atom 1847 because residue number 229  < previous residue 298 
Skipped atom 1848 because residue number 230  < previous residue 298 
Skipped atom 1849 because residue number 230  < previous residue 298 
Skipped atom 1850 because residue number 230  < previous residue 298 
Skipped atom 1851 because residue number 230  < previous residue 298 
Skipped atom 1852 because residue number 230  < previous residue 298 
Skipped atom 1853 because residue number 230  < previous residue 298 
Skipped atom 1854 because residue number 230  < previous residue 298 
Skipped atom 1855 because residue number 230  < previous residue 298 
Skipped atom 1856 because residue number 230  < previous residue 298 
Skipped atom 1857 because residue number 231  < previous residue 298 
Skipped atom 1858 because residue number 231  < previous residue 298 
Skipped atom 1859 because residue number 231  < previous residue 298 
Skipped atom 1860 because residue number 231  < previous residue 298 
Skipped atom 1861 because residue number 231  < previous residue 298 
Skipped atom 1862 because residue number 231  < previous residue 298 
Skipped atom 1863 because residue number 231  < previous residue 298 
Skipped atom 1864 because residue number 232  < previous residue 298 
Skipped atom 1865 because residue number 232  < previous residue 298 
Skipped atom 1866 because residue number 232  < previous residue 298 
Skipped atom 1867 because residue number 232  < previous residue 298 
Skipped atom 1868 because residue number 232  < previous residue 298 
Skipped atom 1869 because residue number 233  < previous residue 298 
Skipped atom 1870 because residue number 233  < previous residue 298 
Skipped atom 1871 because residue number 233  < previous residue 298 
Skipped atom 1872 because residue number 233  < previous residue 298 
Skipped atom 1873 because residue number 233  < previous residue 298 
Skipped atom 1874 because residue number 233  < previous residue 298 
Skipped atom 1875 because residue number 233  < previous residue 298 
Skipped atom 1876 because residue number 233  < previous residue 298 
Skipped atom 1877 because residue number 234  < previous residue 298 
Skipped atom 1878 because residue number 234  < previous residue 298 
Skipped atom 1879 because residue number 234  < previous residue 298 
Skipped atom 1880 because residue number 234  < previous residue 298 
Skipped atom 1881 because residue number 234  < previous residue 298 
Skipped atom 1882 because residue number 234  < previous residue 298 
Skipped atom 1883 because residue number 234  < previous residue 298 
Skipped atom 1884 because residue number 234  < previous residue 298 
Skipped atom 1885 because residue number 234  < previous residue 298 
Skipped atom 1886 because residue number 235  < previous residue 298 
Skipped atom 1887 because residue number 235  < previous residue 298 
Skipped atom 1888 because residue number 235  < previous residue 298 
Skipped atom 1889 because residue number 235  < previous residue 298 
Skipped atom 1890 because residue number 235  < previous residue 298 
Skipped atom 1891 because residue number 235  < previous residue 298 
Skipped atom 1892 because residue number 236  < previous residue 298 
Skipped atom 1893 because residue number 236  < previous residue 298 
Skipped atom 1894 because residue number 236  < previous residue 298 
Skipped atom 1895 because residue number 236  < previous residue 298 
Skipped atom 1896 because residue number 237  < previous residue 298 
Skipped atom 1897 because residue number 237  < previous residue 298 
Skipped atom 1898 because residue number 237  < previous residue 298 
Skipped atom 1899 because residue number 237  < previous residue 298 
Skipped atom 1900 because residue number 237  < previous residue 298 
Skipped atom 1901 because residue number 237  < previous residue 298 
Skipped atom 1902 because residue number 237  < previous residue 298 
Skipped atom 1903 because residue number 237  < previous residue 298 
Skipped atom 1904 because residue number 237  < previous residue 298 
Skipped atom 1905 because residue number 238  < previous residue 298 
Skipped atom 1906 because residue number 238  < previous residue 298 
Skipped atom 1907 because residue number 238  < previous residue 298 
Skipped atom 1908 because residue number 238  < previous residue 298 
Skipped atom 1909 because residue number 238  < previous residue 298 
Skipped atom 1910 because residue number 239  < previous residue 298 
Skipped atom 1911 because residue number 239  < previous residue 298 
Skipped atom 1912 because residue number 239  < previous residue 298 
Skipped atom 1913 because residue number 239  < previous residue 298 
Skipped atom 1914 because residue number 239  < previous residue 298 
Skipped atom 1915 because residue number 239  < previous residue 298 
Skipped atom 1916 because residue number 239  < previous residue 298 
Skipped atom 1917 because residue number 239  < previous residue 298 
Skipped atom 1918 because residue number 240  < previous residue 298 
Skipped atom 1919 because residue number 240  < previous residue 298 
Skipped atom 1920 because residue number 240  < previous residue 298 
Skipped atom 1921 because residue number 240  < previous residue 298 
Skipped atom 1922 because residue number 240  < previous residue 298 
Skipped atom 1923 because residue number 240  < previous residue 298 
Skipped atom 1924 because residue number 240  < previous residue 298 
Skipped atom 1925 because residue number 241  < previous residue 298 
Skipped atom 1926 because residue number 241  < previous residue 298 
Skipped atom 1927 because residue number 241  < previous residue 298 
Skipped atom 1928 because residue number 241  < previous residue 298 
Skipped atom 1929 because residue number 241  < previous residue 298 
Skipped atom 1930 because residue number 241  < previous residue 298 
Skipped atom 1931 because residue number 241  < previous residue 298 
Skipped atom 1932 because residue number 241  < previous residue 298 
Skipped atom 1933 because residue number 241  < previous residue 298 
Skipped atom 1934 because residue number 241  < previous residue 298 
Skipped atom 1935 because residue number 241  < previous residue 298 
Skipped atom 1936 because residue number 241  < previous residue 298 
Skipped atom 1937 because residue number 242  < previous residue 298 
Skipped atom 1938 because residue number 242  < previous residue 298 
Skipped atom 1939 because residue number 242  < previous residue 298 
Skipped atom 1940 because residue number 242  < previous residue 298 
Skipped atom 1941 because residue number 242  < previous residue 298 
Skipped atom 1942 because residue number 243  < previous residue 298 
Skipped atom 1943 because residue number 243  < previous residue 298 
Skipped atom 1944 because residue number 243  < previous residue 298 
Skipped atom 1945 because residue number 243  < previous residue 298 
Skipped atom 1946 because residue number 243  < previous residue 298 
Skipped atom 1947 because residue number 243  < previous residue 298 
Skipped atom 1948 because residue number 244  < previous residue 298 
Skipped atom 1949 because residue number 244  < previous residue 298 
Skipped atom 1950 because residue number 244  < previous residue 298 
Skipped atom 1951 because residue number 244  < previous residue 298 
Skipped atom 1952 because residue number 244  < previous residue 298 
Skipped atom 1953 because residue number 244  < previous residue 298 
Skipped atom 1954 because residue number 244  < previous residue 298 
Skipped atom 1955 because residue number 244  < previous residue 298 
Skipped atom 1956 because residue number 244  < previous residue 298 
Skipped atom 1957 because residue number 244  < previous residue 298 
Skipped atom 1958 because residue number 244  < previous residue 298 
Skipped atom 1959 because residue number 245  < previous residue 298 
Skipped atom 1960 because residue number 245  < previous residue 298 
Skipped atom 1961 because residue number 245  < previous residue 298 
Skipped atom 1962 because residue number 245  < previous residue 298 
Skipped atom 1963 because residue number 245  < previous residue 298 
Skipped atom 1964 because residue number 245  < previous residue 298 
Skipped atom 1965 because residue number 245  < previous residue 298 
Skipped atom 1966 because residue number 245  < previous residue 298 
Skipped atom 1967 because residue number 246  < previous residue 298 
Skipped atom 1968 because residue number 246  < previous residue 298 
Skipped atom 1969 because residue number 246  < previous residue 298 
Skipped atom 1970 because residue number 246  < previous residue 298 
Skipped atom 1971 because residue number 246  < previous residue 298 
Skipped atom 1972 because residue number 246  < previous residue 298 
Skipped atom 1973 because residue number 246  < previous residue 298 
Skipped atom 1974 because residue number 246  < previous residue 298 
Skipped atom 1975 because residue number 247  < previous residue 298 
Skipped atom 1976 because residue number 247  < previous residue 298 
Skipped atom 1977 because residue number 247  < previous residue 298 
Skipped atom 1978 because residue number 247  < previous residue 298 
Skipped atom 1979 because residue number 247  < previous residue 298 
Skipped atom 1980 because residue number 247  < previous residue 298 
Skipped atom 1981 because residue number 247  < previous residue 298 
Skipped atom 1982 because residue number 248  < previous residue 298 
Skipped atom 1983 because residue number 248  < previous residue 298 
Skipped atom 1984 because residue number 248  < previous residue 298 
Skipped atom 1985 because residue number 248  < previous residue 298 
Skipped atom 1986 because residue number 248  < previous residue 298 
Skipped atom 1987 because residue number 249  < previous residue 298 
Skipped atom 1988 because residue number 249  < previous residue 298 
Skipped atom 1989 because residue number 249  < previous residue 298 
Skipped atom 1990 because residue number 249  < previous residue 298 
Skipped atom 1991 because residue number 249  < previous residue 298 
Skipped atom 1992 because residue number 249  < previous residue 298 
Skipped atom 1993 because residue number 249  < previous residue 298 
Skipped atom 1994 because residue number 249  < previous residue 298 
Skipped atom 1995 because residue number 249  < previous residue 298 
Skipped atom 1996 because residue number 249  < previous residue 298 
Skipped atom 1997 because residue number 249  < previous residue 298 
Skipped atom 1998 because residue number 250  < previous residue 298 
Skipped atom 1999 because residue number 250  < previous residue 298 
Skipped atom 2000 because residue number 250  < previous residue 298 
Skipped atom 2001 because residue number 250  < previous residue 298 
Skipped atom 2002 because residue number 250  < previous residue 298 
Skipped atom 2003 because residue number 250  < previous residue 298 
Skipped atom 2004 because residue number 250  < previous residue 298 
Skipped atom 2005 because residue number 251  < previous residue 298 
Skipped atom 2006 because residue number 251  < previous residue 298 
Skipped atom 2007 because residue number 251  < previous residue 298 
Skipped atom 2008 because residue number 251  < previous residue 298 
Skipped atom 2009 because residue number 251  < previous residue 298 
Skipped atom 2010 because residue number 251  < previous residue 298 
Skipped atom 2011 because residue number 251  < previous residue 298 
Skipped atom 2012 because residue number 251  < previous residue 298 
Skipped atom 2013 because residue number 251  < previous residue 298 
Skipped atom 2014 because residue number 251  < previous residue 298 
Skipped atom 2015 because residue number 251  < previous residue 298 
Skipped atom 2016 because residue number 251  < previous residue 298 
Skipped atom 2017 because residue number 252  < previous residue 298 
Skipped atom 2018 because residue number 252  < previous residue 298 
Skipped atom 2019 because residue number 252  < previous residue 298 
Skipped atom 2020 because residue number 252  < previous residue 298 
Skipped atom 2021 because residue number 252  < previous residue 298 
Skipped atom 2022 because residue number 252  < previous residue 298 
Skipped atom 2023 because residue number 252  < previous residue 298 
Skipped atom 2024 because residue number 253  < previous residue 298 
Skipped atom 2025 because residue number 253  < previous residue 298 
Skipped atom 2026 because residue number 253  < previous residue 298 
Skipped atom 2027 because residue number 253  < previous residue 298 
Skipped atom 2028 because residue number 253  < previous residue 298 
Skipped atom 2029 because residue number 253  < previous residue 298 
Skipped atom 2030 because residue number 253  < previous residue 298 
Skipped atom 2031 because residue number 253  < previous residue 298 
Skipped atom 2032 because residue number 253  < previous residue 298 
Skipped atom 2033 because residue number 253  < previous residue 298 
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1alq-orig.a2m
Writing a2m file: tmp/1alq-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8936


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8936/tmp -alignfile tmp/1alq-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1alq-orig.a2m (1 sequences, 266 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8936/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8936/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8936/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8936/tmp.a2m (1 sequences, 266 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8936/tmp.mod tmp/1alq-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8936 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1alq-align.mod
tmp/1alq-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8936/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1alq-orig.a2m tmp/1alq-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1alq-align.mod
Running w0.5 tmp/1alq-orig.a2m tmp/1alq-align.mod
Running align2model tmp/1alq-align -i tmp/1alq-align.mod -db tmp/1alq-orig.a2m -db tmp/1alq-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1alq.146.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1alq.147.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1alq.147.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1alq.147.1.a2m \
	-target T0124 -template 1alq \
	-out T0124-1alq.147.1 -outdir und
Skipped atom 298 because residue number 31  < previous residue 298 
Skipped atom 299 because residue number 31  < previous residue 298 
Skipped atom 300 because residue number 31  < previous residue 298 
Skipped atom 301 because residue number 31  < previous residue 298 
Skipped atom 302 because residue number 31  < previous residue 298 
Skipped atom 303 because residue number 31  < previous residue 298 
Skipped atom 304 because residue number 31  < previous residue 298 
Skipped atom 305 because residue number 31  < previous residue 298 
Skipped atom 306 because residue number 31  < previous residue 298 
Skipped atom 307 because residue number 32  < previous residue 298 
Skipped atom 308 because residue number 32  < previous residue 298 
Skipped atom 309 because residue number 32  < previous residue 298 
Skipped atom 310 because residue number 32  < previous residue 298 
Skipped atom 311 because residue number 32  < previous residue 298 
Skipped atom 312 because residue number 32  < previous residue 298 
Skipped atom 313 because residue number 32  < previous residue 298 
Skipped atom 314 because residue number 32  < previous residue 298 
Skipped atom 315 because residue number 32  < previous residue 298 
Skipped atom 316 because residue number 33  < previous residue 298 
Skipped atom 317 because residue number 33  < previous residue 298 
Skipped atom 318 because residue number 33  < previous residue 298 
Skipped atom 319 because residue number 33  < previous residue 298 
Skipped atom 320 because residue number 33  < previous residue 298 
Skipped atom 321 because residue number 33  < previous residue 298 
Skipped atom 322 because residue number 33  < previous residue 298 
Skipped atom 323 because residue number 33  < previous residue 298 
Skipped atom 324 because residue number 34  < previous residue 298 
Skipped atom 325 because residue number 34  < previous residue 298 
Skipped atom 326 because residue number 34  < previous residue 298 
Skipped atom 327 because residue number 34  < previous residue 298 
Skipped atom 328 because residue number 34  < previous residue 298 
Skipped atom 329 because residue number 34  < previous residue 298 
Skipped atom 330 because residue number 34  < previous residue 298 
Skipped atom 331 because residue number 34  < previous residue 298 
Skipped atom 332 because residue number 35  < previous residue 298 
Skipped atom 333 because residue number 35  < previous residue 298 
Skipped atom 334 because residue number 35  < previous residue 298 
Skipped atom 335 because residue number 35  < previous residue 298 
Skipped atom 336 because residue number 35  < previous residue 298 
Skipped atom 337 because residue number 35  < previous residue 298 
Skipped atom 338 because residue number 35  < previous residue 298 
Skipped atom 339 because residue number 35  < previous residue 298 
Skipped atom 340 because residue number 36  < previous residue 298 
Skipped atom 341 because residue number 36  < previous residue 298 
Skipped atom 342 because residue number 36  < previous residue 298 
Skipped atom 343 because residue number 36  < previous residue 298 
Skipped atom 344 because residue number 36  < previous residue 298 
Skipped atom 345 because residue number 36  < previous residue 298 
Skipped atom 346 because residue number 36  < previous residue 298 
Skipped atom 347 because residue number 36  < previous residue 298 
Skipped atom 348 because residue number 37  < previous residue 298 
Skipped atom 349 because residue number 37  < previous residue 298 
Skipped atom 350 because residue number 37  < previous residue 298 
Skipped atom 351 because residue number 37  < previous residue 298 
Skipped atom 352 because residue number 37  < previous residue 298 
Skipped atom 353 because residue number 37  < previous residue 298 
Skipped atom 354 because residue number 37  < previous residue 298 
Skipped atom 355 because residue number 37  < previous residue 298 
Skipped atom 356 because residue number 37  < previous residue 298 
Skipped atom 357 because residue number 38  < previous residue 298 
Skipped atom 358 because residue number 38  < previous residue 298 
Skipped atom 359 because residue number 38  < previous residue 298 
Skipped atom 360 because residue number 38  < previous residue 298 
Skipped atom 361 because residue number 38  < previous residue 298 
Skipped atom 362 because residue number 38  < previous residue 298 
Skipped atom 363 because residue number 38  < previous residue 298 
Skipped atom 364 because residue number 38  < previous residue 298 
Skipped atom 365 because residue number 38  < previous residue 298 
Skipped atom 366 because residue number 39  < previous residue 298 
Skipped atom 367 because residue number 39  < previous residue 298 
Skipped atom 368 because residue number 39  < previous residue 298 
Skipped atom 369 because residue number 39  < previous residue 298 
Skipped atom 370 because residue number 39  < previous residue 298 
Skipped atom 371 because residue number 39  < previous residue 298 
Skipped atom 372 because residue number 39  < previous residue 298 
Skipped atom 373 because residue number 39  < previous residue 298 
Skipped atom 374 because residue number 39  < previous residue 298 
Skipped atom 375 because residue number 40  < previous residue 298 
Skipped atom 376 because residue number 40  < previous residue 298 
Skipped atom 377 because residue number 40  < previous residue 298 
Skipped atom 378 because residue number 40  < previous residue 298 
Skipped atom 379 because residue number 40  < previous residue 298 
Skipped atom 380 because residue number 40  < previous residue 298 
Skipped atom 381 because residue number 40  < previous residue 298 
Skipped atom 382 because residue number 40  < previous residue 298 
Skipped atom 383 because residue number 40  < previous residue 298 
Skipped atom 384 because residue number 40  < previous residue 298 
Skipped atom 385 because residue number 40  < previous residue 298 
Skipped atom 386 because residue number 40  < previous residue 298 
Skipped atom 387 because residue number 41  < previous residue 298 
Skipped atom 388 because residue number 41  < previous residue 298 
Skipped atom 389 because residue number 41  < previous residue 298 
Skipped atom 390 because residue number 41  < previous residue 298 
Skipped atom 391 because residue number 41  < previous residue 298 
Skipped atom 392 because residue number 41  < previous residue 298 
Skipped atom 393 because residue number 41  < previous residue 298 
Skipped atom 394 because residue number 41  < previous residue 298 
Skipped atom 395 because residue number 42  < previous residue 298 
Skipped atom 396 because residue number 42  < previous residue 298 
Skipped atom 397 because residue number 42  < previous residue 298 
Skipped atom 398 because residue number 42  < previous residue 298 
Skipped atom 399 because residue number 42  < previous residue 298 
Skipped atom 400 because residue number 43  < previous residue 298 
Skipped atom 401 because residue number 43  < previous residue 298 
Skipped atom 402 because residue number 43  < previous residue 298 
Skipped atom 403 because residue number 43  < previous residue 298 
Skipped atom 404 because residue number 43  < previous residue 298 
Skipped atom 405 because residue number 43  < previous residue 298 
Skipped atom 406 because residue number 43  < previous residue 298 
Skipped atom 407 because residue number 43  < previous residue 298 
Skipped atom 408 because residue number 43  < previous residue 298 
Skipped atom 409 because residue number 43  < previous residue 298 
Skipped atom 410 because residue number 44  < previous residue 298 
Skipped atom 411 because residue number 44  < previous residue 298 
Skipped atom 412 because residue number 44  < previous residue 298 
Skipped atom 413 because residue number 44  < previous residue 298 
Skipped atom 414 because residue number 44  < previous residue 298 
Skipped atom 415 because residue number 44  < previous residue 298 
Skipped atom 416 because residue number 44  < previous residue 298 
Skipped atom 417 because residue number 44  < previous residue 298 
Skipped atom 418 because residue number 45  < previous residue 298 
Skipped atom 419 because residue number 45  < previous residue 298 
Skipped atom 420 because residue number 45  < previous residue 298 
Skipped atom 421 because residue number 45  < previous residue 298 
Skipped atom 422 because residue number 46  < previous residue 298 
Skipped atom 423 because residue number 46  < previous residue 298 
Skipped atom 424 because residue number 46  < previous residue 298 
Skipped atom 425 because residue number 46  < previous residue 298 
Skipped atom 426 because residue number 46  < previous residue 298 
Skipped atom 427 because residue number 46  < previous residue 298 
Skipped atom 428 because residue number 46  < previous residue 298 
Skipped atom 429 because residue number 47  < previous residue 298 
Skipped atom 430 because residue number 47  < previous residue 298 
Skipped atom 431 because residue number 47  < previous residue 298 
Skipped atom 432 because residue number 47  < previous residue 298 
Skipped atom 433 because residue number 47  < previous residue 298 
Skipped atom 434 because residue number 47  < previous residue 298 
Skipped atom 435 because residue number 47  < previous residue 298 
Skipped atom 436 because residue number 47  < previous residue 298 
Skipped atom 437 because residue number 47  < previous residue 298 
Skipped atom 438 because residue number 47  < previous residue 298 
Skipped atom 439 because residue number 47  < previous residue 298 
Skipped atom 440 because residue number 47  < previous residue 298 
Skipped atom 441 because residue number 48  < previous residue 298 
Skipped atom 442 because residue number 48  < previous residue 298 
Skipped atom 443 because residue number 48  < previous residue 298 
Skipped atom 444 because residue number 48  < previous residue 298 
Skipped atom 445 because residue number 48  < previous residue 298 
Skipped atom 446 because residue number 49  < previous residue 298 
Skipped atom 447 because residue number 49  < previous residue 298 
Skipped atom 448 because residue number 49  < previous residue 298 
Skipped atom 449 because residue number 49  < previous residue 298 
Skipped atom 450 because residue number 49  < previous residue 298 
Skipped atom 451 because residue number 49  < previous residue 298 
Skipped atom 452 because residue number 49  < previous residue 298 
Skipped atom 453 because residue number 49  < previous residue 298 
Skipped atom 454 because residue number 50  < previous residue 298 
Skipped atom 455 because residue number 50  < previous residue 298 
Skipped atom 456 because residue number 50  < previous residue 298 
Skipped atom 457 because residue number 50  < previous residue 298 
Skipped atom 458 because residue number 50  < previous residue 298 
Skipped atom 459 because residue number 50  < previous residue 298 
Skipped atom 460 because residue number 50  < previous residue 298 
Skipped atom 461 because residue number 50  < previous residue 298 
Skipped atom 462 because residue number 51  < previous residue 298 
Skipped atom 463 because residue number 51  < previous residue 298 
Skipped atom 464 because residue number 51  < previous residue 298 
Skipped atom 465 because residue number 51  < previous residue 298 
Skipped atom 466 because residue number 51  < previous residue 298 
Skipped atom 467 because residue number 51  < previous residue 298 
Skipped atom 468 because residue number 51  < previous residue 298 
Skipped atom 469 because residue number 52  < previous residue 298 
Skipped atom 470 because residue number 52  < previous residue 298 
Skipped atom 471 because residue number 52  < previous residue 298 
Skipped atom 472 because residue number 52  < previous residue 298 
Skipped atom 473 because residue number 52  < previous residue 298 
Skipped atom 474 because residue number 52  < previous residue 298 
Skipped atom 475 because residue number 52  < previous residue 298 
Skipped atom 476 because residue number 52  < previous residue 298 
Skipped atom 477 because residue number 52  < previous residue 298 
Skipped atom 478 because residue number 53  < previous residue 298 
Skipped atom 479 because residue number 53  < previous residue 298 
Skipped atom 480 because residue number 53  < previous residue 298 
Skipped atom 481 because residue number 53  < previous residue 298 
Skipped atom 482 because residue number 53  < previous residue 298 
Skipped atom 483 because residue number 53  < previous residue 298 
Skipped atom 484 because residue number 54  < previous residue 298 
Skipped atom 485 because residue number 54  < previous residue 298 
Skipped atom 486 because residue number 54  < previous residue 298 
Skipped atom 487 because residue number 54  < previous residue 298 
Skipped atom 488 because residue number 55  < previous residue 298 
Skipped atom 489 because residue number 55  < previous residue 298 
Skipped atom 490 because residue number 55  < previous residue 298 
Skipped atom 491 because residue number 55  < previous residue 298 
Skipped atom 492 because residue number 55  < previous residue 298 
Skipped atom 493 because residue number 55  < previous residue 298 
Skipped atom 494 because residue number 55  < previous residue 298 
Skipped atom 495 because residue number 55  < previous residue 298 
Skipped atom 496 because residue number 55  < previous residue 298 
Skipped atom 497 because residue number 56  < previous residue 298 
Skipped atom 498 because residue number 56  < previous residue 298 
Skipped atom 499 because residue number 56  < previous residue 298 
Skipped atom 500 because residue number 56  < previous residue 298 
Skipped atom 501 because residue number 56  < previous residue 298 
Skipped atom 502 because residue number 56  < previous residue 298 
Skipped atom 503 because residue number 56  < previous residue 298 
Skipped atom 504 because residue number 56  < previous residue 298 
Skipped atom 505 because residue number 56  < previous residue 298 
Skipped atom 506 because residue number 57  < previous residue 298 
Skipped atom 507 because residue number 57  < previous residue 298 
Skipped atom 508 because residue number 57  < previous residue 298 
Skipped atom 509 because residue number 57  < previous residue 298 
Skipped atom 510 because residue number 57  < previous residue 298 
Skipped atom 511 because residue number 57  < previous residue 298 
Skipped atom 512 because residue number 57  < previous residue 298 
Skipped atom 513 because residue number 59  < previous residue 298 
Skipped atom 514 because residue number 59  < previous residue 298 
Skipped atom 515 because residue number 59  < previous residue 298 
Skipped atom 516 because residue number 59  < previous residue 298 
Skipped atom 517 because residue number 59  < previous residue 298 
Skipped atom 518 because residue number 59  < previous residue 298 
Skipped atom 519 because residue number 59  < previous residue 298 
Skipped atom 520 because residue number 59  < previous residue 298 
Skipped atom 521 because residue number 59  < previous residue 298 
Skipped atom 522 because residue number 60  < previous residue 298 
Skipped atom 523 because residue number 60  < previous residue 298 
Skipped atom 524 because residue number 60  < previous residue 298 
Skipped atom 525 because residue number 60  < previous residue 298 
Skipped atom 526 because residue number 60  < previous residue 298 
Skipped atom 527 because residue number 60  < previous residue 298 
Skipped atom 528 because residue number 60  < previous residue 298 
Skipped atom 529 because residue number 60  < previous residue 298 
Skipped atom 530 because residue number 60  < previous residue 298 
Skipped atom 531 because residue number 60  < previous residue 298 
Skipped atom 532 because residue number 60  < previous residue 298 
Skipped atom 533 because residue number 61  < previous residue 298 
Skipped atom 534 because residue number 61  < previous residue 298 
Skipped atom 535 because residue number 61  < previous residue 298 
Skipped atom 536 because residue number 61  < previous residue 298 
Skipped atom 537 because residue number 61  < previous residue 298 
Skipped atom 538 because residue number 61  < previous residue 298 
Skipped atom 539 because residue number 61  < previous residue 298 
Skipped atom 540 because residue number 61  < previous residue 298 
Skipped atom 541 because residue number 62  < previous residue 298 
Skipped atom 542 because residue number 62  < previous residue 298 
Skipped atom 543 because residue number 62  < previous residue 298 
Skipped atom 544 because residue number 62  < previous residue 298 
Skipped atom 545 because residue number 62  < previous residue 298 
Skipped atom 546 because residue number 62  < previous residue 298 
Skipped atom 547 because residue number 63  < previous residue 298 
Skipped atom 548 because residue number 63  < previous residue 298 
Skipped atom 549 because residue number 63  < previous residue 298 
Skipped atom 550 because residue number 63  < previous residue 298 
Skipped atom 551 because residue number 63  < previous residue 298 
Skipped atom 552 because residue number 63  < previous residue 298 
Skipped atom 553 because residue number 63  < previous residue 298 
Skipped atom 554 because residue number 63  < previous residue 298 
Skipped atom 555 because residue number 64  < previous residue 298 
Skipped atom 556 because residue number 64  < previous residue 298 
Skipped atom 557 because residue number 64  < previous residue 298 
Skipped atom 558 because residue number 64  < previous residue 298 
Skipped atom 559 because residue number 64  < previous residue 298 
Skipped atom 560 because residue number 64  < previous residue 298 
Skipped atom 561 because residue number 64  < previous residue 298 
Skipped atom 562 because residue number 64  < previous residue 298 
Skipped atom 563 because residue number 64  < previous residue 298 
Skipped atom 564 because residue number 65  < previous residue 298 
Skipped atom 565 because residue number 65  < previous residue 298 
Skipped atom 566 because residue number 65  < previous residue 298 
Skipped atom 567 because residue number 65  < previous residue 298 
Skipped atom 568 because residue number 65  < previous residue 298 
Skipped atom 569 because residue number 65  < previous residue 298 
Skipped atom 570 because residue number 65  < previous residue 298 
Skipped atom 571 because residue number 65  < previous residue 298 
Skipped atom 572 because residue number 65  < previous residue 298 
Skipped atom 573 because residue number 65  < previous residue 298 
Skipped atom 574 because residue number 65  < previous residue 298 
Skipped atom 575 because residue number 66  < previous residue 298 
Skipped atom 576 because residue number 66  < previous residue 298 
Skipped atom 577 because residue number 66  < previous residue 298 
Skipped atom 578 because residue number 66  < previous residue 298 
Skipped atom 579 because residue number 66  < previous residue 298 
Skipped atom 580 because residue number 66  < previous residue 298 
Skipped atom 581 because residue number 66  < previous residue 298 
Skipped atom 582 because residue number 66  < previous residue 298 
Skipped atom 583 because residue number 66  < previous residue 298 
Skipped atom 584 because residue number 66  < previous residue 298 
Skipped atom 585 because residue number 66  < previous residue 298 
Skipped atom 586 because residue number 67  < previous residue 298 
Skipped atom 587 because residue number 67  < previous residue 298 
Skipped atom 588 because residue number 67  < previous residue 298 
Skipped atom 589 because residue number 67  < previous residue 298 
Skipped atom 590 because residue number 67  < previous residue 298 
Skipped atom 591 because residue number 68  < previous residue 298 
Skipped atom 592 because residue number 68  < previous residue 298 
Skipped atom 593 because residue number 68  < previous residue 298 
Skipped atom 594 because residue number 68  < previous residue 298 
Skipped atom 595 because residue number 68  < previous residue 298 
Skipped atom 596 because residue number 68  < previous residue 298 
Skipped atom 597 because residue number 68  < previous residue 298 
Skipped atom 598 because residue number 68  < previous residue 298 
Skipped atom 599 because residue number 68  < previous residue 298 
Skipped atom 600 because residue number 68  < previous residue 298 
Skipped atom 601 because residue number 68  < previous residue 298 
Skipped atom 602 because residue number 68  < previous residue 298 
Skipped atom 603 because residue number 69  < previous residue 298 
Skipped atom 604 because residue number 69  < previous residue 298 
Skipped atom 605 because residue number 69  < previous residue 298 
Skipped atom 606 because residue number 69  < previous residue 298 
Skipped atom 607 because residue number 69  < previous residue 298 
Skipped atom 608 because residue number 70  < previous residue 298 
Skipped atom 609 because residue number 70  < previous residue 298 
Skipped atom 610 because residue number 70  < previous residue 298 
Skipped atom 611 because residue number 70  < previous residue 298 
Skipped atom 612 because residue number 70  < previous residue 298 
Skipped atom 613 because residue number 70  < previous residue 298 
Skipped atom 614 because residue number 71  < previous residue 298 
Skipped atom 615 because residue number 71  < previous residue 298 
Skipped atom 616 because residue number 71  < previous residue 298 
Skipped atom 617 because residue number 71  < previous residue 298 
Skipped atom 618 because residue number 71  < previous residue 298 
Skipped atom 619 because residue number 71  < previous residue 298 
Skipped atom 620 because residue number 71  < previous residue 298 
Skipped atom 621 because residue number 72  < previous residue 298 
Skipped atom 622 because residue number 72  < previous residue 298 
Skipped atom 623 because residue number 72  < previous residue 298 
Skipped atom 624 because residue number 72  < previous residue 298 
Skipped atom 625 because residue number 72  < previous residue 298 
Skipped atom 626 because residue number 72  < previous residue 298 
Skipped atom 627 because residue number 73  < previous residue 298 
Skipped atom 628 because residue number 73  < previous residue 298 
Skipped atom 629 because residue number 73  < previous residue 298 
Skipped atom 630 because residue number 73  < previous residue 298 
Skipped atom 631 because residue number 73  < previous residue 298 
Skipped atom 632 because residue number 73  < previous residue 298 
Skipped atom 633 because residue number 73  < previous residue 298 
Skipped atom 634 because residue number 73  < previous residue 298 
Skipped atom 635 because residue number 73  < previous residue 298 
Skipped atom 636 because residue number 74  < previous residue 298 
Skipped atom 637 because residue number 74  < previous residue 298 
Skipped atom 638 because residue number 74  < previous residue 298 
Skipped atom 639 because residue number 74  < previous residue 298 
Skipped atom 640 because residue number 74  < previous residue 298 
Skipped atom 641 because residue number 75  < previous residue 298 
Skipped atom 642 because residue number 75  < previous residue 298 
Skipped atom 643 because residue number 75  < previous residue 298 
Skipped atom 644 because residue number 75  < previous residue 298 
Skipped atom 645 because residue number 75  < previous residue 298 
Skipped atom 646 because residue number 75  < previous residue 298 
Skipped atom 647 because residue number 75  < previous residue 298 
Skipped atom 648 because residue number 75  < previous residue 298 
Skipped atom 649 because residue number 76  < previous residue 298 
Skipped atom 650 because residue number 76  < previous residue 298 
Skipped atom 651 because residue number 76  < previous residue 298 
Skipped atom 652 because residue number 76  < previous residue 298 
Skipped atom 653 because residue number 76  < previous residue 298 
Skipped atom 654 because residue number 76  < previous residue 298 
Skipped atom 655 because residue number 76  < previous residue 298 
Skipped atom 656 because residue number 76  < previous residue 298 
Skipped atom 657 because residue number 77  < previous residue 298 
Skipped atom 658 because residue number 77  < previous residue 298 
Skipped atom 659 because residue number 77  < previous residue 298 
Skipped atom 660 because residue number 77  < previous residue 298 
Skipped atom 661 because residue number 77  < previous residue 298 
Skipped atom 662 because residue number 77  < previous residue 298 
Skipped atom 663 because residue number 78  < previous residue 298 
Skipped atom 664 because residue number 78  < previous residue 298 
Skipped atom 665 because residue number 78  < previous residue 298 
Skipped atom 666 because residue number 78  < previous residue 298 
Skipped atom 667 because residue number 78  < previous residue 298 
Skipped atom 668 because residue number 79  < previous residue 298 
Skipped atom 669 because residue number 79  < previous residue 298 
Skipped atom 670 because residue number 79  < previous residue 298 
Skipped atom 671 because residue number 79  < previous residue 298 
Skipped atom 672 because residue number 79  < previous residue 298 
Skipped atom 673 because residue number 79  < previous residue 298 
Skipped atom 674 because residue number 79  < previous residue 298 
Skipped atom 675 because residue number 79  < previous residue 298 
Skipped atom 676 because residue number 80  < previous residue 298 
Skipped atom 677 because residue number 80  < previous residue 298 
Skipped atom 678 because residue number 80  < previous residue 298 
Skipped atom 679 because residue number 80  < previous residue 298 
Skipped atom 680 because residue number 80  < previous residue 298 
Skipped atom 681 because residue number 80  < previous residue 298 
Skipped atom 682 because residue number 80  < previous residue 298 
Skipped atom 683 because residue number 80  < previous residue 298 
Skipped atom 684 because residue number 81  < previous residue 298 
Skipped atom 685 because residue number 81  < previous residue 298 
Skipped atom 686 because residue number 81  < previous residue 298 
Skipped atom 687 because residue number 81  < previous residue 298 
Skipped atom 688 because residue number 81  < previous residue 298 
Skipped atom 689 because residue number 81  < previous residue 298 
Skipped atom 690 because residue number 81  < previous residue 298 
Skipped atom 691 because residue number 81  < previous residue 298 
Skipped atom 692 because residue number 82  < previous residue 298 
Skipped atom 693 because residue number 82  < previous residue 298 
Skipped atom 694 because residue number 82  < previous residue 298 
Skipped atom 695 because residue number 82  < previous residue 298 
Skipped atom 696 because residue number 82  < previous residue 298 
Skipped atom 697 because residue number 82  < previous residue 298 
Skipped atom 698 because residue number 82  < previous residue 298 
Skipped atom 699 because residue number 82  < previous residue 298 
Skipped atom 700 because residue number 82  < previous residue 298 
Skipped atom 701 because residue number 83  < previous residue 298 
Skipped atom 702 because residue number 83  < previous residue 298 
Skipped atom 703 because residue number 83  < previous residue 298 
Skipped atom 704 because residue number 83  < previous residue 298 
Skipped atom 705 because residue number 83  < previous residue 298 
Skipped atom 706 because residue number 83  < previous residue 298 
Skipped atom 707 because residue number 83  < previous residue 298 
Skipped atom 708 because residue number 83  < previous residue 298 
Skipped atom 709 because residue number 83  < previous residue 298 
Skipped atom 710 because residue number 84  < previous residue 298 
Skipped atom 711 because residue number 84  < previous residue 298 
Skipped atom 712 because residue number 84  < previous residue 298 
Skipped atom 713 because residue number 84  < previous residue 298 
Skipped atom 714 because residue number 84  < previous residue 298 
Skipped atom 715 because residue number 84  < previous residue 298 
Skipped atom 716 because residue number 84  < previous residue 298 
Skipped atom 717 because residue number 87  < previous residue 298 
Skipped atom 718 because residue number 87  < previous residue 298 
Skipped atom 719 because residue number 87  < previous residue 298 
Skipped atom 720 because residue number 87  < previous residue 298 
Skipped atom 721 because residue number 87  < previous residue 298 
Skipped atom 722 because residue number 87  < previous residue 298 
Skipped atom 723 because residue number 87  < previous residue 298 
Skipped atom 724 because residue number 88  < previous residue 298 
Skipped atom 725 because residue number 88  < previous residue 298 
Skipped atom 726 because residue number 88  < previous residue 298 
Skipped atom 727 because residue number 88  < previous residue 298 
Skipped atom 728 because residue number 88  < previous residue 298 
Skipped atom 729 because residue number 88  < previous residue 298 
Skipped atom 730 because residue number 88  < previous residue 298 
Skipped atom 731 because residue number 88  < previous residue 298 
Skipped atom 732 because residue number 88  < previous residue 298 
Skipped atom 733 because residue number 88  < previous residue 298 
Skipped atom 734 because residue number 88  < previous residue 298 
Skipped atom 735 because residue number 88  < previous residue 298 
Skipped atom 736 because residue number 89  < previous residue 298 
Skipped atom 737 because residue number 89  < previous residue 298 
Skipped atom 738 because residue number 89  < previous residue 298 
Skipped atom 739 because residue number 89  < previous residue 298 
Skipped atom 740 because residue number 89  < previous residue 298 
Skipped atom 741 because residue number 89  < previous residue 298 
Skipped atom 742 because residue number 89  < previous residue 298 
Skipped atom 743 because residue number 89  < previous residue 298 
Skipped atom 744 because residue number 90  < previous residue 298 
Skipped atom 745 because residue number 90  < previous residue 298 
Skipped atom 746 because residue number 90  < previous residue 298 
Skipped atom 747 because residue number 90  < previous residue 298 
Skipped atom 748 because residue number 90  < previous residue 298 
Skipped atom 749 because residue number 90  < previous residue 298 
Skipped atom 750 because residue number 90  < previous residue 298 
Skipped atom 751 because residue number 90  < previous residue 298 
Skipped atom 752 because residue number 90  < previous residue 298 
Skipped atom 753 because residue number 91  < previous residue 298 
Skipped atom 754 because residue number 91  < previous residue 298 
Skipped atom 755 because residue number 91  < previous residue 298 
Skipped atom 756 because residue number 91  < previous residue 298 
Skipped atom 757 because residue number 91  < previous residue 298 
Skipped atom 758 because residue number 91  < previous residue 298 
Skipped atom 759 because residue number 91  < previous residue 298 
Skipped atom 760 because residue number 91  < previous residue 298 
Skipped atom 761 because residue number 92  < previous residue 298 
Skipped atom 762 because residue number 92  < previous residue 298 
Skipped atom 763 because residue number 92  < previous residue 298 
Skipped atom 764 because residue number 92  < previous residue 298 
Skipped atom 765 because residue number 92  < previous residue 298 
Skipped atom 766 because residue number 92  < previous residue 298 
Skipped atom 767 because residue number 92  < previous residue 298 
Skipped atom 768 because residue number 92  < previous residue 298 
Skipped atom 769 because residue number 93  < previous residue 298 
Skipped atom 770 because residue number 93  < previous residue 298 
Skipped atom 771 because residue number 93  < previous residue 298 
Skipped atom 772 because residue number 93  < previous residue 298 
Skipped atom 773 because residue number 93  < previous residue 298 
Skipped atom 774 because residue number 93  < previous residue 298 
Skipped atom 775 because residue number 93  < previous residue 298 
Skipped atom 776 because residue number 93  < previous residue 298 
Skipped atom 777 because residue number 93  < previous residue 298 
Skipped atom 778 because residue number 94  < previous residue 298 
Skipped atom 779 because residue number 94  < previous residue 298 
Skipped atom 780 because residue number 94  < previous residue 298 
Skipped atom 781 because residue number 94  < previous residue 298 
Skipped atom 782 because residue number 94  < previous residue 298 
Skipped atom 783 because residue number 94  < previous residue 298 
Skipped atom 784 because residue number 94  < previous residue 298 
Skipped atom 785 because residue number 94  < previous residue 298 
Skipped atom 786 because residue number 94  < previous residue 298 
Skipped atom 787 because residue number 95  < previous residue 298 
Skipped atom 788 because residue number 95  < previous residue 298 
Skipped atom 789 because residue number 95  < previous residue 298 
Skipped atom 790 because residue number 95  < previous residue 298 
Skipped atom 791 because residue number 95  < previous residue 298 
Skipped atom 792 because residue number 95  < previous residue 298 
Skipped atom 793 because residue number 95  < previous residue 298 
Skipped atom 794 because residue number 96  < previous residue 298 
Skipped atom 795 because residue number 96  < previous residue 298 
Skipped atom 796 because residue number 96  < previous residue 298 
Skipped atom 797 because residue number 96  < previous residue 298 
Skipped atom 798 because residue number 96  < previous residue 298 
Skipped atom 799 because residue number 96  < previous residue 298 
Skipped atom 800 because residue number 96  < previous residue 298 
Skipped atom 801 because residue number 96  < previous residue 298 
Skipped atom 802 because residue number 96  < previous residue 298 
Skipped atom 803 because residue number 96  < previous residue 298 
Skipped atom 804 because residue number 97  < previous residue 298 
Skipped atom 805 because residue number 97  < previous residue 298 
Skipped atom 806 because residue number 97  < previous residue 298 
Skipped atom 807 because residue number 97  < previous residue 298 
Skipped atom 808 because residue number 97  < previous residue 298 
Skipped atom 809 because residue number 97  < previous residue 298 
Skipped atom 810 because residue number 97  < previous residue 298 
Skipped atom 811 because residue number 97  < previous residue 298 
Skipped atom 812 because residue number 98  < previous residue 298 
Skipped atom 813 because residue number 98  < previous residue 298 
Skipped atom 814 because residue number 98  < previous residue 298 
Skipped atom 815 because residue number 98  < previous residue 298 
Skipped atom 816 because residue number 98  < previous residue 298 
Skipped atom 817 because residue number 98  < previous residue 298 
Skipped atom 818 because residue number 98  < previous residue 298 
Skipped atom 819 because residue number 98  < previous residue 298 
Skipped atom 820 because residue number 99  < previous residue 298 
Skipped atom 821 because residue number 99  < previous residue 298 
Skipped atom 822 because residue number 99  < previous residue 298 
Skipped atom 823 because residue number 99  < previous residue 298 
Skipped atom 824 because residue number 99  < previous residue 298 
Skipped atom 825 because residue number 99  < previous residue 298 
Skipped atom 826 because residue number 99  < previous residue 298 
Skipped atom 827 because residue number 99  < previous residue 298 
Skipped atom 828 because residue number 99  < previous residue 298 
Skipped atom 829 because residue number 100  < previous residue 298 
Skipped atom 830 because residue number 100  < previous residue 298 
Skipped atom 831 because residue number 100  < previous residue 298 
Skipped atom 832 because residue number 100  < previous residue 298 
Skipped atom 833 because residue number 100  < previous residue 298 
Skipped atom 834 because residue number 100  < previous residue 298 
Skipped atom 835 because residue number 100  < previous residue 298 
Skipped atom 836 because residue number 100  < previous residue 298 
Skipped atom 837 because residue number 101  < previous residue 298 
Skipped atom 838 because residue number 101  < previous residue 298 
Skipped atom 839 because residue number 101  < previous residue 298 
Skipped atom 840 because residue number 101  < previous residue 298 
Skipped atom 841 because residue number 101  < previous residue 298 
Skipped atom 842 because residue number 101  < previous residue 298 
Skipped atom 843 because residue number 101  < previous residue 298 
Skipped atom 844 because residue number 101  < previous residue 298 
Skipped atom 845 because residue number 102  < previous residue 298 
Skipped atom 846 because residue number 102  < previous residue 298 
Skipped atom 847 because residue number 102  < previous residue 298 
Skipped atom 848 because residue number 102  < previous residue 298 
Skipped atom 849 because residue number 102  < previous residue 298 
Skipped atom 850 because residue number 102  < previous residue 298 
Skipped atom 851 because residue number 102  < previous residue 298 
Skipped atom 852 because residue number 102  < previous residue 298 
Skipped atom 853 because residue number 103  < previous residue 298 
Skipped atom 854 because residue number 103  < previous residue 298 
Skipped atom 855 because residue number 103  < previous residue 298 
Skipped atom 856 because residue number 103  < previous residue 298 
Skipped atom 857 because residue number 103  < previous residue 298 
Skipped atom 858 because residue number 103  < previous residue 298 
Skipped atom 859 because residue number 103  < previous residue 298 
Skipped atom 860 because residue number 104  < previous residue 298 
Skipped atom 861 because residue number 104  < previous residue 298 
Skipped atom 862 because residue number 104  < previous residue 298 
Skipped atom 863 because residue number 104  < previous residue 298 
Skipped atom 864 because residue number 104  < previous residue 298 
Skipped atom 865 because residue number 105  < previous residue 298 
Skipped atom 866 because residue number 105  < previous residue 298 
Skipped atom 867 because residue number 105  < previous residue 298 
Skipped atom 868 because residue number 105  < previous residue 298 
Skipped atom 869 because residue number 105  < previous residue 298 
Skipped atom 870 because residue number 105  < previous residue 298 
Skipped atom 871 because residue number 105  < previous residue 298 
Skipped atom 872 because residue number 105  < previous residue 298 
Skipped atom 873 because residue number 105  < previous residue 298 
Skipped atom 874 because residue number 105  < previous residue 298 
Skipped atom 875 because residue number 105  < previous residue 298 
Skipped atom 876 because residue number 105  < previous residue 298 
Skipped atom 877 because residue number 106  < previous residue 298 
Skipped atom 878 because residue number 106  < previous residue 298 
Skipped atom 879 because residue number 106  < previous residue 298 
Skipped atom 880 because residue number 106  < previous residue 298 
Skipped atom 881 because residue number 106  < previous residue 298 
Skipped atom 882 because residue number 106  < previous residue 298 
Skipped atom 883 because residue number 107  < previous residue 298 
Skipped atom 884 because residue number 107  < previous residue 298 
Skipped atom 885 because residue number 107  < previous residue 298 
Skipped atom 886 because residue number 107  < previous residue 298 
Skipped atom 887 because residue number 107  < previous residue 298 
Skipped atom 888 because residue number 107  < previous residue 298 
Skipped atom 889 because residue number 107  < previous residue 298 
Skipped atom 890 because residue number 108  < previous residue 298 
Skipped atom 891 because residue number 108  < previous residue 298 
Skipped atom 892 because residue number 108  < previous residue 298 
Skipped atom 893 because residue number 108  < previous residue 298 
Skipped atom 894 because residue number 108  < previous residue 298 
Skipped atom 895 because residue number 108  < previous residue 298 
Skipped atom 896 because residue number 108  < previous residue 298 
Skipped atom 897 because residue number 108  < previous residue 298 
Skipped atom 898 because residue number 109  < previous residue 298 
Skipped atom 899 because residue number 109  < previous residue 298 
Skipped atom 900 because residue number 109  < previous residue 298 
Skipped atom 901 because residue number 109  < previous residue 298 
Skipped atom 902 because residue number 109  < previous residue 298 
Skipped atom 903 because residue number 109  < previous residue 298 
Skipped atom 904 because residue number 109  < previous residue 298 
Skipped atom 905 because residue number 109  < previous residue 298 
Skipped atom 906 because residue number 110  < previous residue 298 
Skipped atom 907 because residue number 110  < previous residue 298 
Skipped atom 908 because residue number 110  < previous residue 298 
Skipped atom 909 because residue number 110  < previous residue 298 
Skipped atom 910 because residue number 110  < previous residue 298 
Skipped atom 911 because residue number 110  < previous residue 298 
Skipped atom 912 because residue number 110  < previous residue 298 
Skipped atom 913 because residue number 110  < previous residue 298 
Skipped atom 914 because residue number 110  < previous residue 298 
Skipped atom 915 because residue number 111  < previous residue 298 
Skipped atom 916 because residue number 111  < previous residue 298 
Skipped atom 917 because residue number 111  < previous residue 298 
Skipped atom 918 because residue number 111  < previous residue 298 
Skipped atom 919 because residue number 111  < previous residue 298 
Skipped atom 920 because residue number 111  < previous residue 298 
Skipped atom 921 because residue number 111  < previous residue 298 
Skipped atom 922 because residue number 111  < previous residue 298 
Skipped atom 923 because residue number 111  < previous residue 298 
Skipped atom 924 because residue number 112  < previous residue 298 
Skipped atom 925 because residue number 112  < previous residue 298 
Skipped atom 926 because residue number 112  < previous residue 298 
Skipped atom 927 because residue number 112  < previous residue 298 
Skipped atom 928 because residue number 112  < previous residue 298 
Skipped atom 929 because residue number 112  < previous residue 298 
Skipped atom 930 because residue number 112  < previous residue 298 
Skipped atom 931 because residue number 112  < previous residue 298 
Skipped atom 932 because residue number 112  < previous residue 298 
Skipped atom 933 because residue number 112  < previous residue 298 
Skipped atom 934 because residue number 112  < previous residue 298 
Skipped atom 935 because residue number 112  < previous residue 298 
Skipped atom 936 because residue number 113  < previous residue 298 
Skipped atom 937 because residue number 113  < previous residue 298 
Skipped atom 938 because residue number 113  < previous residue 298 
Skipped atom 939 because residue number 113  < previous residue 298 
Skipped atom 940 because residue number 113  < previous residue 298 
Skipped atom 941 because residue number 113  < previous residue 298 
Skipped atom 942 because residue number 113  < previous residue 298 
Skipped atom 943 because residue number 114  < previous residue 298 
Skipped atom 944 because residue number 114  < previous residue 298 
Skipped atom 945 because residue number 114  < previous residue 298 
Skipped atom 946 because residue number 114  < previous residue 298 
Skipped atom 947 because residue number 115  < previous residue 298 
Skipped atom 948 because residue number 115  < previous residue 298 
Skipped atom 949 because residue number 115  < previous residue 298 
Skipped atom 950 because residue number 115  < previous residue 298 
Skipped atom 951 because residue number 115  < previous residue 298 
Skipped atom 952 because residue number 115  < previous residue 298 
Skipped atom 953 because residue number 115  < previous residue 298 
Skipped atom 954 because residue number 115  < previous residue 298 
Skipped atom 955 because residue number 115  < previous residue 298 
Skipped atom 956 because residue number 116  < previous residue 298 
Skipped atom 957 because residue number 116  < previous residue 298 
Skipped atom 958 because residue number 116  < previous residue 298 
Skipped atom 959 because residue number 116  < previous residue 298 
Skipped atom 960 because residue number 116  < previous residue 298 
Skipped atom 961 because residue number 116  < previous residue 298 
Skipped atom 962 because residue number 116  < previous residue 298 
Skipped atom 963 because residue number 116  < previous residue 298 
Skipped atom 964 because residue number 117  < previous residue 298 
Skipped atom 965 because residue number 117  < previous residue 298 
Skipped atom 966 because residue number 117  < previous residue 298 
Skipped atom 967 because residue number 117  < previous residue 298 
Skipped atom 968 because residue number 117  < previous residue 298 
Skipped atom 969 because residue number 117  < previous residue 298 
Skipped atom 970 because residue number 117  < previous residue 298 
Skipped atom 971 because residue number 117  < previous residue 298 
Skipped atom 972 because residue number 118  < previous residue 298 
Skipped atom 973 because residue number 118  < previous residue 298 
Skipped atom 974 because residue number 118  < previous residue 298 
Skipped atom 975 because residue number 118  < previous residue 298 
Skipped atom 976 because residue number 118  < previous residue 298 
Skipped atom 977 because residue number 118  < previous residue 298 
Skipped atom 978 because residue number 118  < previous residue 298 
Skipped atom 979 because residue number 119  < previous residue 298 
Skipped atom 980 because residue number 119  < previous residue 298 
Skipped atom 981 because residue number 119  < previous residue 298 
Skipped atom 982 because residue number 119  < previous residue 298 
Skipped atom 983 because residue number 119  < previous residue 298 
Skipped atom 984 because residue number 119  < previous residue 298 
Skipped atom 985 because residue number 119  < previous residue 298 
Skipped atom 986 because residue number 119  < previous residue 298 
Skipped atom 987 because residue number 120  < previous residue 298 
Skipped atom 988 because residue number 120  < previous residue 298 
Skipped atom 989 because residue number 120  < previous residue 298 
Skipped atom 990 because residue number 120  < previous residue 298 
Skipped atom 991 because residue number 120  < previous residue 298 
Skipped atom 992 because residue number 120  < previous residue 298 
Skipped atom 993 because residue number 120  < previous residue 298 
Skipped atom 994 because residue number 120  < previous residue 298 
Skipped atom 995 because residue number 120  < previous residue 298 
Skipped atom 996 because residue number 121  < previous residue 298 
Skipped atom 997 because residue number 121  < previous residue 298 
Skipped atom 998 because residue number 121  < previous residue 298 
Skipped atom 999 because residue number 121  < previous residue 298 
Skipped atom 1000 because residue number 121  < previous residue 298 
Skipped atom 1001 because residue number 122  < previous residue 298 
Skipped atom 1002 because residue number 122  < previous residue 298 
Skipped atom 1003 because residue number 122  < previous residue 298 
Skipped atom 1004 because residue number 122  < previous residue 298 
Skipped atom 1005 because residue number 122  < previous residue 298 
Skipped atom 1006 because residue number 122  < previous residue 298 
Skipped atom 1007 because residue number 122  < previous residue 298 
Skipped atom 1008 because residue number 122  < previous residue 298 
Skipped atom 1009 because residue number 123  < previous residue 298 
Skipped atom 1010 because residue number 123  < previous residue 298 
Skipped atom 1011 because residue number 123  < previous residue 298 
Skipped atom 1012 because residue number 123  < previous residue 298 
Skipped atom 1013 because residue number 123  < previous residue 298 
Skipped atom 1014 because residue number 123  < previous residue 298 
Skipped atom 1015 because residue number 123  < previous residue 298 
Skipped atom 1016 because residue number 123  < previous residue 298 
Skipped atom 1017 because residue number 124  < previous residue 298 
Skipped atom 1018 because residue number 124  < previous residue 298 
Skipped atom 1019 because residue number 124  < previous residue 298 
Skipped atom 1020 because residue number 124  < previous residue 298 
Skipped atom 1021 because residue number 124  < previous residue 298 
Skipped atom 1022 because residue number 124  < previous residue 298 
Skipped atom 1023 because residue number 124  < previous residue 298 
Skipped atom 1024 because residue number 124  < previous residue 298 
Skipped atom 1025 because residue number 124  < previous residue 298 
Skipped atom 1026 because residue number 125  < previous residue 298 
Skipped atom 1027 because residue number 125  < previous residue 298 
Skipped atom 1028 because residue number 125  < previous residue 298 
Skipped atom 1029 because residue number 125  < previous residue 298 
Skipped atom 1030 because residue number 125  < previous residue 298 
Skipped atom 1031 because residue number 126  < previous residue 298 
Skipped atom 1032 because residue number 126  < previous residue 298 
Skipped atom 1033 because residue number 126  < previous residue 298 
Skipped atom 1034 because residue number 126  < previous residue 298 
Skipped atom 1035 because residue number 126  < previous residue 298 
Skipped atom 1036 because residue number 126  < previous residue 298 
Skipped atom 1037 because residue number 127  < previous residue 298 
Skipped atom 1038 because residue number 127  < previous residue 298 
Skipped atom 1039 because residue number 127  < previous residue 298 
Skipped atom 1040 because residue number 127  < previous residue 298 
Skipped atom 1041 because residue number 127  < previous residue 298 
Skipped atom 1042 because residue number 127  < previous residue 298 
Skipped atom 1043 because residue number 127  < previous residue 298 
Skipped atom 1044 because residue number 127  < previous residue 298 
Skipped atom 1045 because residue number 128  < previous residue 298 
Skipped atom 1046 because residue number 128  < previous residue 298 
Skipped atom 1047 because residue number 128  < previous residue 298 
Skipped atom 1048 because residue number 128  < previous residue 298 
Skipped atom 1049 because residue number 128  < previous residue 298 
Skipped atom 1050 because residue number 128  < previous residue 298 
Skipped atom 1051 because residue number 128  < previous residue 298 
Skipped atom 1052 because residue number 129  < previous residue 298 
Skipped atom 1053 because residue number 129  < previous residue 298 
Skipped atom 1054 because residue number 129  < previous residue 298 
Skipped atom 1055 because residue number 129  < previous residue 298 
Skipped atom 1056 because residue number 129  < previous residue 298 
Skipped atom 1057 because residue number 129  < previous residue 298 
Skipped atom 1058 because residue number 129  < previous residue 298 
Skipped atom 1059 because residue number 129  < previous residue 298 
Skipped atom 1060 because residue number 129  < previous residue 298 
Skipped atom 1061 because residue number 129  < previous residue 298 
Skipped atom 1062 because residue number 129  < previous residue 298 
Skipped atom 1063 because residue number 129  < previous residue 298 
Skipped atom 1064 because residue number 130  < previous residue 298 
Skipped atom 1065 because residue number 130  < previous residue 298 
Skipped atom 1066 because residue number 130  < previous residue 298 
Skipped atom 1067 because residue number 130  < previous residue 298 
Skipped atom 1068 because residue number 130  < previous residue 298 
Skipped atom 1069 because residue number 130  < previous residue 298 
Skipped atom 1070 because residue number 131  < previous residue 298 
Skipped atom 1071 because residue number 131  < previous residue 298 
Skipped atom 1072 because residue number 131  < previous residue 298 
Skipped atom 1073 because residue number 131  < previous residue 298 
Skipped atom 1074 because residue number 131  < previous residue 298 
Skipped atom 1075 because residue number 131  < previous residue 298 
Skipped atom 1076 because residue number 131  < previous residue 298 
Skipped atom 1077 because residue number 131  < previous residue 298 
Skipped atom 1078 because residue number 132  < previous residue 298 
Skipped atom 1079 because residue number 132  < previous residue 298 
Skipped atom 1080 because residue number 132  < previous residue 298 
Skipped atom 1081 because residue number 132  < previous residue 298 
Skipped atom 1082 because residue number 132  < previous residue 298 
Skipped atom 1083 because residue number 132  < previous residue 298 
Skipped atom 1084 because residue number 132  < previous residue 298 
Skipped atom 1085 because residue number 132  < previous residue 298 
Skipped atom 1086 because residue number 133  < previous residue 298 
Skipped atom 1087 because residue number 133  < previous residue 298 
Skipped atom 1088 because residue number 133  < previous residue 298 
Skipped atom 1089 because residue number 133  < previous residue 298 
Skipped atom 1090 because residue number 133  < previous residue 298 
Skipped atom 1091 because residue number 133  < previous residue 298 
Skipped atom 1092 because residue number 133  < previous residue 298 
Skipped atom 1093 because residue number 134  < previous residue 298 
Skipped atom 1094 because residue number 134  < previous residue 298 
Skipped atom 1095 because residue number 134  < previous residue 298 
Skipped atom 1096 because residue number 134  < previous residue 298 
Skipped atom 1097 because residue number 134  < previous residue 298 
Skipped atom 1098 because residue number 135  < previous residue 298 
Skipped atom 1099 because residue number 135  < previous residue 298 
Skipped atom 1100 because residue number 135  < previous residue 298 
Skipped atom 1101 because residue number 135  < previous residue 298 
Skipped atom 1102 because residue number 135  < previous residue 298 
Skipped atom 1103 because residue number 135  < previous residue 298 
Skipped atom 1104 because residue number 135  < previous residue 298 
Skipped atom 1105 because residue number 135  < previous residue 298 
Skipped atom 1106 because residue number 136  < previous residue 298 
Skipped atom 1107 because residue number 136  < previous residue 298 
Skipped atom 1108 because residue number 136  < previous residue 298 
Skipped atom 1109 because residue number 136  < previous residue 298 
Skipped atom 1110 because residue number 136  < previous residue 298 
Skipped atom 1111 because residue number 136  < previous residue 298 
Skipped atom 1112 because residue number 136  < previous residue 298 
Skipped atom 1113 because residue number 136  < previous residue 298 
Skipped atom 1114 because residue number 137  < previous residue 298 
Skipped atom 1115 because residue number 137  < previous residue 298 
Skipped atom 1116 because residue number 137  < previous residue 298 
Skipped atom 1117 because residue number 137  < previous residue 298 
Skipped atom 1118 because residue number 137  < previous residue 298 
Skipped atom 1119 because residue number 137  < previous residue 298 
Skipped atom 1120 because residue number 137  < previous residue 298 
Skipped atom 1121 because residue number 137  < previous residue 298 
Skipped atom 1122 because residue number 137  < previous residue 298 
Skipped atom 1123 because residue number 138  < previous residue 298 
Skipped atom 1124 because residue number 138  < previous residue 298 
Skipped atom 1125 because residue number 138  < previous residue 298 
Skipped atom 1126 because residue number 138  < previous residue 298 
Skipped atom 1127 because residue number 138  < previous residue 298 
Skipped atom 1128 because residue number 138  < previous residue 298 
Skipped atom 1129 because residue number 138  < previous residue 298 
Skipped atom 1130 because residue number 138  < previous residue 298 
Skipped atom 1131 because residue number 139  < previous residue 298 
Skipped atom 1132 because residue number 139  < previous residue 298 
Skipped atom 1133 because residue number 139  < previous residue 298 
Skipped atom 1134 because residue number 139  < previous residue 298 
Skipped atom 1135 because residue number 139  < previous residue 298 
Skipped atom 1136 because residue number 139  < previous residue 298 
Skipped atom 1137 because residue number 139  < previous residue 298 
Skipped atom 1138 because residue number 139  < previous residue 298 
Skipped atom 1139 because residue number 140  < previous residue 298 
Skipped atom 1140 because residue number 140  < previous residue 298 
Skipped atom 1141 because residue number 140  < previous residue 298 
Skipped atom 1142 because residue number 140  < previous residue 298 
Skipped atom 1143 because residue number 140  < previous residue 298 
Skipped atom 1144 because residue number 140  < previous residue 298 
Skipped atom 1145 because residue number 140  < previous residue 298 
Skipped atom 1146 because residue number 140  < previous residue 298 
Skipped atom 1147 because residue number 140  < previous residue 298 
Skipped atom 1148 because residue number 141  < previous residue 298 
Skipped atom 1149 because residue number 141  < previous residue 298 
Skipped atom 1150 because residue number 141  < previous residue 298 
Skipped atom 1151 because residue number 141  < previous residue 298 
Skipped atom 1152 because residue number 141  < previous residue 298 
Skipped atom 1153 because residue number 141  < previous residue 298 
Skipped atom 1154 because residue number 141  < previous residue 298 
Skipped atom 1155 because residue number 141  < previous residue 298 
Skipped atom 1156 because residue number 141  < previous residue 298 
Skipped atom 1157 because residue number 142  < previous residue 298 
Skipped atom 1158 because residue number 142  < previous residue 298 
Skipped atom 1159 because residue number 142  < previous residue 298 
Skipped atom 1160 because residue number 142  < previous residue 298 
Skipped atom 1161 because residue number 142  < previous residue 298 
Skipped atom 1162 because residue number 142  < previous residue 298 
Skipped atom 1163 because residue number 142  < previous residue 298 
Skipped atom 1164 because residue number 142  < previous residue 298 
Skipped atom 1165 because residue number 143  < previous residue 298 
Skipped atom 1166 because residue number 143  < previous residue 298 
Skipped atom 1167 because residue number 143  < previous residue 298 
Skipped atom 1168 because residue number 143  < previous residue 298 
Skipped atom 1169 because residue number 144  < previous residue 298 
Skipped atom 1170 because residue number 144  < previous residue 298 
Skipped atom 1171 because residue number 144  < previous residue 298 
Skipped atom 1172 because residue number 144  < previous residue 298 
Skipped atom 1173 because residue number 145  < previous residue 298 
Skipped atom 1174 because residue number 145  < previous residue 298 
Skipped atom 1175 because residue number 145  < previous residue 298 
Skipped atom 1176 because residue number 145  < previous residue 298 
Skipped atom 1177 because residue number 145  < previous residue 298 
Skipped atom 1178 because residue number 145  < previous residue 298 
Skipped atom 1179 because residue number 145  < previous residue 298 
Skipped atom 1180 because residue number 145  < previous residue 298 
Skipped atom 1181 because residue number 146  < previous residue 298 
Skipped atom 1182 because residue number 146  < previous residue 298 
Skipped atom 1183 because residue number 146  < previous residue 298 
Skipped atom 1184 because residue number 146  < previous residue 298 
Skipped atom 1185 because residue number 146  < previous residue 298 
Skipped atom 1186 because residue number 146  < previous residue 298 
Skipped atom 1187 because residue number 146  < previous residue 298 
Skipped atom 1188 because residue number 146  < previous residue 298 
Skipped atom 1189 because residue number 146  < previous residue 298 
Skipped atom 1190 because residue number 147  < previous residue 298 
Skipped atom 1191 because residue number 147  < previous residue 298 
Skipped atom 1192 because residue number 147  < previous residue 298 
Skipped atom 1193 because residue number 147  < previous residue 298 
Skipped atom 1194 because residue number 147  < previous residue 298 
Skipped atom 1195 because residue number 147  < previous residue 298 
Skipped atom 1196 because residue number 147  < previous residue 298 
Skipped atom 1197 because residue number 147  < previous residue 298 
Skipped atom 1198 because residue number 147  < previous residue 298 
Skipped atom 1199 because residue number 148  < previous residue 298 
Skipped atom 1200 because residue number 148  < previous residue 298 
Skipped atom 1201 because residue number 148  < previous residue 298 
Skipped atom 1202 because residue number 148  < previous residue 298 
Skipped atom 1203 because residue number 148  < previous residue 298 
Skipped atom 1204 because residue number 148  < previous residue 298 
Skipped atom 1205 because residue number 148  < previous residue 298 
Skipped atom 1206 because residue number 149  < previous residue 298 
Skipped atom 1207 because residue number 149  < previous residue 298 
Skipped atom 1208 because residue number 149  < previous residue 298 
Skipped atom 1209 because residue number 149  < previous residue 298 
Skipped atom 1210 because residue number 149  < previous residue 298 
Skipped atom 1211 because residue number 149  < previous residue 298 
Skipped atom 1212 because residue number 149  < previous residue 298 
Skipped atom 1213 because residue number 149  < previous residue 298 
Skipped atom 1214 because residue number 149  < previous residue 298 
Skipped atom 1215 because residue number 150  < previous residue 298 
Skipped atom 1216 because residue number 150  < previous residue 298 
Skipped atom 1217 because residue number 150  < previous residue 298 
Skipped atom 1218 because residue number 150  < previous residue 298 
Skipped atom 1219 because residue number 150  < previous residue 298 
Skipped atom 1220 because residue number 150  < previous residue 298 
Skipped atom 1221 because residue number 150  < previous residue 298 
Skipped atom 1222 because residue number 150  < previous residue 298 
Skipped atom 1223 because residue number 150  < previous residue 298 
Skipped atom 1224 because residue number 151  < previous residue 298 
Skipped atom 1225 because residue number 151  < previous residue 298 
Skipped atom 1226 because residue number 151  < previous residue 298 
Skipped atom 1227 because residue number 151  < previous residue 298 
Skipped atom 1228 because residue number 151  < previous residue 298 
Skipped atom 1229 because residue number 151  < previous residue 298 
Skipped atom 1230 because residue number 151  < previous residue 298 
Skipped atom 1231 because residue number 151  < previous residue 298 
Skipped atom 1232 because residue number 151  < previous residue 298 
Skipped atom 1233 because residue number 151  < previous residue 298 
Skipped atom 1234 because residue number 151  < previous residue 298 
Skipped atom 1235 because residue number 152  < previous residue 298 
Skipped atom 1236 because residue number 152  < previous residue 298 
Skipped atom 1237 because residue number 152  < previous residue 298 
Skipped atom 1238 because residue number 152  < previous residue 298 
Skipped atom 1239 because residue number 152  < previous residue 298 
Skipped atom 1240 because residue number 152  < previous residue 298 
Skipped atom 1241 because residue number 152  < previous residue 298 
Skipped atom 1242 because residue number 152  < previous residue 298 
Skipped atom 1243 because residue number 153  < previous residue 298 
Skipped atom 1244 because residue number 153  < previous residue 298 
Skipped atom 1245 because residue number 153  < previous residue 298 
Skipped atom 1246 because residue number 153  < previous residue 298 
Skipped atom 1247 because residue number 153  < previous residue 298 
Skipped atom 1248 because residue number 153  < previous residue 298 
Skipped atom 1249 because residue number 153  < previous residue 298 
Skipped atom 1250 because residue number 153  < previous residue 298 
Skipped atom 1251 because residue number 153  < previous residue 298 
Skipped atom 1252 because residue number 154  < previous residue 298 
Skipped atom 1253 because residue number 154  < previous residue 298 
Skipped atom 1254 because residue number 154  < previous residue 298 
Skipped atom 1255 because residue number 154  < previous residue 298 
Skipped atom 1256 because residue number 154  < previous residue 298 
Skipped atom 1257 because residue number 154  < previous residue 298 
Skipped atom 1258 because residue number 154  < previous residue 298 
Skipped atom 1259 because residue number 154  < previous residue 298 
Skipped atom 1260 because residue number 154  < previous residue 298 
Skipped atom 1261 because residue number 155  < previous residue 298 
Skipped atom 1262 because residue number 155  < previous residue 298 
Skipped atom 1263 because residue number 155  < previous residue 298 
Skipped atom 1264 because residue number 155  < previous residue 298 
Skipped atom 1265 because residue number 155  < previous residue 298 
Skipped atom 1266 because residue number 155  < previous residue 298 
Skipped atom 1267 because residue number 155  < previous residue 298 
Skipped atom 1268 because residue number 155  < previous residue 298 
Skipped atom 1269 because residue number 156  < previous residue 298 
Skipped atom 1270 because residue number 156  < previous residue 298 
Skipped atom 1271 because residue number 156  < previous residue 298 
Skipped atom 1272 because residue number 156  < previous residue 298 
Skipped atom 1273 because residue number 157  < previous residue 298 
Skipped atom 1274 because residue number 157  < previous residue 298 
Skipped atom 1275 because residue number 157  < previous residue 298 
Skipped atom 1276 because residue number 157  < previous residue 298 
Skipped atom 1277 because residue number 157  < previous residue 298 
Skipped atom 1278 because residue number 157  < previous residue 298 
Skipped atom 1279 because residue number 157  < previous residue 298 
Skipped atom 1280 because residue number 157  < previous residue 298 
Skipped atom 1281 because residue number 158  < previous residue 298 
Skipped atom 1282 because residue number 158  < previous residue 298 
Skipped atom 1283 because residue number 158  < previous residue 298 
Skipped atom 1284 because residue number 158  < previous residue 298 
Skipped atom 1285 because residue number 158  < previous residue 298 
Skipped atom 1286 because residue number 158  < previous residue 298 
Skipped atom 1287 because residue number 158  < previous residue 298 
Skipped atom 1288 because residue number 158  < previous residue 298 
Skipped atom 1289 because residue number 158  < previous residue 298 
Skipped atom 1290 because residue number 159  < previous residue 298 
Skipped atom 1291 because residue number 159  < previous residue 298 
Skipped atom 1292 because residue number 159  < previous residue 298 
Skipped atom 1293 because residue number 159  < previous residue 298 
Skipped atom 1294 because residue number 159  < previous residue 298 
Skipped atom 1295 because residue number 159  < previous residue 298 
Skipped atom 1296 because residue number 159  < previous residue 298 
Skipped atom 1297 because residue number 160  < previous residue 298 
Skipped atom 1298 because residue number 160  < previous residue 298 
Skipped atom 1299 because residue number 160  < previous residue 298 
Skipped atom 1300 because residue number 160  < previous residue 298 
Skipped atom 1301 because residue number 160  < previous residue 298 
Skipped atom 1302 because residue number 160  < previous residue 298 
Skipped atom 1303 because residue number 160  < previous residue 298 
Skipped atom 1304 because residue number 161  < previous residue 298 
Skipped atom 1305 because residue number 161  < previous residue 298 
Skipped atom 1306 because residue number 161  < previous residue 298 
Skipped atom 1307 because residue number 161  < previous residue 298 
Skipped atom 1308 because residue number 161  < previous residue 298 
Skipped atom 1309 because residue number 161  < previous residue 298 
Skipped atom 1310 because residue number 161  < previous residue 298 
Skipped atom 1311 because residue number 161  < previous residue 298 
Skipped atom 1312 because residue number 162  < previous residue 298 
Skipped atom 1313 because residue number 162  < previous residue 298 
Skipped atom 1314 because residue number 162  < previous residue 298 
Skipped atom 1315 because residue number 162  < previous residue 298 
Skipped atom 1316 because residue number 162  < previous residue 298 
Skipped atom 1317 because residue number 162  < previous residue 298 
Skipped atom 1318 because residue number 162  < previous residue 298 
Skipped atom 1319 because residue number 163  < previous residue 298 
Skipped atom 1320 because residue number 163  < previous residue 298 
Skipped atom 1321 because residue number 163  < previous residue 298 
Skipped atom 1322 because residue number 163  < previous residue 298 
Skipped atom 1323 because residue number 163  < previous residue 298 
Skipped atom 1324 because residue number 163  < previous residue 298 
Skipped atom 1325 because residue number 163  < previous residue 298 
Skipped atom 1326 because residue number 164  < previous residue 298 
Skipped atom 1327 because residue number 164  < previous residue 298 
Skipped atom 1328 because residue number 164  < previous residue 298 
Skipped atom 1329 because residue number 164  < previous residue 298 
Skipped atom 1330 because residue number 164  < previous residue 298 
Skipped atom 1331 because residue number 164  < previous residue 298 
Skipped atom 1332 because residue number 164  < previous residue 298 
Skipped atom 1333 because residue number 164  < previous residue 298 
Skipped atom 1334 because residue number 164  < previous residue 298 
Skipped atom 1335 because residue number 164  < previous residue 298 
Skipped atom 1336 because residue number 164  < previous residue 298 
Skipped atom 1337 because residue number 165  < previous residue 298 
Skipped atom 1338 because residue number 165  < previous residue 298 
Skipped atom 1339 because residue number 165  < previous residue 298 
Skipped atom 1340 because residue number 165  < previous residue 298 
Skipped atom 1341 because residue number 165  < previous residue 298 
Skipped atom 1342 because residue number 165  < previous residue 298 
Skipped atom 1343 because residue number 165  < previous residue 298 
Skipped atom 1344 because residue number 165  < previous residue 298 
Skipped atom 1345 because residue number 165  < previous residue 298 
Skipped atom 1346 because residue number 165  < previous residue 298 
Skipped atom 1347 because residue number 165  < previous residue 298 
Skipped atom 1348 because residue number 165  < previous residue 298 
Skipped atom 1349 because residue number 166  < previous residue 298 
Skipped atom 1350 because residue number 166  < previous residue 298 
Skipped atom 1351 because residue number 166  < previous residue 298 
Skipped atom 1352 because residue number 166  < previous residue 298 
Skipped atom 1353 because residue number 166  < previous residue 298 
Skipped atom 1354 because residue number 166  < previous residue 298 
Skipped atom 1355 because residue number 166  < previous residue 298 
Skipped atom 1356 because residue number 166  < previous residue 298 
Skipped atom 1357 because residue number 166  < previous residue 298 
Skipped atom 1358 because residue number 167  < previous residue 298 
Skipped atom 1359 because residue number 167  < previous residue 298 
Skipped atom 1360 because residue number 167  < previous residue 298 
Skipped atom 1361 because residue number 167  < previous residue 298 
Skipped atom 1362 because residue number 167  < previous residue 298 
Skipped atom 1363 because residue number 167  < previous residue 298 
Skipped atom 1364 because residue number 167  < previous residue 298 
Skipped atom 1365 because residue number 167  < previous residue 298 
Skipped atom 1366 because residue number 168  < previous residue 298 
Skipped atom 1367 because residue number 168  < previous residue 298 
Skipped atom 1368 because residue number 168  < previous residue 298 
Skipped atom 1369 because residue number 168  < previous residue 298 
Skipped atom 1370 because residue number 168  < previous residue 298 
Skipped atom 1371 because residue number 168  < previous residue 298 
Skipped atom 1372 because residue number 168  < previous residue 298 
Skipped atom 1373 because residue number 168  < previous residue 298 
Skipped atom 1374 because residue number 168  < previous residue 298 
Skipped atom 1375 because residue number 169  < previous residue 298 
Skipped atom 1376 because residue number 169  < previous residue 298 
Skipped atom 1377 because residue number 169  < previous residue 298 
Skipped atom 1378 because residue number 169  < previous residue 298 
Skipped atom 1379 because residue number 169  < previous residue 298 
Skipped atom 1380 because residue number 169  < previous residue 298 
Skipped atom 1381 because residue number 169  < previous residue 298 
Skipped atom 1382 because residue number 169  < previous residue 298 
Skipped atom 1383 because residue number 170  < previous residue 298 
Skipped atom 1384 because residue number 170  < previous residue 298 
Skipped atom 1385 because residue number 170  < previous residue 298 
Skipped atom 1386 because residue number 170  < previous residue 298 
Skipped atom 1387 because residue number 170  < previous residue 298 
Skipped atom 1388 because residue number 170  < previous residue 298 
Skipped atom 1389 because residue number 170  < previous residue 298 
Skipped atom 1390 because residue number 170  < previous residue 298 
Skipped atom 1391 because residue number 171  < previous residue 298 
Skipped atom 1392 because residue number 171  < previous residue 298 
Skipped atom 1393 because residue number 171  < previous residue 298 
Skipped atom 1394 because residue number 171  < previous residue 298 
Skipped atom 1395 because residue number 171  < previous residue 298 
Skipped atom 1396 because residue number 171  < previous residue 298 
Skipped atom 1397 because residue number 171  < previous residue 298 
Skipped atom 1398 because residue number 171  < previous residue 298 
Skipped atom 1399 because residue number 171  < previous residue 298 
Skipped atom 1400 because residue number 171  < previous residue 298 
Skipped atom 1401 because residue number 171  < previous residue 298 
Skipped atom 1402 because residue number 171  < previous residue 298 
Skipped atom 1403 because residue number 172  < previous residue 298 
Skipped atom 1404 because residue number 172  < previous residue 298 
Skipped atom 1405 because residue number 172  < previous residue 298 
Skipped atom 1406 because residue number 172  < previous residue 298 
Skipped atom 1407 because residue number 172  < previous residue 298 
Skipped atom 1408 because residue number 172  < previous residue 298 
Skipped atom 1409 because residue number 172  < previous residue 298 
Skipped atom 1410 because residue number 172  < previous residue 298 
Skipped atom 1411 because residue number 172  < previous residue 298 
Skipped atom 1412 because residue number 172  < previous residue 298 
Skipped atom 1413 because residue number 172  < previous residue 298 
Skipped atom 1414 because residue number 172  < previous residue 298 
Skipped atom 1415 because residue number 173  < previous residue 298 
Skipped atom 1416 because residue number 173  < previous residue 298 
Skipped atom 1417 because residue number 173  < previous residue 298 
Skipped atom 1418 because residue number 173  < previous residue 298 
Skipped atom 1419 because residue number 173  < previous residue 298 
Skipped atom 1420 because residue number 173  < previous residue 298 
Skipped atom 1421 because residue number 174  < previous residue 298 
Skipped atom 1422 because residue number 174  < previous residue 298 
Skipped atom 1423 because residue number 174  < previous residue 298 
Skipped atom 1424 because residue number 174  < previous residue 298 
Skipped atom 1425 because residue number 174  < previous residue 298 
Skipped atom 1426 because residue number 174  < previous residue 298 
Skipped atom 1427 because residue number 174  < previous residue 298 
Skipped atom 1428 because residue number 175  < previous residue 298 
Skipped atom 1429 because residue number 175  < previous residue 298 
Skipped atom 1430 because residue number 175  < previous residue 298 
Skipped atom 1431 because residue number 175  < previous residue 298 
Skipped atom 1432 because residue number 175  < previous residue 298 
Skipped atom 1433 because residue number 175  < previous residue 298 
Skipped atom 1434 because residue number 175  < previous residue 298 
Skipped atom 1435 because residue number 175  < previous residue 298 
Skipped atom 1436 because residue number 175  < previous residue 298 
Skipped atom 1437 because residue number 176  < previous residue 298 
Skipped atom 1438 because residue number 176  < previous residue 298 
Skipped atom 1439 because residue number 176  < previous residue 298 
Skipped atom 1440 because residue number 176  < previous residue 298 
Skipped atom 1441 because residue number 176  < previous residue 298 
Skipped atom 1442 because residue number 176  < previous residue 298 
Skipped atom 1443 because residue number 177  < previous residue 298 
Skipped atom 1444 because residue number 177  < previous residue 298 
Skipped atom 1445 because residue number 177  < previous residue 298 
Skipped atom 1446 because residue number 177  < previous residue 298 
Skipped atom 1447 because residue number 177  < previous residue 298 
Skipped atom 1448 because residue number 177  < previous residue 298 
Skipped atom 1449 because residue number 177  < previous residue 298 
Skipped atom 1450 because residue number 177  < previous residue 298 
Skipped atom 1451 because residue number 177  < previous residue 298 
Skipped atom 1452 because residue number 178  < previous residue 298 
Skipped atom 1453 because residue number 178  < previous residue 298 
Skipped atom 1454 because residue number 178  < previous residue 298 
Skipped atom 1455 because residue number 178  < previous residue 298 
Skipped atom 1456 because residue number 178  < previous residue 298 
Skipped atom 1457 because residue number 178  < previous residue 298 
Skipped atom 1458 because residue number 178  < previous residue 298 
Skipped atom 1459 because residue number 178  < previous residue 298 
Skipped atom 1460 because residue number 178  < previous residue 298 
Skipped atom 1461 because residue number 179  < previous residue 298 
Skipped atom 1462 because residue number 179  < previous residue 298 
Skipped atom 1463 because residue number 179  < previous residue 298 
Skipped atom 1464 because residue number 179  < previous residue 298 
Skipped atom 1465 because residue number 179  < previous residue 298 
Skipped atom 1466 because residue number 179  < previous residue 298 
Skipped atom 1467 because residue number 179  < previous residue 298 
Skipped atom 1468 because residue number 179  < previous residue 298 
Skipped atom 1469 because residue number 180  < previous residue 298 
Skipped atom 1470 because residue number 180  < previous residue 298 
Skipped atom 1471 because residue number 180  < previous residue 298 
Skipped atom 1472 because residue number 180  < previous residue 298 
Skipped atom 1473 because residue number 180  < previous residue 298 
Skipped atom 1474 because residue number 180  < previous residue 298 
Skipped atom 1475 because residue number 180  < previous residue 298 
Skipped atom 1476 because residue number 181  < previous residue 298 
Skipped atom 1477 because residue number 181  < previous residue 298 
Skipped atom 1478 because residue number 181  < previous residue 298 
Skipped atom 1479 because residue number 181  < previous residue 298 
Skipped atom 1480 because residue number 181  < previous residue 298 
Skipped atom 1481 because residue number 181  < previous residue 298 
Skipped atom 1482 because residue number 182  < previous residue 298 
Skipped atom 1483 because residue number 182  < previous residue 298 
Skipped atom 1484 because residue number 182  < previous residue 298 
Skipped atom 1485 because residue number 182  < previous residue 298 
Skipped atom 1486 because residue number 182  < previous residue 298 
Skipped atom 1487 because residue number 182  < previous residue 298 
Skipped atom 1488 because residue number 182  < previous residue 298 
Skipped atom 1489 because residue number 183  < previous residue 298 
Skipped atom 1490 because residue number 183  < previous residue 298 
Skipped atom 1491 because residue number 183  < previous residue 298 
Skipped atom 1492 because residue number 183  < previous residue 298 
Skipped atom 1493 because residue number 183  < previous residue 298 
Skipped atom 1494 because residue number 183  < previous residue 298 
Skipped atom 1495 because residue number 183  < previous residue 298 
Skipped atom 1496 because residue number 184  < previous residue 298 
Skipped atom 1497 because residue number 184  < previous residue 298 
Skipped atom 1498 because residue number 184  < previous residue 298 
Skipped atom 1499 because residue number 184  < previous residue 298 
Skipped atom 1500 because residue number 184  < previous residue 298 
Skipped atom 1501 because residue number 185  < previous residue 298 
Skipped atom 1502 because residue number 185  < previous residue 298 
Skipped atom 1503 because residue number 185  < previous residue 298 
Skipped atom 1504 because residue number 185  < previous residue 298 
Skipped atom 1505 because residue number 185  < previous residue 298 
Skipped atom 1506 because residue number 186  < previous residue 298 
Skipped atom 1507 because residue number 186  < previous residue 298 
Skipped atom 1508 because residue number 186  < previous residue 298 
Skipped atom 1509 because residue number 186  < previous residue 298 
Skipped atom 1510 because residue number 186  < previous residue 298 
Skipped atom 1511 because residue number 186  < previous residue 298 
Skipped atom 1512 because residue number 186  < previous residue 298 
Skipped atom 1513 because residue number 186  < previous residue 298 
Skipped atom 1514 because residue number 186  < previous residue 298 
Skipped atom 1515 because residue number 186  < previous residue 298 
Skipped atom 1516 because residue number 186  < previous residue 298 
Skipped atom 1517 because residue number 187  < previous residue 298 
Skipped atom 1518 because residue number 187  < previous residue 298 
Skipped atom 1519 because residue number 187  < previous residue 298 
Skipped atom 1520 because residue number 187  < previous residue 298 
Skipped atom 1521 because residue number 188  < previous residue 298 
Skipped atom 1522 because residue number 188  < previous residue 298 
Skipped atom 1523 because residue number 188  < previous residue 298 
Skipped atom 1524 because residue number 188  < previous residue 298 
Skipped atom 1525 because residue number 188  < previous residue 298 
Skipped atom 1526 because residue number 188  < previous residue 298 
Skipped atom 1527 because residue number 188  < previous residue 298 
Skipped atom 1528 because residue number 188  < previous residue 298 
Skipped atom 1529 because residue number 188  < previous residue 298 
Skipped atom 1530 because residue number 189  < previous residue 298 
Skipped atom 1531 because residue number 189  < previous residue 298 
Skipped atom 1532 because residue number 189  < previous residue 298 
Skipped atom 1533 because residue number 189  < previous residue 298 
Skipped atom 1534 because residue number 189  < previous residue 298 
Skipped atom 1535 because residue number 189  < previous residue 298 
Skipped atom 1536 because residue number 189  < previous residue 298 
Skipped atom 1537 because residue number 190  < previous residue 298 
Skipped atom 1538 because residue number 190  < previous residue 298 
Skipped atom 1539 because residue number 190  < previous residue 298 
Skipped atom 1540 because residue number 190  < previous residue 298 
Skipped atom 1541 because residue number 190  < previous residue 298 
Skipped atom 1542 because residue number 190  < previous residue 298 
Skipped atom 1543 because residue number 190  < previous residue 298 
Skipped atom 1544 because residue number 190  < previous residue 298 
Skipped atom 1545 because residue number 191  < previous residue 298 
Skipped atom 1546 because residue number 191  < previous residue 298 
Skipped atom 1547 because residue number 191  < previous residue 298 
Skipped atom 1548 because residue number 191  < previous residue 298 
Skipped atom 1549 because residue number 191  < previous residue 298 
Skipped atom 1550 because residue number 191  < previous residue 298 
Skipped atom 1551 because residue number 191  < previous residue 298 
Skipped atom 1552 because residue number 191  < previous residue 298 
Skipped atom 1553 because residue number 192  < previous residue 298 
Skipped atom 1554 because residue number 192  < previous residue 298 
Skipped atom 1555 because residue number 192  < previous residue 298 
Skipped atom 1556 because residue number 192  < previous residue 298 
Skipped atom 1557 because residue number 192  < previous residue 298 
Skipped atom 1558 because residue number 192  < previous residue 298 
Skipped atom 1559 because residue number 192  < previous residue 298 
Skipped atom 1560 because residue number 192  < previous residue 298 
Skipped atom 1561 because residue number 192  < previous residue 298 
Skipped atom 1562 because residue number 193  < previous residue 298 
Skipped atom 1563 because residue number 193  < previous residue 298 
Skipped atom 1564 because residue number 193  < previous residue 298 
Skipped atom 1565 because residue number 193  < previous residue 298 
Skipped atom 1566 because residue number 193  < previous residue 298 
Skipped atom 1567 because residue number 193  < previous residue 298 
Skipped atom 1568 because residue number 193  < previous residue 298 
Skipped atom 1569 because residue number 193  < previous residue 298 
Skipped atom 1570 because residue number 194  < previous residue 298 
Skipped atom 1571 because residue number 194  < previous residue 298 
Skipped atom 1572 because residue number 194  < previous residue 298 
Skipped atom 1573 because residue number 194  < previous residue 298 
Skipped atom 1574 because residue number 194  < previous residue 298 
Skipped atom 1575 because residue number 194  < previous residue 298 
Skipped atom 1576 because residue number 194  < previous residue 298 
Skipped atom 1577 because residue number 194  < previous residue 298 
Skipped atom 1578 because residue number 195  < previous residue 298 
Skipped atom 1579 because residue number 195  < previous residue 298 
Skipped atom 1580 because residue number 195  < previous residue 298 
Skipped atom 1581 because residue number 195  < previous residue 298 
Skipped atom 1582 because residue number 195  < previous residue 298 
Skipped atom 1583 because residue number 196  < previous residue 298 
Skipped atom 1584 because residue number 196  < previous residue 298 
Skipped atom 1585 because residue number 196  < previous residue 298 
Skipped atom 1586 because residue number 196  < previous residue 298 
Skipped atom 1587 because residue number 196  < previous residue 298 
Skipped atom 1588 because residue number 196  < previous residue 298 
Skipped atom 1589 because residue number 196  < previous residue 298 
Skipped atom 1590 because residue number 196  < previous residue 298 
Skipped atom 1591 because residue number 197  < previous residue 298 
Skipped atom 1592 because residue number 197  < previous residue 298 
Skipped atom 1593 because residue number 197  < previous residue 298 
Skipped atom 1594 because residue number 197  < previous residue 298 
Skipped atom 1595 because residue number 198  < previous residue 298 
Skipped atom 1596 because residue number 198  < previous residue 298 
Skipped atom 1597 because residue number 198  < previous residue 298 
Skipped atom 1598 because residue number 198  < previous residue 298 
Skipped atom 1599 because residue number 198  < previous residue 298 
Skipped atom 1600 because residue number 198  < previous residue 298 
Skipped atom 1601 because residue number 198  < previous residue 298 
Skipped atom 1602 because residue number 198  < previous residue 298 
Skipped atom 1603 because residue number 198  < previous residue 298 
Skipped atom 1604 because residue number 199  < previous residue 298 
Skipped atom 1605 because residue number 199  < previous residue 298 
Skipped atom 1606 because residue number 199  < previous residue 298 
Skipped atom 1607 because residue number 199  < previous residue 298 
Skipped atom 1608 because residue number 199  < previous residue 298 
Skipped atom 1609 because residue number 199  < previous residue 298 
Skipped atom 1610 because residue number 199  < previous residue 298 
Skipped atom 1611 because residue number 199  < previous residue 298 
Skipped atom 1612 because residue number 200  < previous residue 298 
Skipped atom 1613 because residue number 200  < previous residue 298 
Skipped atom 1614 because residue number 200  < previous residue 298 
Skipped atom 1615 because residue number 200  < previous residue 298 
Skipped atom 1616 because residue number 200  < previous residue 298 
Skipped atom 1617 because residue number 200  < previous residue 298 
Skipped atom 1618 because residue number 201  < previous residue 298 
Skipped atom 1619 because residue number 201  < previous residue 298 
Skipped atom 1620 because residue number 201  < previous residue 298 
Skipped atom 1621 because residue number 201  < previous residue 298 
Skipped atom 1622 because residue number 201  < previous residue 298 
Skipped atom 1623 because residue number 201  < previous residue 298 
Skipped atom 1624 because residue number 201  < previous residue 298 
Skipped atom 1625 because residue number 201  < previous residue 298 
Skipped atom 1626 because residue number 201  < previous residue 298 
Skipped atom 1627 because residue number 202  < previous residue 298 
Skipped atom 1628 because residue number 202  < previous residue 298 
Skipped atom 1629 because residue number 202  < previous residue 298 
Skipped atom 1630 because residue number 202  < previous residue 298 
Skipped atom 1631 because residue number 202  < previous residue 298 
Skipped atom 1632 because residue number 202  < previous residue 298 
Skipped atom 1633 because residue number 202  < previous residue 298 
Skipped atom 1634 because residue number 202  < previous residue 298 
Skipped atom 1635 because residue number 202  < previous residue 298 
Skipped atom 1636 because residue number 203  < previous residue 298 
Skipped atom 1637 because residue number 203  < previous residue 298 
Skipped atom 1638 because residue number 203  < previous residue 298 
Skipped atom 1639 because residue number 203  < previous residue 298 
Skipped atom 1640 because residue number 203  < previous residue 298 
Skipped atom 1641 because residue number 203  < previous residue 298 
Skipped atom 1642 because residue number 203  < previous residue 298 
Skipped atom 1643 because residue number 203  < previous residue 298 
Skipped atom 1644 because residue number 204  < previous residue 298 
Skipped atom 1645 because residue number 204  < previous residue 298 
Skipped atom 1646 because residue number 204  < previous residue 298 
Skipped atom 1647 because residue number 204  < previous residue 298 
Skipped atom 1648 because residue number 204  < previous residue 298 
Skipped atom 1649 because residue number 204  < previous residue 298 
Skipped atom 1650 because residue number 204  < previous residue 298 
Skipped atom 1651 because residue number 204  < previous residue 298 
Skipped atom 1652 because residue number 204  < previous residue 298 
Skipped atom 1653 because residue number 205  < previous residue 298 
Skipped atom 1654 because residue number 205  < previous residue 298 
Skipped atom 1655 because residue number 205  < previous residue 298 
Skipped atom 1656 because residue number 205  < previous residue 298 
Skipped atom 1657 because residue number 205  < previous residue 298 
Skipped atom 1658 because residue number 205  < previous residue 298 
Skipped atom 1659 because residue number 205  < previous residue 298 
Skipped atom 1660 because residue number 205  < previous residue 298 
Skipped atom 1661 because residue number 205  < previous residue 298 
Skipped atom 1662 because residue number 206  < previous residue 298 
Skipped atom 1663 because residue number 206  < previous residue 298 
Skipped atom 1664 because residue number 206  < previous residue 298 
Skipped atom 1665 because residue number 206  < previous residue 298 
Skipped atom 1666 because residue number 206  < previous residue 298 
Skipped atom 1667 because residue number 206  < previous residue 298 
Skipped atom 1668 because residue number 206  < previous residue 298 
Skipped atom 1669 because residue number 206  < previous residue 298 
Skipped atom 1670 because residue number 206  < previous residue 298 
Skipped atom 1671 because residue number 206  < previous residue 298 
Skipped atom 1672 because residue number 206  < previous residue 298 
Skipped atom 1673 because residue number 207  < previous residue 298 
Skipped atom 1674 because residue number 207  < previous residue 298 
Skipped atom 1675 because residue number 207  < previous residue 298 
Skipped atom 1676 because residue number 207  < previous residue 298 
Skipped atom 1677 because residue number 207  < previous residue 298 
Skipped atom 1678 because residue number 207  < previous residue 298 
Skipped atom 1679 because residue number 207  < previous residue 298 
Skipped atom 1680 because residue number 207  < previous residue 298 
Skipped atom 1681 because residue number 208  < previous residue 298 
Skipped atom 1682 because residue number 208  < previous residue 298 
Skipped atom 1683 because residue number 208  < previous residue 298 
Skipped atom 1684 because residue number 208  < previous residue 298 
Skipped atom 1685 because residue number 208  < previous residue 298 
Skipped atom 1686 because residue number 208  < previous residue 298 
Skipped atom 1687 because residue number 208  < previous residue 298 
Skipped atom 1688 because residue number 208  < previous residue 298 
Skipped atom 1689 because residue number 209  < previous residue 298 
Skipped atom 1690 because residue number 209  < previous residue 298 
Skipped atom 1691 because residue number 209  < previous residue 298 
Skipped atom 1692 because residue number 209  < previous residue 298 
Skipped atom 1693 because residue number 209  < previous residue 298 
Skipped atom 1694 because residue number 209  < previous residue 298 
Skipped atom 1695 because residue number 209  < previous residue 298 
Skipped atom 1696 because residue number 209  < previous residue 298 
Skipped atom 1697 because residue number 210  < previous residue 298 
Skipped atom 1698 because residue number 210  < previous residue 298 
Skipped atom 1699 because residue number 210  < previous residue 298 
Skipped atom 1700 because residue number 210  < previous residue 298 
Skipped atom 1701 because residue number 210  < previous residue 298 
Skipped atom 1702 because residue number 210  < previous residue 298 
Skipped atom 1703 because residue number 210  < previous residue 298 
Skipped atom 1704 because residue number 210  < previous residue 298 
Skipped atom 1705 because residue number 211  < previous residue 298 
Skipped atom 1706 because residue number 211  < previous residue 298 
Skipped atom 1707 because residue number 211  < previous residue 298 
Skipped atom 1708 because residue number 211  < previous residue 298 
Skipped atom 1709 because residue number 211  < previous residue 298 
Skipped atom 1710 because residue number 211  < previous residue 298 
Skipped atom 1711 because residue number 211  < previous residue 298 
Skipped atom 1712 because residue number 211  < previous residue 298 
Skipped atom 1713 because residue number 212  < previous residue 298 
Skipped atom 1714 because residue number 212  < previous residue 298 
Skipped atom 1715 because residue number 212  < previous residue 298 
Skipped atom 1716 because residue number 212  < previous residue 298 
Skipped atom 1717 because residue number 212  < previous residue 298 
Skipped atom 1718 because residue number 212  < previous residue 298 
Skipped atom 1719 because residue number 212  < previous residue 298 
Skipped atom 1720 because residue number 212  < previous residue 298 
Skipped atom 1721 because residue number 213  < previous residue 298 
Skipped atom 1722 because residue number 213  < previous residue 298 
Skipped atom 1723 because residue number 213  < previous residue 298 
Skipped atom 1724 because residue number 213  < previous residue 298 
Skipped atom 1725 because residue number 213  < previous residue 298 
Skipped atom 1726 because residue number 213  < previous residue 298 
Skipped atom 1727 because residue number 213  < previous residue 298 
Skipped atom 1728 because residue number 213  < previous residue 298 
Skipped atom 1729 because residue number 214  < previous residue 298 
Skipped atom 1730 because residue number 214  < previous residue 298 
Skipped atom 1731 because residue number 214  < previous residue 298 
Skipped atom 1732 because residue number 214  < previous residue 298 
Skipped atom 1733 because residue number 214  < previous residue 298 
Skipped atom 1734 because residue number 214  < previous residue 298 
Skipped atom 1735 because residue number 214  < previous residue 298 
Skipped atom 1736 because residue number 214  < previous residue 298 
Skipped atom 1737 because residue number 215  < previous residue 298 
Skipped atom 1738 because residue number 215  < previous residue 298 
Skipped atom 1739 because residue number 215  < previous residue 298 
Skipped atom 1740 because residue number 215  < previous residue 298 
Skipped atom 1741 because residue number 215  < previous residue 298 
Skipped atom 1742 because residue number 215  < previous residue 298 
Skipped atom 1743 because residue number 215  < previous residue 298 
Skipped atom 1744 because residue number 215  < previous residue 298 
Skipped atom 1745 because residue number 215  < previous residue 298 
Skipped atom 1746 because residue number 216  < previous residue 298 
Skipped atom 1747 because residue number 216  < previous residue 298 
Skipped atom 1748 because residue number 216  < previous residue 298 
Skipped atom 1749 because residue number 216  < previous residue 298 
Skipped atom 1750 because residue number 216  < previous residue 298 
Skipped atom 1751 because residue number 216  < previous residue 298 
Skipped atom 1752 because residue number 217  < previous residue 298 
Skipped atom 1753 because residue number 217  < previous residue 298 
Skipped atom 1754 because residue number 217  < previous residue 298 
Skipped atom 1755 because residue number 217  < previous residue 298 
Skipped atom 1756 because residue number 218  < previous residue 298 
Skipped atom 1757 because residue number 218  < previous residue 298 
Skipped atom 1758 because residue number 218  < previous residue 298 
Skipped atom 1759 because residue number 218  < previous residue 298 
Skipped atom 1760 because residue number 218  < previous residue 298 
Skipped atom 1761 because residue number 218  < previous residue 298 
Skipped atom 1762 because residue number 218  < previous residue 298 
Skipped atom 1763 because residue number 218  < previous residue 298 
Skipped atom 1764 because residue number 219  < previous residue 298 
Skipped atom 1765 because residue number 219  < previous residue 298 
Skipped atom 1766 because residue number 219  < previous residue 298 
Skipped atom 1767 because residue number 219  < previous residue 298 
Skipped atom 1768 because residue number 219  < previous residue 298 
Skipped atom 1769 because residue number 219  < previous residue 298 
Skipped atom 1770 because residue number 219  < previous residue 298 
Skipped atom 1771 because residue number 220  < previous residue 298 
Skipped atom 1772 because residue number 220  < previous residue 298 
Skipped atom 1773 because residue number 220  < previous residue 298 
Skipped atom 1774 because residue number 220  < previous residue 298 
Skipped atom 1775 because residue number 220  < previous residue 298 
Skipped atom 1776 because residue number 220  < previous residue 298 
Skipped atom 1777 because residue number 220  < previous residue 298 
Skipped atom 1778 because residue number 220  < previous residue 298 
Skipped atom 1779 because residue number 221  < previous residue 298 
Skipped atom 1780 because residue number 221  < previous residue 298 
Skipped atom 1781 because residue number 221  < previous residue 298 
Skipped atom 1782 because residue number 221  < previous residue 298 
Skipped atom 1783 because residue number 221  < previous residue 298 
Skipped atom 1784 because residue number 221  < previous residue 298 
Skipped atom 1785 because residue number 221  < previous residue 298 
Skipped atom 1786 because residue number 221  < previous residue 298 
Skipped atom 1787 because residue number 222  < previous residue 298 
Skipped atom 1788 because residue number 222  < previous residue 298 
Skipped atom 1789 because residue number 222  < previous residue 298 
Skipped atom 1790 because residue number 222  < previous residue 298 
Skipped atom 1791 because residue number 222  < previous residue 298 
Skipped atom 1792 because residue number 222  < previous residue 298 
Skipped atom 1793 because residue number 222  < previous residue 298 
Skipped atom 1794 because residue number 222  < previous residue 298 
Skipped atom 1795 because residue number 222  < previous residue 298 
Skipped atom 1796 because residue number 223  < previous residue 298 
Skipped atom 1797 because residue number 223  < previous residue 298 
Skipped atom 1798 because residue number 223  < previous residue 298 
Skipped atom 1799 because residue number 223  < previous residue 298 
Skipped atom 1800 because residue number 223  < previous residue 298 
Skipped atom 1801 because residue number 223  < previous residue 298 
Skipped atom 1802 because residue number 223  < previous residue 298 
Skipped atom 1803 because residue number 223  < previous residue 298 
Skipped atom 1804 because residue number 224  < previous residue 298 
Skipped atom 1805 because residue number 224  < previous residue 298 
Skipped atom 1806 because residue number 224  < previous residue 298 
Skipped atom 1807 because residue number 224  < previous residue 298 
Skipped atom 1808 because residue number 225  < previous residue 298 
Skipped atom 1809 because residue number 225  < previous residue 298 
Skipped atom 1810 because residue number 225  < previous residue 298 
Skipped atom 1811 because residue number 225  < previous residue 298 
Skipped atom 1812 because residue number 225  < previous residue 298 
Skipped atom 1813 because residue number 225  < previous residue 298 
Skipped atom 1814 because residue number 225  < previous residue 298 
Skipped atom 1815 because residue number 226  < previous residue 298 
Skipped atom 1816 because residue number 226  < previous residue 298 
Skipped atom 1817 because residue number 226  < previous residue 298 
Skipped atom 1818 because residue number 226  < previous residue 298 
Skipped atom 1819 because residue number 226  < previous residue 298 
Skipped atom 1820 because residue number 226  < previous residue 298 
Skipped atom 1821 because residue number 226  < previous residue 298 
Skipped atom 1822 because residue number 227  < previous residue 298 
Skipped atom 1823 because residue number 227  < previous residue 298 
Skipped atom 1824 because residue number 227  < previous residue 298 
Skipped atom 1825 because residue number 227  < previous residue 298 
Skipped atom 1826 because residue number 227  < previous residue 298 
Skipped atom 1827 because residue number 227  < previous residue 298 
Skipped atom 1828 because residue number 228  < previous residue 298 
Skipped atom 1829 because residue number 228  < previous residue 298 
Skipped atom 1830 because residue number 228  < previous residue 298 
Skipped atom 1831 because residue number 228  < previous residue 298 
Skipped atom 1832 because residue number 228  < previous residue 298 
Skipped atom 1833 because residue number 228  < previous residue 298 
Skipped atom 1834 because residue number 228  < previous residue 298 
Skipped atom 1835 because residue number 228  < previous residue 298 
Skipped atom 1836 because residue number 229  < previous residue 298 
Skipped atom 1837 because residue number 229  < previous residue 298 
Skipped atom 1838 because residue number 229  < previous residue 298 
Skipped atom 1839 because residue number 229  < previous residue 298 
Skipped atom 1840 because residue number 229  < previous residue 298 
Skipped atom 1841 because residue number 229  < previous residue 298 
Skipped atom 1842 because residue number 229  < previous residue 298 
Skipped atom 1843 because residue number 229  < previous residue 298 
Skipped atom 1844 because residue number 229  < previous residue 298 
Skipped atom 1845 because residue number 229  < previous residue 298 
Skipped atom 1846 because residue number 229  < previous residue 298 
Skipped atom 1847 because residue number 229  < previous residue 298 
Skipped atom 1848 because residue number 230  < previous residue 298 
Skipped atom 1849 because residue number 230  < previous residue 298 
Skipped atom 1850 because residue number 230  < previous residue 298 
Skipped atom 1851 because residue number 230  < previous residue 298 
Skipped atom 1852 because residue number 230  < previous residue 298 
Skipped atom 1853 because residue number 230  < previous residue 298 
Skipped atom 1854 because residue number 230  < previous residue 298 
Skipped atom 1855 because residue number 230  < previous residue 298 
Skipped atom 1856 because residue number 230  < previous residue 298 
Skipped atom 1857 because residue number 231  < previous residue 298 
Skipped atom 1858 because residue number 231  < previous residue 298 
Skipped atom 1859 because residue number 231  < previous residue 298 
Skipped atom 1860 because residue number 231  < previous residue 298 
Skipped atom 1861 because residue number 231  < previous residue 298 
Skipped atom 1862 because residue number 231  < previous residue 298 
Skipped atom 1863 because residue number 231  < previous residue 298 
Skipped atom 1864 because residue number 232  < previous residue 298 
Skipped atom 1865 because residue number 232  < previous residue 298 
Skipped atom 1866 because residue number 232  < previous residue 298 
Skipped atom 1867 because residue number 232  < previous residue 298 
Skipped atom 1868 because residue number 232  < previous residue 298 
Skipped atom 1869 because residue number 233  < previous residue 298 
Skipped atom 1870 because residue number 233  < previous residue 298 
Skipped atom 1871 because residue number 233  < previous residue 298 
Skipped atom 1872 because residue number 233  < previous residue 298 
Skipped atom 1873 because residue number 233  < previous residue 298 
Skipped atom 1874 because residue number 233  < previous residue 298 
Skipped atom 1875 because residue number 233  < previous residue 298 
Skipped atom 1876 because residue number 233  < previous residue 298 
Skipped atom 1877 because residue number 234  < previous residue 298 
Skipped atom 1878 because residue number 234  < previous residue 298 
Skipped atom 1879 because residue number 234  < previous residue 298 
Skipped atom 1880 because residue number 234  < previous residue 298 
Skipped atom 1881 because residue number 234  < previous residue 298 
Skipped atom 1882 because residue number 234  < previous residue 298 
Skipped atom 1883 because residue number 234  < previous residue 298 
Skipped atom 1884 because residue number 234  < previous residue 298 
Skipped atom 1885 because residue number 234  < previous residue 298 
Skipped atom 1886 because residue number 235  < previous residue 298 
Skipped atom 1887 because residue number 235  < previous residue 298 
Skipped atom 1888 because residue number 235  < previous residue 298 
Skipped atom 1889 because residue number 235  < previous residue 298 
Skipped atom 1890 because residue number 235  < previous residue 298 
Skipped atom 1891 because residue number 235  < previous residue 298 
Skipped atom 1892 because residue number 236  < previous residue 298 
Skipped atom 1893 because residue number 236  < previous residue 298 
Skipped atom 1894 because residue number 236  < previous residue 298 
Skipped atom 1895 because residue number 236  < previous residue 298 
Skipped atom 1896 because residue number 237  < previous residue 298 
Skipped atom 1897 because residue number 237  < previous residue 298 
Skipped atom 1898 because residue number 237  < previous residue 298 
Skipped atom 1899 because residue number 237  < previous residue 298 
Skipped atom 1900 because residue number 237  < previous residue 298 
Skipped atom 1901 because residue number 237  < previous residue 298 
Skipped atom 1902 because residue number 237  < previous residue 298 
Skipped atom 1903 because residue number 237  < previous residue 298 
Skipped atom 1904 because residue number 237  < previous residue 298 
Skipped atom 1905 because residue number 238  < previous residue 298 
Skipped atom 1906 because residue number 238  < previous residue 298 
Skipped atom 1907 because residue number 238  < previous residue 298 
Skipped atom 1908 because residue number 238  < previous residue 298 
Skipped atom 1909 because residue number 238  < previous residue 298 
Skipped atom 1910 because residue number 239  < previous residue 298 
Skipped atom 1911 because residue number 239  < previous residue 298 
Skipped atom 1912 because residue number 239  < previous residue 298 
Skipped atom 1913 because residue number 239  < previous residue 298 
Skipped atom 1914 because residue number 239  < previous residue 298 
Skipped atom 1915 because residue number 239  < previous residue 298 
Skipped atom 1916 because residue number 239  < previous residue 298 
Skipped atom 1917 because residue number 239  < previous residue 298 
Skipped atom 1918 because residue number 240  < previous residue 298 
Skipped atom 1919 because residue number 240  < previous residue 298 
Skipped atom 1920 because residue number 240  < previous residue 298 
Skipped atom 1921 because residue number 240  < previous residue 298 
Skipped atom 1922 because residue number 240  < previous residue 298 
Skipped atom 1923 because residue number 240  < previous residue 298 
Skipped atom 1924 because residue number 240  < previous residue 298 
Skipped atom 1925 because residue number 241  < previous residue 298 
Skipped atom 1926 because residue number 241  < previous residue 298 
Skipped atom 1927 because residue number 241  < previous residue 298 
Skipped atom 1928 because residue number 241  < previous residue 298 
Skipped atom 1929 because residue number 241  < previous residue 298 
Skipped atom 1930 because residue number 241  < previous residue 298 
Skipped atom 1931 because residue number 241  < previous residue 298 
Skipped atom 1932 because residue number 241  < previous residue 298 
Skipped atom 1933 because residue number 241  < previous residue 298 
Skipped atom 1934 because residue number 241  < previous residue 298 
Skipped atom 1935 because residue number 241  < previous residue 298 
Skipped atom 1936 because residue number 241  < previous residue 298 
Skipped atom 1937 because residue number 242  < previous residue 298 
Skipped atom 1938 because residue number 242  < previous residue 298 
Skipped atom 1939 because residue number 242  < previous residue 298 
Skipped atom 1940 because residue number 242  < previous residue 298 
Skipped atom 1941 because residue number 242  < previous residue 298 
Skipped atom 1942 because residue number 243  < previous residue 298 
Skipped atom 1943 because residue number 243  < previous residue 298 
Skipped atom 1944 because residue number 243  < previous residue 298 
Skipped atom 1945 because residue number 243  < previous residue 298 
Skipped atom 1946 because residue number 243  < previous residue 298 
Skipped atom 1947 because residue number 243  < previous residue 298 
Skipped atom 1948 because residue number 244  < previous residue 298 
Skipped atom 1949 because residue number 244  < previous residue 298 
Skipped atom 1950 because residue number 244  < previous residue 298 
Skipped atom 1951 because residue number 244  < previous residue 298 
Skipped atom 1952 because residue number 244  < previous residue 298 
Skipped atom 1953 because residue number 244  < previous residue 298 
Skipped atom 1954 because residue number 244  < previous residue 298 
Skipped atom 1955 because residue number 244  < previous residue 298 
Skipped atom 1956 because residue number 244  < previous residue 298 
Skipped atom 1957 because residue number 244  < previous residue 298 
Skipped atom 1958 because residue number 244  < previous residue 298 
Skipped atom 1959 because residue number 245  < previous residue 298 
Skipped atom 1960 because residue number 245  < previous residue 298 
Skipped atom 1961 because residue number 245  < previous residue 298 
Skipped atom 1962 because residue number 245  < previous residue 298 
Skipped atom 1963 because residue number 245  < previous residue 298 
Skipped atom 1964 because residue number 245  < previous residue 298 
Skipped atom 1965 because residue number 245  < previous residue 298 
Skipped atom 1966 because residue number 245  < previous residue 298 
Skipped atom 1967 because residue number 246  < previous residue 298 
Skipped atom 1968 because residue number 246  < previous residue 298 
Skipped atom 1969 because residue number 246  < previous residue 298 
Skipped atom 1970 because residue number 246  < previous residue 298 
Skipped atom 1971 because residue number 246  < previous residue 298 
Skipped atom 1972 because residue number 246  < previous residue 298 
Skipped atom 1973 because residue number 246  < previous residue 298 
Skipped atom 1974 because residue number 246  < previous residue 298 
Skipped atom 1975 because residue number 247  < previous residue 298 
Skipped atom 1976 because residue number 247  < previous residue 298 
Skipped atom 1977 because residue number 247  < previous residue 298 
Skipped atom 1978 because residue number 247  < previous residue 298 
Skipped atom 1979 because residue number 247  < previous residue 298 
Skipped atom 1980 because residue number 247  < previous residue 298 
Skipped atom 1981 because residue number 247  < previous residue 298 
Skipped atom 1982 because residue number 248  < previous residue 298 
Skipped atom 1983 because residue number 248  < previous residue 298 
Skipped atom 1984 because residue number 248  < previous residue 298 
Skipped atom 1985 because residue number 248  < previous residue 298 
Skipped atom 1986 because residue number 248  < previous residue 298 
Skipped atom 1987 because residue number 249  < previous residue 298 
Skipped atom 1988 because residue number 249  < previous residue 298 
Skipped atom 1989 because residue number 249  < previous residue 298 
Skipped atom 1990 because residue number 249  < previous residue 298 
Skipped atom 1991 because residue number 249  < previous residue 298 
Skipped atom 1992 because residue number 249  < previous residue 298 
Skipped atom 1993 because residue number 249  < previous residue 298 
Skipped atom 1994 because residue number 249  < previous residue 298 
Skipped atom 1995 because residue number 249  < previous residue 298 
Skipped atom 1996 because residue number 249  < previous residue 298 
Skipped atom 1997 because residue number 249  < previous residue 298 
Skipped atom 1998 because residue number 250  < previous residue 298 
Skipped atom 1999 because residue number 250  < previous residue 298 
Skipped atom 2000 because residue number 250  < previous residue 298 
Skipped atom 2001 because residue number 250  < previous residue 298 
Skipped atom 2002 because residue number 250  < previous residue 298 
Skipped atom 2003 because residue number 250  < previous residue 298 
Skipped atom 2004 because residue number 250  < previous residue 298 
Skipped atom 2005 because residue number 251  < previous residue 298 
Skipped atom 2006 because residue number 251  < previous residue 298 
Skipped atom 2007 because residue number 251  < previous residue 298 
Skipped atom 2008 because residue number 251  < previous residue 298 
Skipped atom 2009 because residue number 251  < previous residue 298 
Skipped atom 2010 because residue number 251  < previous residue 298 
Skipped atom 2011 because residue number 251  < previous residue 298 
Skipped atom 2012 because residue number 251  < previous residue 298 
Skipped atom 2013 because residue number 251  < previous residue 298 
Skipped atom 2014 because residue number 251  < previous residue 298 
Skipped atom 2015 because residue number 251  < previous residue 298 
Skipped atom 2016 because residue number 251  < previous residue 298 
Skipped atom 2017 because residue number 252  < previous residue 298 
Skipped atom 2018 because residue number 252  < previous residue 298 
Skipped atom 2019 because residue number 252  < previous residue 298 
Skipped atom 2020 because residue number 252  < previous residue 298 
Skipped atom 2021 because residue number 252  < previous residue 298 
Skipped atom 2022 because residue number 252  < previous residue 298 
Skipped atom 2023 because residue number 252  < previous residue 298 
Skipped atom 2024 because residue number 253  < previous residue 298 
Skipped atom 2025 because residue number 253  < previous residue 298 
Skipped atom 2026 because residue number 253  < previous residue 298 
Skipped atom 2027 because residue number 253  < previous residue 298 
Skipped atom 2028 because residue number 253  < previous residue 298 
Skipped atom 2029 because residue number 253  < previous residue 298 
Skipped atom 2030 because residue number 253  < previous residue 298 
Skipped atom 2031 because residue number 253  < previous residue 298 
Skipped atom 2032 because residue number 253  < previous residue 298 
Skipped atom 2033 because residue number 253  < previous residue 298 
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1alq-orig.a2m
Writing a2m file: tmp/1alq-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14931


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14931/tmp -alignfile tmp/1alq-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1alq-orig.a2m (1 sequences, 266 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14931/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14931/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14931/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14931/tmp.a2m (1 sequences, 266 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14931/tmp.mod tmp/1alq-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14931 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1alq-align.mod
tmp/1alq-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14931/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1alq-orig.a2m tmp/1alq-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1alq-align.mod
Running w0.5 tmp/1alq-orig.a2m tmp/1alq-align.mod
Running align2model tmp/1alq-align -i tmp/1alq-align.mod -db tmp/1alq-orig.a2m -db tmp/1alq-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1alq.147.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1alq.94.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1alq.94.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1alq.94.5.a2m \
	-target T0124 -template 1alq \
	-out T0124-1alq.94.5 -outdir und
Skipped atom 298 because residue number 31  < previous residue 298 
Skipped atom 299 because residue number 31  < previous residue 298 
Skipped atom 300 because residue number 31  < previous residue 298 
Skipped atom 301 because residue number 31  < previous residue 298 
Skipped atom 302 because residue number 31  < previous residue 298 
Skipped atom 303 because residue number 31  < previous residue 298 
Skipped atom 304 because residue number 31  < previous residue 298 
Skipped atom 305 because residue number 31  < previous residue 298 
Skipped atom 306 because residue number 31  < previous residue 298 
Skipped atom 307 because residue number 32  < previous residue 298 
Skipped atom 308 because residue number 32  < previous residue 298 
Skipped atom 309 because residue number 32  < previous residue 298 
Skipped atom 310 because residue number 32  < previous residue 298 
Skipped atom 311 because residue number 32  < previous residue 298 
Skipped atom 312 because residue number 32  < previous residue 298 
Skipped atom 313 because residue number 32  < previous residue 298 
Skipped atom 314 because residue number 32  < previous residue 298 
Skipped atom 315 because residue number 32  < previous residue 298 
Skipped atom 316 because residue number 33  < previous residue 298 
Skipped atom 317 because residue number 33  < previous residue 298 
Skipped atom 318 because residue number 33  < previous residue 298 
Skipped atom 319 because residue number 33  < previous residue 298 
Skipped atom 320 because residue number 33  < previous residue 298 
Skipped atom 321 because residue number 33  < previous residue 298 
Skipped atom 322 because residue number 33  < previous residue 298 
Skipped atom 323 because residue number 33  < previous residue 298 
Skipped atom 324 because residue number 34  < previous residue 298 
Skipped atom 325 because residue number 34  < previous residue 298 
Skipped atom 326 because residue number 34  < previous residue 298 
Skipped atom 327 because residue number 34  < previous residue 298 
Skipped atom 328 because residue number 34  < previous residue 298 
Skipped atom 329 because residue number 34  < previous residue 298 
Skipped atom 330 because residue number 34  < previous residue 298 
Skipped atom 331 because residue number 34  < previous residue 298 
Skipped atom 332 because residue number 35  < previous residue 298 
Skipped atom 333 because residue number 35  < previous residue 298 
Skipped atom 334 because residue number 35  < previous residue 298 
Skipped atom 335 because residue number 35  < previous residue 298 
Skipped atom 336 because residue number 35  < previous residue 298 
Skipped atom 337 because residue number 35  < previous residue 298 
Skipped atom 338 because residue number 35  < previous residue 298 
Skipped atom 339 because residue number 35  < previous residue 298 
Skipped atom 340 because residue number 36  < previous residue 298 
Skipped atom 341 because residue number 36  < previous residue 298 
Skipped atom 342 because residue number 36  < previous residue 298 
Skipped atom 343 because residue number 36  < previous residue 298 
Skipped atom 344 because residue number 36  < previous residue 298 
Skipped atom 345 because residue number 36  < previous residue 298 
Skipped atom 346 because residue number 36  < previous residue 298 
Skipped atom 347 because residue number 36  < previous residue 298 
Skipped atom 348 because residue number 37  < previous residue 298 
Skipped atom 349 because residue number 37  < previous residue 298 
Skipped atom 350 because residue number 37  < previous residue 298 
Skipped atom 351 because residue number 37  < previous residue 298 
Skipped atom 352 because residue number 37  < previous residue 298 
Skipped atom 353 because residue number 37  < previous residue 298 
Skipped atom 354 because residue number 37  < previous residue 298 
Skipped atom 355 because residue number 37  < previous residue 298 
Skipped atom 356 because residue number 37  < previous residue 298 
Skipped atom 357 because residue number 38  < previous residue 298 
Skipped atom 358 because residue number 38  < previous residue 298 
Skipped atom 359 because residue number 38  < previous residue 298 
Skipped atom 360 because residue number 38  < previous residue 298 
Skipped atom 361 because residue number 38  < previous residue 298 
Skipped atom 362 because residue number 38  < previous residue 298 
Skipped atom 363 because residue number 38  < previous residue 298 
Skipped atom 364 because residue number 38  < previous residue 298 
Skipped atom 365 because residue number 38  < previous residue 298 
Skipped atom 366 because residue number 39  < previous residue 298 
Skipped atom 367 because residue number 39  < previous residue 298 
Skipped atom 368 because residue number 39  < previous residue 298 
Skipped atom 369 because residue number 39  < previous residue 298 
Skipped atom 370 because residue number 39  < previous residue 298 
Skipped atom 371 because residue number 39  < previous residue 298 
Skipped atom 372 because residue number 39  < previous residue 298 
Skipped atom 373 because residue number 39  < previous residue 298 
Skipped atom 374 because residue number 39  < previous residue 298 
Skipped atom 375 because residue number 40  < previous residue 298 
Skipped atom 376 because residue number 40  < previous residue 298 
Skipped atom 377 because residue number 40  < previous residue 298 
Skipped atom 378 because residue number 40  < previous residue 298 
Skipped atom 379 because residue number 40  < previous residue 298 
Skipped atom 380 because residue number 40  < previous residue 298 
Skipped atom 381 because residue number 40  < previous residue 298 
Skipped atom 382 because residue number 40  < previous residue 298 
Skipped atom 383 because residue number 40  < previous residue 298 
Skipped atom 384 because residue number 40  < previous residue 298 
Skipped atom 385 because residue number 40  < previous residue 298 
Skipped atom 386 because residue number 40  < previous residue 298 
Skipped atom 387 because residue number 41  < previous residue 298 
Skipped atom 388 because residue number 41  < previous residue 298 
Skipped atom 389 because residue number 41  < previous residue 298 
Skipped atom 390 because residue number 41  < previous residue 298 
Skipped atom 391 because residue number 41  < previous residue 298 
Skipped atom 392 because residue number 41  < previous residue 298 
Skipped atom 393 because residue number 41  < previous residue 298 
Skipped atom 394 because residue number 41  < previous residue 298 
Skipped atom 395 because residue number 42  < previous residue 298 
Skipped atom 396 because residue number 42  < previous residue 298 
Skipped atom 397 because residue number 42  < previous residue 298 
Skipped atom 398 because residue number 42  < previous residue 298 
Skipped atom 399 because residue number 42  < previous residue 298 
Skipped atom 400 because residue number 43  < previous residue 298 
Skipped atom 401 because residue number 43  < previous residue 298 
Skipped atom 402 because residue number 43  < previous residue 298 
Skipped atom 403 because residue number 43  < previous residue 298 
Skipped atom 404 because residue number 43  < previous residue 298 
Skipped atom 405 because residue number 43  < previous residue 298 
Skipped atom 406 because residue number 43  < previous residue 298 
Skipped atom 407 because residue number 43  < previous residue 298 
Skipped atom 408 because residue number 43  < previous residue 298 
Skipped atom 409 because residue number 43  < previous residue 298 
Skipped atom 410 because residue number 44  < previous residue 298 
Skipped atom 411 because residue number 44  < previous residue 298 
Skipped atom 412 because residue number 44  < previous residue 298 
Skipped atom 413 because residue number 44  < previous residue 298 
Skipped atom 414 because residue number 44  < previous residue 298 
Skipped atom 415 because residue number 44  < previous residue 298 
Skipped atom 416 because residue number 44  < previous residue 298 
Skipped atom 417 because residue number 44  < previous residue 298 
Skipped atom 418 because residue number 45  < previous residue 298 
Skipped atom 419 because residue number 45  < previous residue 298 
Skipped atom 420 because residue number 45  < previous residue 298 
Skipped atom 421 because residue number 45  < previous residue 298 
Skipped atom 422 because residue number 46  < previous residue 298 
Skipped atom 423 because residue number 46  < previous residue 298 
Skipped atom 424 because residue number 46  < previous residue 298 
Skipped atom 425 because residue number 46  < previous residue 298 
Skipped atom 426 because residue number 46  < previous residue 298 
Skipped atom 427 because residue number 46  < previous residue 298 
Skipped atom 428 because residue number 46  < previous residue 298 
Skipped atom 429 because residue number 47  < previous residue 298 
Skipped atom 430 because residue number 47  < previous residue 298 
Skipped atom 431 because residue number 47  < previous residue 298 
Skipped atom 432 because residue number 47  < previous residue 298 
Skipped atom 433 because residue number 47  < previous residue 298 
Skipped atom 434 because residue number 47  < previous residue 298 
Skipped atom 435 because residue number 47  < previous residue 298 
Skipped atom 436 because residue number 47  < previous residue 298 
Skipped atom 437 because residue number 47  < previous residue 298 
Skipped atom 438 because residue number 47  < previous residue 298 
Skipped atom 439 because residue number 47  < previous residue 298 
Skipped atom 440 because residue number 47  < previous residue 298 
Skipped atom 441 because residue number 48  < previous residue 298 
Skipped atom 442 because residue number 48  < previous residue 298 
Skipped atom 443 because residue number 48  < previous residue 298 
Skipped atom 444 because residue number 48  < previous residue 298 
Skipped atom 445 because residue number 48  < previous residue 298 
Skipped atom 446 because residue number 49  < previous residue 298 
Skipped atom 447 because residue number 49  < previous residue 298 
Skipped atom 448 because residue number 49  < previous residue 298 
Skipped atom 449 because residue number 49  < previous residue 298 
Skipped atom 450 because residue number 49  < previous residue 298 
Skipped atom 451 because residue number 49  < previous residue 298 
Skipped atom 452 because residue number 49  < previous residue 298 
Skipped atom 453 because residue number 49  < previous residue 298 
Skipped atom 454 because residue number 50  < previous residue 298 
Skipped atom 455 because residue number 50  < previous residue 298 
Skipped atom 456 because residue number 50  < previous residue 298 
Skipped atom 457 because residue number 50  < previous residue 298 
Skipped atom 458 because residue number 50  < previous residue 298 
Skipped atom 459 because residue number 50  < previous residue 298 
Skipped atom 460 because residue number 50  < previous residue 298 
Skipped atom 461 because residue number 50  < previous residue 298 
Skipped atom 462 because residue number 51  < previous residue 298 
Skipped atom 463 because residue number 51  < previous residue 298 
Skipped atom 464 because residue number 51  < previous residue 298 
Skipped atom 465 because residue number 51  < previous residue 298 
Skipped atom 466 because residue number 51  < previous residue 298 
Skipped atom 467 because residue number 51  < previous residue 298 
Skipped atom 468 because residue number 51  < previous residue 298 
Skipped atom 469 because residue number 52  < previous residue 298 
Skipped atom 470 because residue number 52  < previous residue 298 
Skipped atom 471 because residue number 52  < previous residue 298 
Skipped atom 472 because residue number 52  < previous residue 298 
Skipped atom 473 because residue number 52  < previous residue 298 
Skipped atom 474 because residue number 52  < previous residue 298 
Skipped atom 475 because residue number 52  < previous residue 298 
Skipped atom 476 because residue number 52  < previous residue 298 
Skipped atom 477 because residue number 52  < previous residue 298 
Skipped atom 478 because residue number 53  < previous residue 298 
Skipped atom 479 because residue number 53  < previous residue 298 
Skipped atom 480 because residue number 53  < previous residue 298 
Skipped atom 481 because residue number 53  < previous residue 298 
Skipped atom 482 because residue number 53  < previous residue 298 
Skipped atom 483 because residue number 53  < previous residue 298 
Skipped atom 484 because residue number 54  < previous residue 298 
Skipped atom 485 because residue number 54  < previous residue 298 
Skipped atom 486 because residue number 54  < previous residue 298 
Skipped atom 487 because residue number 54  < previous residue 298 
Skipped atom 488 because residue number 55  < previous residue 298 
Skipped atom 489 because residue number 55  < previous residue 298 
Skipped atom 490 because residue number 55  < previous residue 298 
Skipped atom 491 because residue number 55  < previous residue 298 
Skipped atom 492 because residue number 55  < previous residue 298 
Skipped atom 493 because residue number 55  < previous residue 298 
Skipped atom 494 because residue number 55  < previous residue 298 
Skipped atom 495 because residue number 55  < previous residue 298 
Skipped atom 496 because residue number 55  < previous residue 298 
Skipped atom 497 because residue number 56  < previous residue 298 
Skipped atom 498 because residue number 56  < previous residue 298 
Skipped atom 499 because residue number 56  < previous residue 298 
Skipped atom 500 because residue number 56  < previous residue 298 
Skipped atom 501 because residue number 56  < previous residue 298 
Skipped atom 502 because residue number 56  < previous residue 298 
Skipped atom 503 because residue number 56  < previous residue 298 
Skipped atom 504 because residue number 56  < previous residue 298 
Skipped atom 505 because residue number 56  < previous residue 298 
Skipped atom 506 because residue number 57  < previous residue 298 
Skipped atom 507 because residue number 57  < previous residue 298 
Skipped atom 508 because residue number 57  < previous residue 298 
Skipped atom 509 because residue number 57  < previous residue 298 
Skipped atom 510 because residue number 57  < previous residue 298 
Skipped atom 511 because residue number 57  < previous residue 298 
Skipped atom 512 because residue number 57  < previous residue 298 
Skipped atom 513 because residue number 59  < previous residue 298 
Skipped atom 514 because residue number 59  < previous residue 298 
Skipped atom 515 because residue number 59  < previous residue 298 
Skipped atom 516 because residue number 59  < previous residue 298 
Skipped atom 517 because residue number 59  < previous residue 298 
Skipped atom 518 because residue number 59  < previous residue 298 
Skipped atom 519 because residue number 59  < previous residue 298 
Skipped atom 520 because residue number 59  < previous residue 298 
Skipped atom 521 because residue number 59  < previous residue 298 
Skipped atom 522 because residue number 60  < previous residue 298 
Skipped atom 523 because residue number 60  < previous residue 298 
Skipped atom 524 because residue number 60  < previous residue 298 
Skipped atom 525 because residue number 60  < previous residue 298 
Skipped atom 526 because residue number 60  < previous residue 298 
Skipped atom 527 because residue number 60  < previous residue 298 
Skipped atom 528 because residue number 60  < previous residue 298 
Skipped atom 529 because residue number 60  < previous residue 298 
Skipped atom 530 because residue number 60  < previous residue 298 
Skipped atom 531 because residue number 60  < previous residue 298 
Skipped atom 532 because residue number 60  < previous residue 298 
Skipped atom 533 because residue number 61  < previous residue 298 
Skipped atom 534 because residue number 61  < previous residue 298 
Skipped atom 535 because residue number 61  < previous residue 298 
Skipped atom 536 because residue number 61  < previous residue 298 
Skipped atom 537 because residue number 61  < previous residue 298 
Skipped atom 538 because residue number 61  < previous residue 298 
Skipped atom 539 because residue number 61  < previous residue 298 
Skipped atom 540 because residue number 61  < previous residue 298 
Skipped atom 541 because residue number 62  < previous residue 298 
Skipped atom 542 because residue number 62  < previous residue 298 
Skipped atom 543 because residue number 62  < previous residue 298 
Skipped atom 544 because residue number 62  < previous residue 298 
Skipped atom 545 because residue number 62  < previous residue 298 
Skipped atom 546 because residue number 62  < previous residue 298 
Skipped atom 547 because residue number 63  < previous residue 298 
Skipped atom 548 because residue number 63  < previous residue 298 
Skipped atom 549 because residue number 63  < previous residue 298 
Skipped atom 550 because residue number 63  < previous residue 298 
Skipped atom 551 because residue number 63  < previous residue 298 
Skipped atom 552 because residue number 63  < previous residue 298 
Skipped atom 553 because residue number 63  < previous residue 298 
Skipped atom 554 because residue number 63  < previous residue 298 
Skipped atom 555 because residue number 64  < previous residue 298 
Skipped atom 556 because residue number 64  < previous residue 298 
Skipped atom 557 because residue number 64  < previous residue 298 
Skipped atom 558 because residue number 64  < previous residue 298 
Skipped atom 559 because residue number 64  < previous residue 298 
Skipped atom 560 because residue number 64  < previous residue 298 
Skipped atom 561 because residue number 64  < previous residue 298 
Skipped atom 562 because residue number 64  < previous residue 298 
Skipped atom 563 because residue number 64  < previous residue 298 
Skipped atom 564 because residue number 65  < previous residue 298 
Skipped atom 565 because residue number 65  < previous residue 298 
Skipped atom 566 because residue number 65  < previous residue 298 
Skipped atom 567 because residue number 65  < previous residue 298 
Skipped atom 568 because residue number 65  < previous residue 298 
Skipped atom 569 because residue number 65  < previous residue 298 
Skipped atom 570 because residue number 65  < previous residue 298 
Skipped atom 571 because residue number 65  < previous residue 298 
Skipped atom 572 because residue number 65  < previous residue 298 
Skipped atom 573 because residue number 65  < previous residue 298 
Skipped atom 574 because residue number 65  < previous residue 298 
Skipped atom 575 because residue number 66  < previous residue 298 
Skipped atom 576 because residue number 66  < previous residue 298 
Skipped atom 577 because residue number 66  < previous residue 298 
Skipped atom 578 because residue number 66  < previous residue 298 
Skipped atom 579 because residue number 66  < previous residue 298 
Skipped atom 580 because residue number 66  < previous residue 298 
Skipped atom 581 because residue number 66  < previous residue 298 
Skipped atom 582 because residue number 66  < previous residue 298 
Skipped atom 583 because residue number 66  < previous residue 298 
Skipped atom 584 because residue number 66  < previous residue 298 
Skipped atom 585 because residue number 66  < previous residue 298 
Skipped atom 586 because residue number 67  < previous residue 298 
Skipped atom 587 because residue number 67  < previous residue 298 
Skipped atom 588 because residue number 67  < previous residue 298 
Skipped atom 589 because residue number 67  < previous residue 298 
Skipped atom 590 because residue number 67  < previous residue 298 
Skipped atom 591 because residue number 68  < previous residue 298 
Skipped atom 592 because residue number 68  < previous residue 298 
Skipped atom 593 because residue number 68  < previous residue 298 
Skipped atom 594 because residue number 68  < previous residue 298 
Skipped atom 595 because residue number 68  < previous residue 298 
Skipped atom 596 because residue number 68  < previous residue 298 
Skipped atom 597 because residue number 68  < previous residue 298 
Skipped atom 598 because residue number 68  < previous residue 298 
Skipped atom 599 because residue number 68  < previous residue 298 
Skipped atom 600 because residue number 68  < previous residue 298 
Skipped atom 601 because residue number 68  < previous residue 298 
Skipped atom 602 because residue number 68  < previous residue 298 
Skipped atom 603 because residue number 69  < previous residue 298 
Skipped atom 604 because residue number 69  < previous residue 298 
Skipped atom 605 because residue number 69  < previous residue 298 
Skipped atom 606 because residue number 69  < previous residue 298 
Skipped atom 607 because residue number 69  < previous residue 298 
Skipped atom 608 because residue number 70  < previous residue 298 
Skipped atom 609 because residue number 70  < previous residue 298 
Skipped atom 610 because residue number 70  < previous residue 298 
Skipped atom 611 because residue number 70  < previous residue 298 
Skipped atom 612 because residue number 70  < previous residue 298 
Skipped atom 613 because residue number 70  < previous residue 298 
Skipped atom 614 because residue number 71  < previous residue 298 
Skipped atom 615 because residue number 71  < previous residue 298 
Skipped atom 616 because residue number 71  < previous residue 298 
Skipped atom 617 because residue number 71  < previous residue 298 
Skipped atom 618 because residue number 71  < previous residue 298 
Skipped atom 619 because residue number 71  < previous residue 298 
Skipped atom 620 because residue number 71  < previous residue 298 
Skipped atom 621 because residue number 72  < previous residue 298 
Skipped atom 622 because residue number 72  < previous residue 298 
Skipped atom 623 because residue number 72  < previous residue 298 
Skipped atom 624 because residue number 72  < previous residue 298 
Skipped atom 625 because residue number 72  < previous residue 298 
Skipped atom 626 because residue number 72  < previous residue 298 
Skipped atom 627 because residue number 73  < previous residue 298 
Skipped atom 628 because residue number 73  < previous residue 298 
Skipped atom 629 because residue number 73  < previous residue 298 
Skipped atom 630 because residue number 73  < previous residue 298 
Skipped atom 631 because residue number 73  < previous residue 298 
Skipped atom 632 because residue number 73  < previous residue 298 
Skipped atom 633 because residue number 73  < previous residue 298 
Skipped atom 634 because residue number 73  < previous residue 298 
Skipped atom 635 because residue number 73  < previous residue 298 
Skipped atom 636 because residue number 74  < previous residue 298 
Skipped atom 637 because residue number 74  < previous residue 298 
Skipped atom 638 because residue number 74  < previous residue 298 
Skipped atom 639 because residue number 74  < previous residue 298 
Skipped atom 640 because residue number 74  < previous residue 298 
Skipped atom 641 because residue number 75  < previous residue 298 
Skipped atom 642 because residue number 75  < previous residue 298 
Skipped atom 643 because residue number 75  < previous residue 298 
Skipped atom 644 because residue number 75  < previous residue 298 
Skipped atom 645 because residue number 75  < previous residue 298 
Skipped atom 646 because residue number 75  < previous residue 298 
Skipped atom 647 because residue number 75  < previous residue 298 
Skipped atom 648 because residue number 75  < previous residue 298 
Skipped atom 649 because residue number 76  < previous residue 298 
Skipped atom 650 because residue number 76  < previous residue 298 
Skipped atom 651 because residue number 76  < previous residue 298 
Skipped atom 652 because residue number 76  < previous residue 298 
Skipped atom 653 because residue number 76  < previous residue 298 
Skipped atom 654 because residue number 76  < previous residue 298 
Skipped atom 655 because residue number 76  < previous residue 298 
Skipped atom 656 because residue number 76  < previous residue 298 
Skipped atom 657 because residue number 77  < previous residue 298 
Skipped atom 658 because residue number 77  < previous residue 298 
Skipped atom 659 because residue number 77  < previous residue 298 
Skipped atom 660 because residue number 77  < previous residue 298 
Skipped atom 661 because residue number 77  < previous residue 298 
Skipped atom 662 because residue number 77  < previous residue 298 
Skipped atom 663 because residue number 78  < previous residue 298 
Skipped atom 664 because residue number 78  < previous residue 298 
Skipped atom 665 because residue number 78  < previous residue 298 
Skipped atom 666 because residue number 78  < previous residue 298 
Skipped atom 667 because residue number 78  < previous residue 298 
Skipped atom 668 because residue number 79  < previous residue 298 
Skipped atom 669 because residue number 79  < previous residue 298 
Skipped atom 670 because residue number 79  < previous residue 298 
Skipped atom 671 because residue number 79  < previous residue 298 
Skipped atom 672 because residue number 79  < previous residue 298 
Skipped atom 673 because residue number 79  < previous residue 298 
Skipped atom 674 because residue number 79  < previous residue 298 
Skipped atom 675 because residue number 79  < previous residue 298 
Skipped atom 676 because residue number 80  < previous residue 298 
Skipped atom 677 because residue number 80  < previous residue 298 
Skipped atom 678 because residue number 80  < previous residue 298 
Skipped atom 679 because residue number 80  < previous residue 298 
Skipped atom 680 because residue number 80  < previous residue 298 
Skipped atom 681 because residue number 80  < previous residue 298 
Skipped atom 682 because residue number 80  < previous residue 298 
Skipped atom 683 because residue number 80  < previous residue 298 
Skipped atom 684 because residue number 81  < previous residue 298 
Skipped atom 685 because residue number 81  < previous residue 298 
Skipped atom 686 because residue number 81  < previous residue 298 
Skipped atom 687 because residue number 81  < previous residue 298 
Skipped atom 688 because residue number 81  < previous residue 298 
Skipped atom 689 because residue number 81  < previous residue 298 
Skipped atom 690 because residue number 81  < previous residue 298 
Skipped atom 691 because residue number 81  < previous residue 298 
Skipped atom 692 because residue number 82  < previous residue 298 
Skipped atom 693 because residue number 82  < previous residue 298 
Skipped atom 694 because residue number 82  < previous residue 298 
Skipped atom 695 because residue number 82  < previous residue 298 
Skipped atom 696 because residue number 82  < previous residue 298 
Skipped atom 697 because residue number 82  < previous residue 298 
Skipped atom 698 because residue number 82  < previous residue 298 
Skipped atom 699 because residue number 82  < previous residue 298 
Skipped atom 700 because residue number 82  < previous residue 298 
Skipped atom 701 because residue number 83  < previous residue 298 
Skipped atom 702 because residue number 83  < previous residue 298 
Skipped atom 703 because residue number 83  < previous residue 298 
Skipped atom 704 because residue number 83  < previous residue 298 
Skipped atom 705 because residue number 83  < previous residue 298 
Skipped atom 706 because residue number 83  < previous residue 298 
Skipped atom 707 because residue number 83  < previous residue 298 
Skipped atom 708 because residue number 83  < previous residue 298 
Skipped atom 709 because residue number 83  < previous residue 298 
Skipped atom 710 because residue number 84  < previous residue 298 
Skipped atom 711 because residue number 84  < previous residue 298 
Skipped atom 712 because residue number 84  < previous residue 298 
Skipped atom 713 because residue number 84  < previous residue 298 
Skipped atom 714 because residue number 84  < previous residue 298 
Skipped atom 715 because residue number 84  < previous residue 298 
Skipped atom 716 because residue number 84  < previous residue 298 
Skipped atom 717 because residue number 87  < previous residue 298 
Skipped atom 718 because residue number 87  < previous residue 298 
Skipped atom 719 because residue number 87  < previous residue 298 
Skipped atom 720 because residue number 87  < previous residue 298 
Skipped atom 721 because residue number 87  < previous residue 298 
Skipped atom 722 because residue number 87  < previous residue 298 
Skipped atom 723 because residue number 87  < previous residue 298 
Skipped atom 724 because residue number 88  < previous residue 298 
Skipped atom 725 because residue number 88  < previous residue 298 
Skipped atom 726 because residue number 88  < previous residue 298 
Skipped atom 727 because residue number 88  < previous residue 298 
Skipped atom 728 because residue number 88  < previous residue 298 
Skipped atom 729 because residue number 88  < previous residue 298 
Skipped atom 730 because residue number 88  < previous residue 298 
Skipped atom 731 because residue number 88  < previous residue 298 
Skipped atom 732 because residue number 88  < previous residue 298 
Skipped atom 733 because residue number 88  < previous residue 298 
Skipped atom 734 because residue number 88  < previous residue 298 
Skipped atom 735 because residue number 88  < previous residue 298 
Skipped atom 736 because residue number 89  < previous residue 298 
Skipped atom 737 because residue number 89  < previous residue 298 
Skipped atom 738 because residue number 89  < previous residue 298 
Skipped atom 739 because residue number 89  < previous residue 298 
Skipped atom 740 because residue number 89  < previous residue 298 
Skipped atom 741 because residue number 89  < previous residue 298 
Skipped atom 742 because residue number 89  < previous residue 298 
Skipped atom 743 because residue number 89  < previous residue 298 
Skipped atom 744 because residue number 90  < previous residue 298 
Skipped atom 745 because residue number 90  < previous residue 298 
Skipped atom 746 because residue number 90  < previous residue 298 
Skipped atom 747 because residue number 90  < previous residue 298 
Skipped atom 748 because residue number 90  < previous residue 298 
Skipped atom 749 because residue number 90  < previous residue 298 
Skipped atom 750 because residue number 90  < previous residue 298 
Skipped atom 751 because residue number 90  < previous residue 298 
Skipped atom 752 because residue number 90  < previous residue 298 
Skipped atom 753 because residue number 91  < previous residue 298 
Skipped atom 754 because residue number 91  < previous residue 298 
Skipped atom 755 because residue number 91  < previous residue 298 
Skipped atom 756 because residue number 91  < previous residue 298 
Skipped atom 757 because residue number 91  < previous residue 298 
Skipped atom 758 because residue number 91  < previous residue 298 
Skipped atom 759 because residue number 91  < previous residue 298 
Skipped atom 760 because residue number 91  < previous residue 298 
Skipped atom 761 because residue number 92  < previous residue 298 
Skipped atom 762 because residue number 92  < previous residue 298 
Skipped atom 763 because residue number 92  < previous residue 298 
Skipped atom 764 because residue number 92  < previous residue 298 
Skipped atom 765 because residue number 92  < previous residue 298 
Skipped atom 766 because residue number 92  < previous residue 298 
Skipped atom 767 because residue number 92  < previous residue 298 
Skipped atom 768 because residue number 92  < previous residue 298 
Skipped atom 769 because residue number 93  < previous residue 298 
Skipped atom 770 because residue number 93  < previous residue 298 
Skipped atom 771 because residue number 93  < previous residue 298 
Skipped atom 772 because residue number 93  < previous residue 298 
Skipped atom 773 because residue number 93  < previous residue 298 
Skipped atom 774 because residue number 93  < previous residue 298 
Skipped atom 775 because residue number 93  < previous residue 298 
Skipped atom 776 because residue number 93  < previous residue 298 
Skipped atom 777 because residue number 93  < previous residue 298 
Skipped atom 778 because residue number 94  < previous residue 298 
Skipped atom 779 because residue number 94  < previous residue 298 
Skipped atom 780 because residue number 94  < previous residue 298 
Skipped atom 781 because residue number 94  < previous residue 298 
Skipped atom 782 because residue number 94  < previous residue 298 
Skipped atom 783 because residue number 94  < previous residue 298 
Skipped atom 784 because residue number 94  < previous residue 298 
Skipped atom 785 because residue number 94  < previous residue 298 
Skipped atom 786 because residue number 94  < previous residue 298 
Skipped atom 787 because residue number 95  < previous residue 298 
Skipped atom 788 because residue number 95  < previous residue 298 
Skipped atom 789 because residue number 95  < previous residue 298 
Skipped atom 790 because residue number 95  < previous residue 298 
Skipped atom 791 because residue number 95  < previous residue 298 
Skipped atom 792 because residue number 95  < previous residue 298 
Skipped atom 793 because residue number 95  < previous residue 298 
Skipped atom 794 because residue number 96  < previous residue 298 
Skipped atom 795 because residue number 96  < previous residue 298 
Skipped atom 796 because residue number 96  < previous residue 298 
Skipped atom 797 because residue number 96  < previous residue 298 
Skipped atom 798 because residue number 96  < previous residue 298 
Skipped atom 799 because residue number 96  < previous residue 298 
Skipped atom 800 because residue number 96  < previous residue 298 
Skipped atom 801 because residue number 96  < previous residue 298 
Skipped atom 802 because residue number 96  < previous residue 298 
Skipped atom 803 because residue number 96  < previous residue 298 
Skipped atom 804 because residue number 97  < previous residue 298 
Skipped atom 805 because residue number 97  < previous residue 298 
Skipped atom 806 because residue number 97  < previous residue 298 
Skipped atom 807 because residue number 97  < previous residue 298 
Skipped atom 808 because residue number 97  < previous residue 298 
Skipped atom 809 because residue number 97  < previous residue 298 
Skipped atom 810 because residue number 97  < previous residue 298 
Skipped atom 811 because residue number 97  < previous residue 298 
Skipped atom 812 because residue number 98  < previous residue 298 
Skipped atom 813 because residue number 98  < previous residue 298 
Skipped atom 814 because residue number 98  < previous residue 298 
Skipped atom 815 because residue number 98  < previous residue 298 
Skipped atom 816 because residue number 98  < previous residue 298 
Skipped atom 817 because residue number 98  < previous residue 298 
Skipped atom 818 because residue number 98  < previous residue 298 
Skipped atom 819 because residue number 98  < previous residue 298 
Skipped atom 820 because residue number 99  < previous residue 298 
Skipped atom 821 because residue number 99  < previous residue 298 
Skipped atom 822 because residue number 99  < previous residue 298 
Skipped atom 823 because residue number 99  < previous residue 298 
Skipped atom 824 because residue number 99  < previous residue 298 
Skipped atom 825 because residue number 99  < previous residue 298 
Skipped atom 826 because residue number 99  < previous residue 298 
Skipped atom 827 because residue number 99  < previous residue 298 
Skipped atom 828 because residue number 99  < previous residue 298 
Skipped atom 829 because residue number 100  < previous residue 298 
Skipped atom 830 because residue number 100  < previous residue 298 
Skipped atom 831 because residue number 100  < previous residue 298 
Skipped atom 832 because residue number 100  < previous residue 298 
Skipped atom 833 because residue number 100  < previous residue 298 
Skipped atom 834 because residue number 100  < previous residue 298 
Skipped atom 835 because residue number 100  < previous residue 298 
Skipped atom 836 because residue number 100  < previous residue 298 
Skipped atom 837 because residue number 101  < previous residue 298 
Skipped atom 838 because residue number 101  < previous residue 298 
Skipped atom 839 because residue number 101  < previous residue 298 
Skipped atom 840 because residue number 101  < previous residue 298 
Skipped atom 841 because residue number 101  < previous residue 298 
Skipped atom 842 because residue number 101  < previous residue 298 
Skipped atom 843 because residue number 101  < previous residue 298 
Skipped atom 844 because residue number 101  < previous residue 298 
Skipped atom 845 because residue number 102  < previous residue 298 
Skipped atom 846 because residue number 102  < previous residue 298 
Skipped atom 847 because residue number 102  < previous residue 298 
Skipped atom 848 because residue number 102  < previous residue 298 
Skipped atom 849 because residue number 102  < previous residue 298 
Skipped atom 850 because residue number 102  < previous residue 298 
Skipped atom 851 because residue number 102  < previous residue 298 
Skipped atom 852 because residue number 102  < previous residue 298 
Skipped atom 853 because residue number 103  < previous residue 298 
Skipped atom 854 because residue number 103  < previous residue 298 
Skipped atom 855 because residue number 103  < previous residue 298 
Skipped atom 856 because residue number 103  < previous residue 298 
Skipped atom 857 because residue number 103  < previous residue 298 
Skipped atom 858 because residue number 103  < previous residue 298 
Skipped atom 859 because residue number 103  < previous residue 298 
Skipped atom 860 because residue number 104  < previous residue 298 
Skipped atom 861 because residue number 104  < previous residue 298 
Skipped atom 862 because residue number 104  < previous residue 298 
Skipped atom 863 because residue number 104  < previous residue 298 
Skipped atom 864 because residue number 104  < previous residue 298 
Skipped atom 865 because residue number 105  < previous residue 298 
Skipped atom 866 because residue number 105  < previous residue 298 
Skipped atom 867 because residue number 105  < previous residue 298 
Skipped atom 868 because residue number 105  < previous residue 298 
Skipped atom 869 because residue number 105  < previous residue 298 
Skipped atom 870 because residue number 105  < previous residue 298 
Skipped atom 871 because residue number 105  < previous residue 298 
Skipped atom 872 because residue number 105  < previous residue 298 
Skipped atom 873 because residue number 105  < previous residue 298 
Skipped atom 874 because residue number 105  < previous residue 298 
Skipped atom 875 because residue number 105  < previous residue 298 
Skipped atom 876 because residue number 105  < previous residue 298 
Skipped atom 877 because residue number 106  < previous residue 298 
Skipped atom 878 because residue number 106  < previous residue 298 
Skipped atom 879 because residue number 106  < previous residue 298 
Skipped atom 880 because residue number 106  < previous residue 298 
Skipped atom 881 because residue number 106  < previous residue 298 
Skipped atom 882 because residue number 106  < previous residue 298 
Skipped atom 883 because residue number 107  < previous residue 298 
Skipped atom 884 because residue number 107  < previous residue 298 
Skipped atom 885 because residue number 107  < previous residue 298 
Skipped atom 886 because residue number 107  < previous residue 298 
Skipped atom 887 because residue number 107  < previous residue 298 
Skipped atom 888 because residue number 107  < previous residue 298 
Skipped atom 889 because residue number 107  < previous residue 298 
Skipped atom 890 because residue number 108  < previous residue 298 
Skipped atom 891 because residue number 108  < previous residue 298 
Skipped atom 892 because residue number 108  < previous residue 298 
Skipped atom 893 because residue number 108  < previous residue 298 
Skipped atom 894 because residue number 108  < previous residue 298 
Skipped atom 895 because residue number 108  < previous residue 298 
Skipped atom 896 because residue number 108  < previous residue 298 
Skipped atom 897 because residue number 108  < previous residue 298 
Skipped atom 898 because residue number 109  < previous residue 298 
Skipped atom 899 because residue number 109  < previous residue 298 
Skipped atom 900 because residue number 109  < previous residue 298 
Skipped atom 901 because residue number 109  < previous residue 298 
Skipped atom 902 because residue number 109  < previous residue 298 
Skipped atom 903 because residue number 109  < previous residue 298 
Skipped atom 904 because residue number 109  < previous residue 298 
Skipped atom 905 because residue number 109  < previous residue 298 
Skipped atom 906 because residue number 110  < previous residue 298 
Skipped atom 907 because residue number 110  < previous residue 298 
Skipped atom 908 because residue number 110  < previous residue 298 
Skipped atom 909 because residue number 110  < previous residue 298 
Skipped atom 910 because residue number 110  < previous residue 298 
Skipped atom 911 because residue number 110  < previous residue 298 
Skipped atom 912 because residue number 110  < previous residue 298 
Skipped atom 913 because residue number 110  < previous residue 298 
Skipped atom 914 because residue number 110  < previous residue 298 
Skipped atom 915 because residue number 111  < previous residue 298 
Skipped atom 916 because residue number 111  < previous residue 298 
Skipped atom 917 because residue number 111  < previous residue 298 
Skipped atom 918 because residue number 111  < previous residue 298 
Skipped atom 919 because residue number 111  < previous residue 298 
Skipped atom 920 because residue number 111  < previous residue 298 
Skipped atom 921 because residue number 111  < previous residue 298 
Skipped atom 922 because residue number 111  < previous residue 298 
Skipped atom 923 because residue number 111  < previous residue 298 
Skipped atom 924 because residue number 112  < previous residue 298 
Skipped atom 925 because residue number 112  < previous residue 298 
Skipped atom 926 because residue number 112  < previous residue 298 
Skipped atom 927 because residue number 112  < previous residue 298 
Skipped atom 928 because residue number 112  < previous residue 298 
Skipped atom 929 because residue number 112  < previous residue 298 
Skipped atom 930 because residue number 112  < previous residue 298 
Skipped atom 931 because residue number 112  < previous residue 298 
Skipped atom 932 because residue number 112  < previous residue 298 
Skipped atom 933 because residue number 112  < previous residue 298 
Skipped atom 934 because residue number 112  < previous residue 298 
Skipped atom 935 because residue number 112  < previous residue 298 
Skipped atom 936 because residue number 113  < previous residue 298 
Skipped atom 937 because residue number 113  < previous residue 298 
Skipped atom 938 because residue number 113  < previous residue 298 
Skipped atom 939 because residue number 113  < previous residue 298 
Skipped atom 940 because residue number 113  < previous residue 298 
Skipped atom 941 because residue number 113  < previous residue 298 
Skipped atom 942 because residue number 113  < previous residue 298 
Skipped atom 943 because residue number 114  < previous residue 298 
Skipped atom 944 because residue number 114  < previous residue 298 
Skipped atom 945 because residue number 114  < previous residue 298 
Skipped atom 946 because residue number 114  < previous residue 298 
Skipped atom 947 because residue number 115  < previous residue 298 
Skipped atom 948 because residue number 115  < previous residue 298 
Skipped atom 949 because residue number 115  < previous residue 298 
Skipped atom 950 because residue number 115  < previous residue 298 
Skipped atom 951 because residue number 115  < previous residue 298 
Skipped atom 952 because residue number 115  < previous residue 298 
Skipped atom 953 because residue number 115  < previous residue 298 
Skipped atom 954 because residue number 115  < previous residue 298 
Skipped atom 955 because residue number 115  < previous residue 298 
Skipped atom 956 because residue number 116  < previous residue 298 
Skipped atom 957 because residue number 116  < previous residue 298 
Skipped atom 958 because residue number 116  < previous residue 298 
Skipped atom 959 because residue number 116  < previous residue 298 
Skipped atom 960 because residue number 116  < previous residue 298 
Skipped atom 961 because residue number 116  < previous residue 298 
Skipped atom 962 because residue number 116  < previous residue 298 
Skipped atom 963 because residue number 116  < previous residue 298 
Skipped atom 964 because residue number 117  < previous residue 298 
Skipped atom 965 because residue number 117  < previous residue 298 
Skipped atom 966 because residue number 117  < previous residue 298 
Skipped atom 967 because residue number 117  < previous residue 298 
Skipped atom 968 because residue number 117  < previous residue 298 
Skipped atom 969 because residue number 117  < previous residue 298 
Skipped atom 970 because residue number 117  < previous residue 298 
Skipped atom 971 because residue number 117  < previous residue 298 
Skipped atom 972 because residue number 118  < previous residue 298 
Skipped atom 973 because residue number 118  < previous residue 298 
Skipped atom 974 because residue number 118  < previous residue 298 
Skipped atom 975 because residue number 118  < previous residue 298 
Skipped atom 976 because residue number 118  < previous residue 298 
Skipped atom 977 because residue number 118  < previous residue 298 
Skipped atom 978 because residue number 118  < previous residue 298 
Skipped atom 979 because residue number 119  < previous residue 298 
Skipped atom 980 because residue number 119  < previous residue 298 
Skipped atom 981 because residue number 119  < previous residue 298 
Skipped atom 982 because residue number 119  < previous residue 298 
Skipped atom 983 because residue number 119  < previous residue 298 
Skipped atom 984 because residue number 119  < previous residue 298 
Skipped atom 985 because residue number 119  < previous residue 298 
Skipped atom 986 because residue number 119  < previous residue 298 
Skipped atom 987 because residue number 120  < previous residue 298 
Skipped atom 988 because residue number 120  < previous residue 298 
Skipped atom 989 because residue number 120  < previous residue 298 
Skipped atom 990 because residue number 120  < previous residue 298 
Skipped atom 991 because residue number 120  < previous residue 298 
Skipped atom 992 because residue number 120  < previous residue 298 
Skipped atom 993 because residue number 120  < previous residue 298 
Skipped atom 994 because residue number 120  < previous residue 298 
Skipped atom 995 because residue number 120  < previous residue 298 
Skipped atom 996 because residue number 121  < previous residue 298 
Skipped atom 997 because residue number 121  < previous residue 298 
Skipped atom 998 because residue number 121  < previous residue 298 
Skipped atom 999 because residue number 121  < previous residue 298 
Skipped atom 1000 because residue number 121  < previous residue 298 
Skipped atom 1001 because residue number 122  < previous residue 298 
Skipped atom 1002 because residue number 122  < previous residue 298 
Skipped atom 1003 because residue number 122  < previous residue 298 
Skipped atom 1004 because residue number 122  < previous residue 298 
Skipped atom 1005 because residue number 122  < previous residue 298 
Skipped atom 1006 because residue number 122  < previous residue 298 
Skipped atom 1007 because residue number 122  < previous residue 298 
Skipped atom 1008 because residue number 122  < previous residue 298 
Skipped atom 1009 because residue number 123  < previous residue 298 
Skipped atom 1010 because residue number 123  < previous residue 298 
Skipped atom 1011 because residue number 123  < previous residue 298 
Skipped atom 1012 because residue number 123  < previous residue 298 
Skipped atom 1013 because residue number 123  < previous residue 298 
Skipped atom 1014 because residue number 123  < previous residue 298 
Skipped atom 1015 because residue number 123  < previous residue 298 
Skipped atom 1016 because residue number 123  < previous residue 298 
Skipped atom 1017 because residue number 124  < previous residue 298 
Skipped atom 1018 because residue number 124  < previous residue 298 
Skipped atom 1019 because residue number 124  < previous residue 298 
Skipped atom 1020 because residue number 124  < previous residue 298 
Skipped atom 1021 because residue number 124  < previous residue 298 
Skipped atom 1022 because residue number 124  < previous residue 298 
Skipped atom 1023 because residue number 124  < previous residue 298 
Skipped atom 1024 because residue number 124  < previous residue 298 
Skipped atom 1025 because residue number 124  < previous residue 298 
Skipped atom 1026 because residue number 125  < previous residue 298 
Skipped atom 1027 because residue number 125  < previous residue 298 
Skipped atom 1028 because residue number 125  < previous residue 298 
Skipped atom 1029 because residue number 125  < previous residue 298 
Skipped atom 1030 because residue number 125  < previous residue 298 
Skipped atom 1031 because residue number 126  < previous residue 298 
Skipped atom 1032 because residue number 126  < previous residue 298 
Skipped atom 1033 because residue number 126  < previous residue 298 
Skipped atom 1034 because residue number 126  < previous residue 298 
Skipped atom 1035 because residue number 126  < previous residue 298 
Skipped atom 1036 because residue number 126  < previous residue 298 
Skipped atom 1037 because residue number 127  < previous residue 298 
Skipped atom 1038 because residue number 127  < previous residue 298 
Skipped atom 1039 because residue number 127  < previous residue 298 
Skipped atom 1040 because residue number 127  < previous residue 298 
Skipped atom 1041 because residue number 127  < previous residue 298 
Skipped atom 1042 because residue number 127  < previous residue 298 
Skipped atom 1043 because residue number 127  < previous residue 298 
Skipped atom 1044 because residue number 127  < previous residue 298 
Skipped atom 1045 because residue number 128  < previous residue 298 
Skipped atom 1046 because residue number 128  < previous residue 298 
Skipped atom 1047 because residue number 128  < previous residue 298 
Skipped atom 1048 because residue number 128  < previous residue 298 
Skipped atom 1049 because residue number 128  < previous residue 298 
Skipped atom 1050 because residue number 128  < previous residue 298 
Skipped atom 1051 because residue number 128  < previous residue 298 
Skipped atom 1052 because residue number 129  < previous residue 298 
Skipped atom 1053 because residue number 129  < previous residue 298 
Skipped atom 1054 because residue number 129  < previous residue 298 
Skipped atom 1055 because residue number 129  < previous residue 298 
Skipped atom 1056 because residue number 129  < previous residue 298 
Skipped atom 1057 because residue number 129  < previous residue 298 
Skipped atom 1058 because residue number 129  < previous residue 298 
Skipped atom 1059 because residue number 129  < previous residue 298 
Skipped atom 1060 because residue number 129  < previous residue 298 
Skipped atom 1061 because residue number 129  < previous residue 298 
Skipped atom 1062 because residue number 129  < previous residue 298 
Skipped atom 1063 because residue number 129  < previous residue 298 
Skipped atom 1064 because residue number 130  < previous residue 298 
Skipped atom 1065 because residue number 130  < previous residue 298 
Skipped atom 1066 because residue number 130  < previous residue 298 
Skipped atom 1067 because residue number 130  < previous residue 298 
Skipped atom 1068 because residue number 130  < previous residue 298 
Skipped atom 1069 because residue number 130  < previous residue 298 
Skipped atom 1070 because residue number 131  < previous residue 298 
Skipped atom 1071 because residue number 131  < previous residue 298 
Skipped atom 1072 because residue number 131  < previous residue 298 
Skipped atom 1073 because residue number 131  < previous residue 298 
Skipped atom 1074 because residue number 131  < previous residue 298 
Skipped atom 1075 because residue number 131  < previous residue 298 
Skipped atom 1076 because residue number 131  < previous residue 298 
Skipped atom 1077 because residue number 131  < previous residue 298 
Skipped atom 1078 because residue number 132  < previous residue 298 
Skipped atom 1079 because residue number 132  < previous residue 298 
Skipped atom 1080 because residue number 132  < previous residue 298 
Skipped atom 1081 because residue number 132  < previous residue 298 
Skipped atom 1082 because residue number 132  < previous residue 298 
Skipped atom 1083 because residue number 132  < previous residue 298 
Skipped atom 1084 because residue number 132  < previous residue 298 
Skipped atom 1085 because residue number 132  < previous residue 298 
Skipped atom 1086 because residue number 133  < previous residue 298 
Skipped atom 1087 because residue number 133  < previous residue 298 
Skipped atom 1088 because residue number 133  < previous residue 298 
Skipped atom 1089 because residue number 133  < previous residue 298 
Skipped atom 1090 because residue number 133  < previous residue 298 
Skipped atom 1091 because residue number 133  < previous residue 298 
Skipped atom 1092 because residue number 133  < previous residue 298 
Skipped atom 1093 because residue number 134  < previous residue 298 
Skipped atom 1094 because residue number 134  < previous residue 298 
Skipped atom 1095 because residue number 134  < previous residue 298 
Skipped atom 1096 because residue number 134  < previous residue 298 
Skipped atom 1097 because residue number 134  < previous residue 298 
Skipped atom 1098 because residue number 135  < previous residue 298 
Skipped atom 1099 because residue number 135  < previous residue 298 
Skipped atom 1100 because residue number 135  < previous residue 298 
Skipped atom 1101 because residue number 135  < previous residue 298 
Skipped atom 1102 because residue number 135  < previous residue 298 
Skipped atom 1103 because residue number 135  < previous residue 298 
Skipped atom 1104 because residue number 135  < previous residue 298 
Skipped atom 1105 because residue number 135  < previous residue 298 
Skipped atom 1106 because residue number 136  < previous residue 298 
Skipped atom 1107 because residue number 136  < previous residue 298 
Skipped atom 1108 because residue number 136  < previous residue 298 
Skipped atom 1109 because residue number 136  < previous residue 298 
Skipped atom 1110 because residue number 136  < previous residue 298 
Skipped atom 1111 because residue number 136  < previous residue 298 
Skipped atom 1112 because residue number 136  < previous residue 298 
Skipped atom 1113 because residue number 136  < previous residue 298 
Skipped atom 1114 because residue number 137  < previous residue 298 
Skipped atom 1115 because residue number 137  < previous residue 298 
Skipped atom 1116 because residue number 137  < previous residue 298 
Skipped atom 1117 because residue number 137  < previous residue 298 
Skipped atom 1118 because residue number 137  < previous residue 298 
Skipped atom 1119 because residue number 137  < previous residue 298 
Skipped atom 1120 because residue number 137  < previous residue 298 
Skipped atom 1121 because residue number 137  < previous residue 298 
Skipped atom 1122 because residue number 137  < previous residue 298 
Skipped atom 1123 because residue number 138  < previous residue 298 
Skipped atom 1124 because residue number 138  < previous residue 298 
Skipped atom 1125 because residue number 138  < previous residue 298 
Skipped atom 1126 because residue number 138  < previous residue 298 
Skipped atom 1127 because residue number 138  < previous residue 298 
Skipped atom 1128 because residue number 138  < previous residue 298 
Skipped atom 1129 because residue number 138  < previous residue 298 
Skipped atom 1130 because residue number 138  < previous residue 298 
Skipped atom 1131 because residue number 139  < previous residue 298 
Skipped atom 1132 because residue number 139  < previous residue 298 
Skipped atom 1133 because residue number 139  < previous residue 298 
Skipped atom 1134 because residue number 139  < previous residue 298 
Skipped atom 1135 because residue number 139  < previous residue 298 
Skipped atom 1136 because residue number 139  < previous residue 298 
Skipped atom 1137 because residue number 139  < previous residue 298 
Skipped atom 1138 because residue number 139  < previous residue 298 
Skipped atom 1139 because residue number 140  < previous residue 298 
Skipped atom 1140 because residue number 140  < previous residue 298 
Skipped atom 1141 because residue number 140  < previous residue 298 
Skipped atom 1142 because residue number 140  < previous residue 298 
Skipped atom 1143 because residue number 140  < previous residue 298 
Skipped atom 1144 because residue number 140  < previous residue 298 
Skipped atom 1145 because residue number 140  < previous residue 298 
Skipped atom 1146 because residue number 140  < previous residue 298 
Skipped atom 1147 because residue number 140  < previous residue 298 
Skipped atom 1148 because residue number 141  < previous residue 298 
Skipped atom 1149 because residue number 141  < previous residue 298 
Skipped atom 1150 because residue number 141  < previous residue 298 
Skipped atom 1151 because residue number 141  < previous residue 298 
Skipped atom 1152 because residue number 141  < previous residue 298 
Skipped atom 1153 because residue number 141  < previous residue 298 
Skipped atom 1154 because residue number 141  < previous residue 298 
Skipped atom 1155 because residue number 141  < previous residue 298 
Skipped atom 1156 because residue number 141  < previous residue 298 
Skipped atom 1157 because residue number 142  < previous residue 298 
Skipped atom 1158 because residue number 142  < previous residue 298 
Skipped atom 1159 because residue number 142  < previous residue 298 
Skipped atom 1160 because residue number 142  < previous residue 298 
Skipped atom 1161 because residue number 142  < previous residue 298 
Skipped atom 1162 because residue number 142  < previous residue 298 
Skipped atom 1163 because residue number 142  < previous residue 298 
Skipped atom 1164 because residue number 142  < previous residue 298 
Skipped atom 1165 because residue number 143  < previous residue 298 
Skipped atom 1166 because residue number 143  < previous residue 298 
Skipped atom 1167 because residue number 143  < previous residue 298 
Skipped atom 1168 because residue number 143  < previous residue 298 
Skipped atom 1169 because residue number 144  < previous residue 298 
Skipped atom 1170 because residue number 144  < previous residue 298 
Skipped atom 1171 because residue number 144  < previous residue 298 
Skipped atom 1172 because residue number 144  < previous residue 298 
Skipped atom 1173 because residue number 145  < previous residue 298 
Skipped atom 1174 because residue number 145  < previous residue 298 
Skipped atom 1175 because residue number 145  < previous residue 298 
Skipped atom 1176 because residue number 145  < previous residue 298 
Skipped atom 1177 because residue number 145  < previous residue 298 
Skipped atom 1178 because residue number 145  < previous residue 298 
Skipped atom 1179 because residue number 145  < previous residue 298 
Skipped atom 1180 because residue number 145  < previous residue 298 
Skipped atom 1181 because residue number 146  < previous residue 298 
Skipped atom 1182 because residue number 146  < previous residue 298 
Skipped atom 1183 because residue number 146  < previous residue 298 
Skipped atom 1184 because residue number 146  < previous residue 298 
Skipped atom 1185 because residue number 146  < previous residue 298 
Skipped atom 1186 because residue number 146  < previous residue 298 
Skipped atom 1187 because residue number 146  < previous residue 298 
Skipped atom 1188 because residue number 146  < previous residue 298 
Skipped atom 1189 because residue number 146  < previous residue 298 
Skipped atom 1190 because residue number 147  < previous residue 298 
Skipped atom 1191 because residue number 147  < previous residue 298 
Skipped atom 1192 because residue number 147  < previous residue 298 
Skipped atom 1193 because residue number 147  < previous residue 298 
Skipped atom 1194 because residue number 147  < previous residue 298 
Skipped atom 1195 because residue number 147  < previous residue 298 
Skipped atom 1196 because residue number 147  < previous residue 298 
Skipped atom 1197 because residue number 147  < previous residue 298 
Skipped atom 1198 because residue number 147  < previous residue 298 
Skipped atom 1199 because residue number 148  < previous residue 298 
Skipped atom 1200 because residue number 148  < previous residue 298 
Skipped atom 1201 because residue number 148  < previous residue 298 
Skipped atom 1202 because residue number 148  < previous residue 298 
Skipped atom 1203 because residue number 148  < previous residue 298 
Skipped atom 1204 because residue number 148  < previous residue 298 
Skipped atom 1205 because residue number 148  < previous residue 298 
Skipped atom 1206 because residue number 149  < previous residue 298 
Skipped atom 1207 because residue number 149  < previous residue 298 
Skipped atom 1208 because residue number 149  < previous residue 298 
Skipped atom 1209 because residue number 149  < previous residue 298 
Skipped atom 1210 because residue number 149  < previous residue 298 
Skipped atom 1211 because residue number 149  < previous residue 298 
Skipped atom 1212 because residue number 149  < previous residue 298 
Skipped atom 1213 because residue number 149  < previous residue 298 
Skipped atom 1214 because residue number 149  < previous residue 298 
Skipped atom 1215 because residue number 150  < previous residue 298 
Skipped atom 1216 because residue number 150  < previous residue 298 
Skipped atom 1217 because residue number 150  < previous residue 298 
Skipped atom 1218 because residue number 150  < previous residue 298 
Skipped atom 1219 because residue number 150  < previous residue 298 
Skipped atom 1220 because residue number 150  < previous residue 298 
Skipped atom 1221 because residue number 150  < previous residue 298 
Skipped atom 1222 because residue number 150  < previous residue 298 
Skipped atom 1223 because residue number 150  < previous residue 298 
Skipped atom 1224 because residue number 151  < previous residue 298 
Skipped atom 1225 because residue number 151  < previous residue 298 
Skipped atom 1226 because residue number 151  < previous residue 298 
Skipped atom 1227 because residue number 151  < previous residue 298 
Skipped atom 1228 because residue number 151  < previous residue 298 
Skipped atom 1229 because residue number 151  < previous residue 298 
Skipped atom 1230 because residue number 151  < previous residue 298 
Skipped atom 1231 because residue number 151  < previous residue 298 
Skipped atom 1232 because residue number 151  < previous residue 298 
Skipped atom 1233 because residue number 151  < previous residue 298 
Skipped atom 1234 because residue number 151  < previous residue 298 
Skipped atom 1235 because residue number 152  < previous residue 298 
Skipped atom 1236 because residue number 152  < previous residue 298 
Skipped atom 1237 because residue number 152  < previous residue 298 
Skipped atom 1238 because residue number 152  < previous residue 298 
Skipped atom 1239 because residue number 152  < previous residue 298 
Skipped atom 1240 because residue number 152  < previous residue 298 
Skipped atom 1241 because residue number 152  < previous residue 298 
Skipped atom 1242 because residue number 152  < previous residue 298 
Skipped atom 1243 because residue number 153  < previous residue 298 
Skipped atom 1244 because residue number 153  < previous residue 298 
Skipped atom 1245 because residue number 153  < previous residue 298 
Skipped atom 1246 because residue number 153  < previous residue 298 
Skipped atom 1247 because residue number 153  < previous residue 298 
Skipped atom 1248 because residue number 153  < previous residue 298 
Skipped atom 1249 because residue number 153  < previous residue 298 
Skipped atom 1250 because residue number 153  < previous residue 298 
Skipped atom 1251 because residue number 153  < previous residue 298 
Skipped atom 1252 because residue number 154  < previous residue 298 
Skipped atom 1253 because residue number 154  < previous residue 298 
Skipped atom 1254 because residue number 154  < previous residue 298 
Skipped atom 1255 because residue number 154  < previous residue 298 
Skipped atom 1256 because residue number 154  < previous residue 298 
Skipped atom 1257 because residue number 154  < previous residue 298 
Skipped atom 1258 because residue number 154  < previous residue 298 
Skipped atom 1259 because residue number 154  < previous residue 298 
Skipped atom 1260 because residue number 154  < previous residue 298 
Skipped atom 1261 because residue number 155  < previous residue 298 
Skipped atom 1262 because residue number 155  < previous residue 298 
Skipped atom 1263 because residue number 155  < previous residue 298 
Skipped atom 1264 because residue number 155  < previous residue 298 
Skipped atom 1265 because residue number 155  < previous residue 298 
Skipped atom 1266 because residue number 155  < previous residue 298 
Skipped atom 1267 because residue number 155  < previous residue 298 
Skipped atom 1268 because residue number 155  < previous residue 298 
Skipped atom 1269 because residue number 156  < previous residue 298 
Skipped atom 1270 because residue number 156  < previous residue 298 
Skipped atom 1271 because residue number 156  < previous residue 298 
Skipped atom 1272 because residue number 156  < previous residue 298 
Skipped atom 1273 because residue number 157  < previous residue 298 
Skipped atom 1274 because residue number 157  < previous residue 298 
Skipped atom 1275 because residue number 157  < previous residue 298 
Skipped atom 1276 because residue number 157  < previous residue 298 
Skipped atom 1277 because residue number 157  < previous residue 298 
Skipped atom 1278 because residue number 157  < previous residue 298 
Skipped atom 1279 because residue number 157  < previous residue 298 
Skipped atom 1280 because residue number 157  < previous residue 298 
Skipped atom 1281 because residue number 158  < previous residue 298 
Skipped atom 1282 because residue number 158  < previous residue 298 
Skipped atom 1283 because residue number 158  < previous residue 298 
Skipped atom 1284 because residue number 158  < previous residue 298 
Skipped atom 1285 because residue number 158  < previous residue 298 
Skipped atom 1286 because residue number 158  < previous residue 298 
Skipped atom 1287 because residue number 158  < previous residue 298 
Skipped atom 1288 because residue number 158  < previous residue 298 
Skipped atom 1289 because residue number 158  < previous residue 298 
Skipped atom 1290 because residue number 159  < previous residue 298 
Skipped atom 1291 because residue number 159  < previous residue 298 
Skipped atom 1292 because residue number 159  < previous residue 298 
Skipped atom 1293 because residue number 159  < previous residue 298 
Skipped atom 1294 because residue number 159  < previous residue 298 
Skipped atom 1295 because residue number 159  < previous residue 298 
Skipped atom 1296 because residue number 159  < previous residue 298 
Skipped atom 1297 because residue number 160  < previous residue 298 
Skipped atom 1298 because residue number 160  < previous residue 298 
Skipped atom 1299 because residue number 160  < previous residue 298 
Skipped atom 1300 because residue number 160  < previous residue 298 
Skipped atom 1301 because residue number 160  < previous residue 298 
Skipped atom 1302 because residue number 160  < previous residue 298 
Skipped atom 1303 because residue number 160  < previous residue 298 
Skipped atom 1304 because residue number 161  < previous residue 298 
Skipped atom 1305 because residue number 161  < previous residue 298 
Skipped atom 1306 because residue number 161  < previous residue 298 
Skipped atom 1307 because residue number 161  < previous residue 298 
Skipped atom 1308 because residue number 161  < previous residue 298 
Skipped atom 1309 because residue number 161  < previous residue 298 
Skipped atom 1310 because residue number 161  < previous residue 298 
Skipped atom 1311 because residue number 161  < previous residue 298 
Skipped atom 1312 because residue number 162  < previous residue 298 
Skipped atom 1313 because residue number 162  < previous residue 298 
Skipped atom 1314 because residue number 162  < previous residue 298 
Skipped atom 1315 because residue number 162  < previous residue 298 
Skipped atom 1316 because residue number 162  < previous residue 298 
Skipped atom 1317 because residue number 162  < previous residue 298 
Skipped atom 1318 because residue number 162  < previous residue 298 
Skipped atom 1319 because residue number 163  < previous residue 298 
Skipped atom 1320 because residue number 163  < previous residue 298 
Skipped atom 1321 because residue number 163  < previous residue 298 
Skipped atom 1322 because residue number 163  < previous residue 298 
Skipped atom 1323 because residue number 163  < previous residue 298 
Skipped atom 1324 because residue number 163  < previous residue 298 
Skipped atom 1325 because residue number 163  < previous residue 298 
Skipped atom 1326 because residue number 164  < previous residue 298 
Skipped atom 1327 because residue number 164  < previous residue 298 
Skipped atom 1328 because residue number 164  < previous residue 298 
Skipped atom 1329 because residue number 164  < previous residue 298 
Skipped atom 1330 because residue number 164  < previous residue 298 
Skipped atom 1331 because residue number 164  < previous residue 298 
Skipped atom 1332 because residue number 164  < previous residue 298 
Skipped atom 1333 because residue number 164  < previous residue 298 
Skipped atom 1334 because residue number 164  < previous residue 298 
Skipped atom 1335 because residue number 164  < previous residue 298 
Skipped atom 1336 because residue number 164  < previous residue 298 
Skipped atom 1337 because residue number 165  < previous residue 298 
Skipped atom 1338 because residue number 165  < previous residue 298 
Skipped atom 1339 because residue number 165  < previous residue 298 
Skipped atom 1340 because residue number 165  < previous residue 298 
Skipped atom 1341 because residue number 165  < previous residue 298 
Skipped atom 1342 because residue number 165  < previous residue 298 
Skipped atom 1343 because residue number 165  < previous residue 298 
Skipped atom 1344 because residue number 165  < previous residue 298 
Skipped atom 1345 because residue number 165  < previous residue 298 
Skipped atom 1346 because residue number 165  < previous residue 298 
Skipped atom 1347 because residue number 165  < previous residue 298 
Skipped atom 1348 because residue number 165  < previous residue 298 
Skipped atom 1349 because residue number 166  < previous residue 298 
Skipped atom 1350 because residue number 166  < previous residue 298 
Skipped atom 1351 because residue number 166  < previous residue 298 
Skipped atom 1352 because residue number 166  < previous residue 298 
Skipped atom 1353 because residue number 166  < previous residue 298 
Skipped atom 1354 because residue number 166  < previous residue 298 
Skipped atom 1355 because residue number 166  < previous residue 298 
Skipped atom 1356 because residue number 166  < previous residue 298 
Skipped atom 1357 because residue number 166  < previous residue 298 
Skipped atom 1358 because residue number 167  < previous residue 298 
Skipped atom 1359 because residue number 167  < previous residue 298 
Skipped atom 1360 because residue number 167  < previous residue 298 
Skipped atom 1361 because residue number 167  < previous residue 298 
Skipped atom 1362 because residue number 167  < previous residue 298 
Skipped atom 1363 because residue number 167  < previous residue 298 
Skipped atom 1364 because residue number 167  < previous residue 298 
Skipped atom 1365 because residue number 167  < previous residue 298 
Skipped atom 1366 because residue number 168  < previous residue 298 
Skipped atom 1367 because residue number 168  < previous residue 298 
Skipped atom 1368 because residue number 168  < previous residue 298 
Skipped atom 1369 because residue number 168  < previous residue 298 
Skipped atom 1370 because residue number 168  < previous residue 298 
Skipped atom 1371 because residue number 168  < previous residue 298 
Skipped atom 1372 because residue number 168  < previous residue 298 
Skipped atom 1373 because residue number 168  < previous residue 298 
Skipped atom 1374 because residue number 168  < previous residue 298 
Skipped atom 1375 because residue number 169  < previous residue 298 
Skipped atom 1376 because residue number 169  < previous residue 298 
Skipped atom 1377 because residue number 169  < previous residue 298 
Skipped atom 1378 because residue number 169  < previous residue 298 
Skipped atom 1379 because residue number 169  < previous residue 298 
Skipped atom 1380 because residue number 169  < previous residue 298 
Skipped atom 1381 because residue number 169  < previous residue 298 
Skipped atom 1382 because residue number 169  < previous residue 298 
Skipped atom 1383 because residue number 170  < previous residue 298 
Skipped atom 1384 because residue number 170  < previous residue 298 
Skipped atom 1385 because residue number 170  < previous residue 298 
Skipped atom 1386 because residue number 170  < previous residue 298 
Skipped atom 1387 because residue number 170  < previous residue 298 
Skipped atom 1388 because residue number 170  < previous residue 298 
Skipped atom 1389 because residue number 170  < previous residue 298 
Skipped atom 1390 because residue number 170  < previous residue 298 
Skipped atom 1391 because residue number 171  < previous residue 298 
Skipped atom 1392 because residue number 171  < previous residue 298 
Skipped atom 1393 because residue number 171  < previous residue 298 
Skipped atom 1394 because residue number 171  < previous residue 298 
Skipped atom 1395 because residue number 171  < previous residue 298 
Skipped atom 1396 because residue number 171  < previous residue 298 
Skipped atom 1397 because residue number 171  < previous residue 298 
Skipped atom 1398 because residue number 171  < previous residue 298 
Skipped atom 1399 because residue number 171  < previous residue 298 
Skipped atom 1400 because residue number 171  < previous residue 298 
Skipped atom 1401 because residue number 171  < previous residue 298 
Skipped atom 1402 because residue number 171  < previous residue 298 
Skipped atom 1403 because residue number 172  < previous residue 298 
Skipped atom 1404 because residue number 172  < previous residue 298 
Skipped atom 1405 because residue number 172  < previous residue 298 
Skipped atom 1406 because residue number 172  < previous residue 298 
Skipped atom 1407 because residue number 172  < previous residue 298 
Skipped atom 1408 because residue number 172  < previous residue 298 
Skipped atom 1409 because residue number 172  < previous residue 298 
Skipped atom 1410 because residue number 172  < previous residue 298 
Skipped atom 1411 because residue number 172  < previous residue 298 
Skipped atom 1412 because residue number 172  < previous residue 298 
Skipped atom 1413 because residue number 172  < previous residue 298 
Skipped atom 1414 because residue number 172  < previous residue 298 
Skipped atom 1415 because residue number 173  < previous residue 298 
Skipped atom 1416 because residue number 173  < previous residue 298 
Skipped atom 1417 because residue number 173  < previous residue 298 
Skipped atom 1418 because residue number 173  < previous residue 298 
Skipped atom 1419 because residue number 173  < previous residue 298 
Skipped atom 1420 because residue number 173  < previous residue 298 
Skipped atom 1421 because residue number 174  < previous residue 298 
Skipped atom 1422 because residue number 174  < previous residue 298 
Skipped atom 1423 because residue number 174  < previous residue 298 
Skipped atom 1424 because residue number 174  < previous residue 298 
Skipped atom 1425 because residue number 174  < previous residue 298 
Skipped atom 1426 because residue number 174  < previous residue 298 
Skipped atom 1427 because residue number 174  < previous residue 298 
Skipped atom 1428 because residue number 175  < previous residue 298 
Skipped atom 1429 because residue number 175  < previous residue 298 
Skipped atom 1430 because residue number 175  < previous residue 298 
Skipped atom 1431 because residue number 175  < previous residue 298 
Skipped atom 1432 because residue number 175  < previous residue 298 
Skipped atom 1433 because residue number 175  < previous residue 298 
Skipped atom 1434 because residue number 175  < previous residue 298 
Skipped atom 1435 because residue number 175  < previous residue 298 
Skipped atom 1436 because residue number 175  < previous residue 298 
Skipped atom 1437 because residue number 176  < previous residue 298 
Skipped atom 1438 because residue number 176  < previous residue 298 
Skipped atom 1439 because residue number 176  < previous residue 298 
Skipped atom 1440 because residue number 176  < previous residue 298 
Skipped atom 1441 because residue number 176  < previous residue 298 
Skipped atom 1442 because residue number 176  < previous residue 298 
Skipped atom 1443 because residue number 177  < previous residue 298 
Skipped atom 1444 because residue number 177  < previous residue 298 
Skipped atom 1445 because residue number 177  < previous residue 298 
Skipped atom 1446 because residue number 177  < previous residue 298 
Skipped atom 1447 because residue number 177  < previous residue 298 
Skipped atom 1448 because residue number 177  < previous residue 298 
Skipped atom 1449 because residue number 177  < previous residue 298 
Skipped atom 1450 because residue number 177  < previous residue 298 
Skipped atom 1451 because residue number 177  < previous residue 298 
Skipped atom 1452 because residue number 178  < previous residue 298 
Skipped atom 1453 because residue number 178  < previous residue 298 
Skipped atom 1454 because residue number 178  < previous residue 298 
Skipped atom 1455 because residue number 178  < previous residue 298 
Skipped atom 1456 because residue number 178  < previous residue 298 
Skipped atom 1457 because residue number 178  < previous residue 298 
Skipped atom 1458 because residue number 178  < previous residue 298 
Skipped atom 1459 because residue number 178  < previous residue 298 
Skipped atom 1460 because residue number 178  < previous residue 298 
Skipped atom 1461 because residue number 179  < previous residue 298 
Skipped atom 1462 because residue number 179  < previous residue 298 
Skipped atom 1463 because residue number 179  < previous residue 298 
Skipped atom 1464 because residue number 179  < previous residue 298 
Skipped atom 1465 because residue number 179  < previous residue 298 
Skipped atom 1466 because residue number 179  < previous residue 298 
Skipped atom 1467 because residue number 179  < previous residue 298 
Skipped atom 1468 because residue number 179  < previous residue 298 
Skipped atom 1469 because residue number 180  < previous residue 298 
Skipped atom 1470 because residue number 180  < previous residue 298 
Skipped atom 1471 because residue number 180  < previous residue 298 
Skipped atom 1472 because residue number 180  < previous residue 298 
Skipped atom 1473 because residue number 180  < previous residue 298 
Skipped atom 1474 because residue number 180  < previous residue 298 
Skipped atom 1475 because residue number 180  < previous residue 298 
Skipped atom 1476 because residue number 181  < previous residue 298 
Skipped atom 1477 because residue number 181  < previous residue 298 
Skipped atom 1478 because residue number 181  < previous residue 298 
Skipped atom 1479 because residue number 181  < previous residue 298 
Skipped atom 1480 because residue number 181  < previous residue 298 
Skipped atom 1481 because residue number 181  < previous residue 298 
Skipped atom 1482 because residue number 182  < previous residue 298 
Skipped atom 1483 because residue number 182  < previous residue 298 
Skipped atom 1484 because residue number 182  < previous residue 298 
Skipped atom 1485 because residue number 182  < previous residue 298 
Skipped atom 1486 because residue number 182  < previous residue 298 
Skipped atom 1487 because residue number 182  < previous residue 298 
Skipped atom 1488 because residue number 182  < previous residue 298 
Skipped atom 1489 because residue number 183  < previous residue 298 
Skipped atom 1490 because residue number 183  < previous residue 298 
Skipped atom 1491 because residue number 183  < previous residue 298 
Skipped atom 1492 because residue number 183  < previous residue 298 
Skipped atom 1493 because residue number 183  < previous residue 298 
Skipped atom 1494 because residue number 183  < previous residue 298 
Skipped atom 1495 because residue number 183  < previous residue 298 
Skipped atom 1496 because residue number 184  < previous residue 298 
Skipped atom 1497 because residue number 184  < previous residue 298 
Skipped atom 1498 because residue number 184  < previous residue 298 
Skipped atom 1499 because residue number 184  < previous residue 298 
Skipped atom 1500 because residue number 184  < previous residue 298 
Skipped atom 1501 because residue number 185  < previous residue 298 
Skipped atom 1502 because residue number 185  < previous residue 298 
Skipped atom 1503 because residue number 185  < previous residue 298 
Skipped atom 1504 because residue number 185  < previous residue 298 
Skipped atom 1505 because residue number 185  < previous residue 298 
Skipped atom 1506 because residue number 186  < previous residue 298 
Skipped atom 1507 because residue number 186  < previous residue 298 
Skipped atom 1508 because residue number 186  < previous residue 298 
Skipped atom 1509 because residue number 186  < previous residue 298 
Skipped atom 1510 because residue number 186  < previous residue 298 
Skipped atom 1511 because residue number 186  < previous residue 298 
Skipped atom 1512 because residue number 186  < previous residue 298 
Skipped atom 1513 because residue number 186  < previous residue 298 
Skipped atom 1514 because residue number 186  < previous residue 298 
Skipped atom 1515 because residue number 186  < previous residue 298 
Skipped atom 1516 because residue number 186  < previous residue 298 
Skipped atom 1517 because residue number 187  < previous residue 298 
Skipped atom 1518 because residue number 187  < previous residue 298 
Skipped atom 1519 because residue number 187  < previous residue 298 
Skipped atom 1520 because residue number 187  < previous residue 298 
Skipped atom 1521 because residue number 188  < previous residue 298 
Skipped atom 1522 because residue number 188  < previous residue 298 
Skipped atom 1523 because residue number 188  < previous residue 298 
Skipped atom 1524 because residue number 188  < previous residue 298 
Skipped atom 1525 because residue number 188  < previous residue 298 
Skipped atom 1526 because residue number 188  < previous residue 298 
Skipped atom 1527 because residue number 188  < previous residue 298 
Skipped atom 1528 because residue number 188  < previous residue 298 
Skipped atom 1529 because residue number 188  < previous residue 298 
Skipped atom 1530 because residue number 189  < previous residue 298 
Skipped atom 1531 because residue number 189  < previous residue 298 
Skipped atom 1532 because residue number 189  < previous residue 298 
Skipped atom 1533 because residue number 189  < previous residue 298 
Skipped atom 1534 because residue number 189  < previous residue 298 
Skipped atom 1535 because residue number 189  < previous residue 298 
Skipped atom 1536 because residue number 189  < previous residue 298 
Skipped atom 1537 because residue number 190  < previous residue 298 
Skipped atom 1538 because residue number 190  < previous residue 298 
Skipped atom 1539 because residue number 190  < previous residue 298 
Skipped atom 1540 because residue number 190  < previous residue 298 
Skipped atom 1541 because residue number 190  < previous residue 298 
Skipped atom 1542 because residue number 190  < previous residue 298 
Skipped atom 1543 because residue number 190  < previous residue 298 
Skipped atom 1544 because residue number 190  < previous residue 298 
Skipped atom 1545 because residue number 191  < previous residue 298 
Skipped atom 1546 because residue number 191  < previous residue 298 
Skipped atom 1547 because residue number 191  < previous residue 298 
Skipped atom 1548 because residue number 191  < previous residue 298 
Skipped atom 1549 because residue number 191  < previous residue 298 
Skipped atom 1550 because residue number 191  < previous residue 298 
Skipped atom 1551 because residue number 191  < previous residue 298 
Skipped atom 1552 because residue number 191  < previous residue 298 
Skipped atom 1553 because residue number 192  < previous residue 298 
Skipped atom 1554 because residue number 192  < previous residue 298 
Skipped atom 1555 because residue number 192  < previous residue 298 
Skipped atom 1556 because residue number 192  < previous residue 298 
Skipped atom 1557 because residue number 192  < previous residue 298 
Skipped atom 1558 because residue number 192  < previous residue 298 
Skipped atom 1559 because residue number 192  < previous residue 298 
Skipped atom 1560 because residue number 192  < previous residue 298 
Skipped atom 1561 because residue number 192  < previous residue 298 
Skipped atom 1562 because residue number 193  < previous residue 298 
Skipped atom 1563 because residue number 193  < previous residue 298 
Skipped atom 1564 because residue number 193  < previous residue 298 
Skipped atom 1565 because residue number 193  < previous residue 298 
Skipped atom 1566 because residue number 193  < previous residue 298 
Skipped atom 1567 because residue number 193  < previous residue 298 
Skipped atom 1568 because residue number 193  < previous residue 298 
Skipped atom 1569 because residue number 193  < previous residue 298 
Skipped atom 1570 because residue number 194  < previous residue 298 
Skipped atom 1571 because residue number 194  < previous residue 298 
Skipped atom 1572 because residue number 194  < previous residue 298 
Skipped atom 1573 because residue number 194  < previous residue 298 
Skipped atom 1574 because residue number 194  < previous residue 298 
Skipped atom 1575 because residue number 194  < previous residue 298 
Skipped atom 1576 because residue number 194  < previous residue 298 
Skipped atom 1577 because residue number 194  < previous residue 298 
Skipped atom 1578 because residue number 195  < previous residue 298 
Skipped atom 1579 because residue number 195  < previous residue 298 
Skipped atom 1580 because residue number 195  < previous residue 298 
Skipped atom 1581 because residue number 195  < previous residue 298 
Skipped atom 1582 because residue number 195  < previous residue 298 
Skipped atom 1583 because residue number 196  < previous residue 298 
Skipped atom 1584 because residue number 196  < previous residue 298 
Skipped atom 1585 because residue number 196  < previous residue 298 
Skipped atom 1586 because residue number 196  < previous residue 298 
Skipped atom 1587 because residue number 196  < previous residue 298 
Skipped atom 1588 because residue number 196  < previous residue 298 
Skipped atom 1589 because residue number 196  < previous residue 298 
Skipped atom 1590 because residue number 196  < previous residue 298 
Skipped atom 1591 because residue number 197  < previous residue 298 
Skipped atom 1592 because residue number 197  < previous residue 298 
Skipped atom 1593 because residue number 197  < previous residue 298 
Skipped atom 1594 because residue number 197  < previous residue 298 
Skipped atom 1595 because residue number 198  < previous residue 298 
Skipped atom 1596 because residue number 198  < previous residue 298 
Skipped atom 1597 because residue number 198  < previous residue 298 
Skipped atom 1598 because residue number 198  < previous residue 298 
Skipped atom 1599 because residue number 198  < previous residue 298 
Skipped atom 1600 because residue number 198  < previous residue 298 
Skipped atom 1601 because residue number 198  < previous residue 298 
Skipped atom 1602 because residue number 198  < previous residue 298 
Skipped atom 1603 because residue number 198  < previous residue 298 
Skipped atom 1604 because residue number 199  < previous residue 298 
Skipped atom 1605 because residue number 199  < previous residue 298 
Skipped atom 1606 because residue number 199  < previous residue 298 
Skipped atom 1607 because residue number 199  < previous residue 298 
Skipped atom 1608 because residue number 199  < previous residue 298 
Skipped atom 1609 because residue number 199  < previous residue 298 
Skipped atom 1610 because residue number 199  < previous residue 298 
Skipped atom 1611 because residue number 199  < previous residue 298 
Skipped atom 1612 because residue number 200  < previous residue 298 
Skipped atom 1613 because residue number 200  < previous residue 298 
Skipped atom 1614 because residue number 200  < previous residue 298 
Skipped atom 1615 because residue number 200  < previous residue 298 
Skipped atom 1616 because residue number 200  < previous residue 298 
Skipped atom 1617 because residue number 200  < previous residue 298 
Skipped atom 1618 because residue number 201  < previous residue 298 
Skipped atom 1619 because residue number 201  < previous residue 298 
Skipped atom 1620 because residue number 201  < previous residue 298 
Skipped atom 1621 because residue number 201  < previous residue 298 
Skipped atom 1622 because residue number 201  < previous residue 298 
Skipped atom 1623 because residue number 201  < previous residue 298 
Skipped atom 1624 because residue number 201  < previous residue 298 
Skipped atom 1625 because residue number 201  < previous residue 298 
Skipped atom 1626 because residue number 201  < previous residue 298 
Skipped atom 1627 because residue number 202  < previous residue 298 
Skipped atom 1628 because residue number 202  < previous residue 298 
Skipped atom 1629 because residue number 202  < previous residue 298 
Skipped atom 1630 because residue number 202  < previous residue 298 
Skipped atom 1631 because residue number 202  < previous residue 298 
Skipped atom 1632 because residue number 202  < previous residue 298 
Skipped atom 1633 because residue number 202  < previous residue 298 
Skipped atom 1634 because residue number 202  < previous residue 298 
Skipped atom 1635 because residue number 202  < previous residue 298 
Skipped atom 1636 because residue number 203  < previous residue 298 
Skipped atom 1637 because residue number 203  < previous residue 298 
Skipped atom 1638 because residue number 203  < previous residue 298 
Skipped atom 1639 because residue number 203  < previous residue 298 
Skipped atom 1640 because residue number 203  < previous residue 298 
Skipped atom 1641 because residue number 203  < previous residue 298 
Skipped atom 1642 because residue number 203  < previous residue 298 
Skipped atom 1643 because residue number 203  < previous residue 298 
Skipped atom 1644 because residue number 204  < previous residue 298 
Skipped atom 1645 because residue number 204  < previous residue 298 
Skipped atom 1646 because residue number 204  < previous residue 298 
Skipped atom 1647 because residue number 204  < previous residue 298 
Skipped atom 1648 because residue number 204  < previous residue 298 
Skipped atom 1649 because residue number 204  < previous residue 298 
Skipped atom 1650 because residue number 204  < previous residue 298 
Skipped atom 1651 because residue number 204  < previous residue 298 
Skipped atom 1652 because residue number 204  < previous residue 298 
Skipped atom 1653 because residue number 205  < previous residue 298 
Skipped atom 1654 because residue number 205  < previous residue 298 
Skipped atom 1655 because residue number 205  < previous residue 298 
Skipped atom 1656 because residue number 205  < previous residue 298 
Skipped atom 1657 because residue number 205  < previous residue 298 
Skipped atom 1658 because residue number 205  < previous residue 298 
Skipped atom 1659 because residue number 205  < previous residue 298 
Skipped atom 1660 because residue number 205  < previous residue 298 
Skipped atom 1661 because residue number 205  < previous residue 298 
Skipped atom 1662 because residue number 206  < previous residue 298 
Skipped atom 1663 because residue number 206  < previous residue 298 
Skipped atom 1664 because residue number 206  < previous residue 298 
Skipped atom 1665 because residue number 206  < previous residue 298 
Skipped atom 1666 because residue number 206  < previous residue 298 
Skipped atom 1667 because residue number 206  < previous residue 298 
Skipped atom 1668 because residue number 206  < previous residue 298 
Skipped atom 1669 because residue number 206  < previous residue 298 
Skipped atom 1670 because residue number 206  < previous residue 298 
Skipped atom 1671 because residue number 206  < previous residue 298 
Skipped atom 1672 because residue number 206  < previous residue 298 
Skipped atom 1673 because residue number 207  < previous residue 298 
Skipped atom 1674 because residue number 207  < previous residue 298 
Skipped atom 1675 because residue number 207  < previous residue 298 
Skipped atom 1676 because residue number 207  < previous residue 298 
Skipped atom 1677 because residue number 207  < previous residue 298 
Skipped atom 1678 because residue number 207  < previous residue 298 
Skipped atom 1679 because residue number 207  < previous residue 298 
Skipped atom 1680 because residue number 207  < previous residue 298 
Skipped atom 1681 because residue number 208  < previous residue 298 
Skipped atom 1682 because residue number 208  < previous residue 298 
Skipped atom 1683 because residue number 208  < previous residue 298 
Skipped atom 1684 because residue number 208  < previous residue 298 
Skipped atom 1685 because residue number 208  < previous residue 298 
Skipped atom 1686 because residue number 208  < previous residue 298 
Skipped atom 1687 because residue number 208  < previous residue 298 
Skipped atom 1688 because residue number 208  < previous residue 298 
Skipped atom 1689 because residue number 209  < previous residue 298 
Skipped atom 1690 because residue number 209  < previous residue 298 
Skipped atom 1691 because residue number 209  < previous residue 298 
Skipped atom 1692 because residue number 209  < previous residue 298 
Skipped atom 1693 because residue number 209  < previous residue 298 
Skipped atom 1694 because residue number 209  < previous residue 298 
Skipped atom 1695 because residue number 209  < previous residue 298 
Skipped atom 1696 because residue number 209  < previous residue 298 
Skipped atom 1697 because residue number 210  < previous residue 298 
Skipped atom 1698 because residue number 210  < previous residue 298 
Skipped atom 1699 because residue number 210  < previous residue 298 
Skipped atom 1700 because residue number 210  < previous residue 298 
Skipped atom 1701 because residue number 210  < previous residue 298 
Skipped atom 1702 because residue number 210  < previous residue 298 
Skipped atom 1703 because residue number 210  < previous residue 298 
Skipped atom 1704 because residue number 210  < previous residue 298 
Skipped atom 1705 because residue number 211  < previous residue 298 
Skipped atom 1706 because residue number 211  < previous residue 298 
Skipped atom 1707 because residue number 211  < previous residue 298 
Skipped atom 1708 because residue number 211  < previous residue 298 
Skipped atom 1709 because residue number 211  < previous residue 298 
Skipped atom 1710 because residue number 211  < previous residue 298 
Skipped atom 1711 because residue number 211  < previous residue 298 
Skipped atom 1712 because residue number 211  < previous residue 298 
Skipped atom 1713 because residue number 212  < previous residue 298 
Skipped atom 1714 because residue number 212  < previous residue 298 
Skipped atom 1715 because residue number 212  < previous residue 298 
Skipped atom 1716 because residue number 212  < previous residue 298 
Skipped atom 1717 because residue number 212  < previous residue 298 
Skipped atom 1718 because residue number 212  < previous residue 298 
Skipped atom 1719 because residue number 212  < previous residue 298 
Skipped atom 1720 because residue number 212  < previous residue 298 
Skipped atom 1721 because residue number 213  < previous residue 298 
Skipped atom 1722 because residue number 213  < previous residue 298 
Skipped atom 1723 because residue number 213  < previous residue 298 
Skipped atom 1724 because residue number 213  < previous residue 298 
Skipped atom 1725 because residue number 213  < previous residue 298 
Skipped atom 1726 because residue number 213  < previous residue 298 
Skipped atom 1727 because residue number 213  < previous residue 298 
Skipped atom 1728 because residue number 213  < previous residue 298 
Skipped atom 1729 because residue number 214  < previous residue 298 
Skipped atom 1730 because residue number 214  < previous residue 298 
Skipped atom 1731 because residue number 214  < previous residue 298 
Skipped atom 1732 because residue number 214  < previous residue 298 
Skipped atom 1733 because residue number 214  < previous residue 298 
Skipped atom 1734 because residue number 214  < previous residue 298 
Skipped atom 1735 because residue number 214  < previous residue 298 
Skipped atom 1736 because residue number 214  < previous residue 298 
Skipped atom 1737 because residue number 215  < previous residue 298 
Skipped atom 1738 because residue number 215  < previous residue 298 
Skipped atom 1739 because residue number 215  < previous residue 298 
Skipped atom 1740 because residue number 215  < previous residue 298 
Skipped atom 1741 because residue number 215  < previous residue 298 
Skipped atom 1742 because residue number 215  < previous residue 298 
Skipped atom 1743 because residue number 215  < previous residue 298 
Skipped atom 1744 because residue number 215  < previous residue 298 
Skipped atom 1745 because residue number 215  < previous residue 298 
Skipped atom 1746 because residue number 216  < previous residue 298 
Skipped atom 1747 because residue number 216  < previous residue 298 
Skipped atom 1748 because residue number 216  < previous residue 298 
Skipped atom 1749 because residue number 216  < previous residue 298 
Skipped atom 1750 because residue number 216  < previous residue 298 
Skipped atom 1751 because residue number 216  < previous residue 298 
Skipped atom 1752 because residue number 217  < previous residue 298 
Skipped atom 1753 because residue number 217  < previous residue 298 
Skipped atom 1754 because residue number 217  < previous residue 298 
Skipped atom 1755 because residue number 217  < previous residue 298 
Skipped atom 1756 because residue number 218  < previous residue 298 
Skipped atom 1757 because residue number 218  < previous residue 298 
Skipped atom 1758 because residue number 218  < previous residue 298 
Skipped atom 1759 because residue number 218  < previous residue 298 
Skipped atom 1760 because residue number 218  < previous residue 298 
Skipped atom 1761 because residue number 218  < previous residue 298 
Skipped atom 1762 because residue number 218  < previous residue 298 
Skipped atom 1763 because residue number 218  < previous residue 298 
Skipped atom 1764 because residue number 219  < previous residue 298 
Skipped atom 1765 because residue number 219  < previous residue 298 
Skipped atom 1766 because residue number 219  < previous residue 298 
Skipped atom 1767 because residue number 219  < previous residue 298 
Skipped atom 1768 because residue number 219  < previous residue 298 
Skipped atom 1769 because residue number 219  < previous residue 298 
Skipped atom 1770 because residue number 219  < previous residue 298 
Skipped atom 1771 because residue number 220  < previous residue 298 
Skipped atom 1772 because residue number 220  < previous residue 298 
Skipped atom 1773 because residue number 220  < previous residue 298 
Skipped atom 1774 because residue number 220  < previous residue 298 
Skipped atom 1775 because residue number 220  < previous residue 298 
Skipped atom 1776 because residue number 220  < previous residue 298 
Skipped atom 1777 because residue number 220  < previous residue 298 
Skipped atom 1778 because residue number 220  < previous residue 298 
Skipped atom 1779 because residue number 221  < previous residue 298 
Skipped atom 1780 because residue number 221  < previous residue 298 
Skipped atom 1781 because residue number 221  < previous residue 298 
Skipped atom 1782 because residue number 221  < previous residue 298 
Skipped atom 1783 because residue number 221  < previous residue 298 
Skipped atom 1784 because residue number 221  < previous residue 298 
Skipped atom 1785 because residue number 221  < previous residue 298 
Skipped atom 1786 because residue number 221  < previous residue 298 
Skipped atom 1787 because residue number 222  < previous residue 298 
Skipped atom 1788 because residue number 222  < previous residue 298 
Skipped atom 1789 because residue number 222  < previous residue 298 
Skipped atom 1790 because residue number 222  < previous residue 298 
Skipped atom 1791 because residue number 222  < previous residue 298 
Skipped atom 1792 because residue number 222  < previous residue 298 
Skipped atom 1793 because residue number 222  < previous residue 298 
Skipped atom 1794 because residue number 222  < previous residue 298 
Skipped atom 1795 because residue number 222  < previous residue 298 
Skipped atom 1796 because residue number 223  < previous residue 298 
Skipped atom 1797 because residue number 223  < previous residue 298 
Skipped atom 1798 because residue number 223  < previous residue 298 
Skipped atom 1799 because residue number 223  < previous residue 298 
Skipped atom 1800 because residue number 223  < previous residue 298 
Skipped atom 1801 because residue number 223  < previous residue 298 
Skipped atom 1802 because residue number 223  < previous residue 298 
Skipped atom 1803 because residue number 223  < previous residue 298 
Skipped atom 1804 because residue number 224  < previous residue 298 
Skipped atom 1805 because residue number 224  < previous residue 298 
Skipped atom 1806 because residue number 224  < previous residue 298 
Skipped atom 1807 because residue number 224  < previous residue 298 
Skipped atom 1808 because residue number 225  < previous residue 298 
Skipped atom 1809 because residue number 225  < previous residue 298 
Skipped atom 1810 because residue number 225  < previous residue 298 
Skipped atom 1811 because residue number 225  < previous residue 298 
Skipped atom 1812 because residue number 225  < previous residue 298 
Skipped atom 1813 because residue number 225  < previous residue 298 
Skipped atom 1814 because residue number 225  < previous residue 298 
Skipped atom 1815 because residue number 226  < previous residue 298 
Skipped atom 1816 because residue number 226  < previous residue 298 
Skipped atom 1817 because residue number 226  < previous residue 298 
Skipped atom 1818 because residue number 226  < previous residue 298 
Skipped atom 1819 because residue number 226  < previous residue 298 
Skipped atom 1820 because residue number 226  < previous residue 298 
Skipped atom 1821 because residue number 226  < previous residue 298 
Skipped atom 1822 because residue number 227  < previous residue 298 
Skipped atom 1823 because residue number 227  < previous residue 298 
Skipped atom 1824 because residue number 227  < previous residue 298 
Skipped atom 1825 because residue number 227  < previous residue 298 
Skipped atom 1826 because residue number 227  < previous residue 298 
Skipped atom 1827 because residue number 227  < previous residue 298 
Skipped atom 1828 because residue number 228  < previous residue 298 
Skipped atom 1829 because residue number 228  < previous residue 298 
Skipped atom 1830 because residue number 228  < previous residue 298 
Skipped atom 1831 because residue number 228  < previous residue 298 
Skipped atom 1832 because residue number 228  < previous residue 298 
Skipped atom 1833 because residue number 228  < previous residue 298 
Skipped atom 1834 because residue number 228  < previous residue 298 
Skipped atom 1835 because residue number 228  < previous residue 298 
Skipped atom 1836 because residue number 229  < previous residue 298 
Skipped atom 1837 because residue number 229  < previous residue 298 
Skipped atom 1838 because residue number 229  < previous residue 298 
Skipped atom 1839 because residue number 229  < previous residue 298 
Skipped atom 1840 because residue number 229  < previous residue 298 
Skipped atom 1841 because residue number 229  < previous residue 298 
Skipped atom 1842 because residue number 229  < previous residue 298 
Skipped atom 1843 because residue number 229  < previous residue 298 
Skipped atom 1844 because residue number 229  < previous residue 298 
Skipped atom 1845 because residue number 229  < previous residue 298 
Skipped atom 1846 because residue number 229  < previous residue 298 
Skipped atom 1847 because residue number 229  < previous residue 298 
Skipped atom 1848 because residue number 230  < previous residue 298 
Skipped atom 1849 because residue number 230  < previous residue 298 
Skipped atom 1850 because residue number 230  < previous residue 298 
Skipped atom 1851 because residue number 230  < previous residue 298 
Skipped atom 1852 because residue number 230  < previous residue 298 
Skipped atom 1853 because residue number 230  < previous residue 298 
Skipped atom 1854 because residue number 230  < previous residue 298 
Skipped atom 1855 because residue number 230  < previous residue 298 
Skipped atom 1856 because residue number 230  < previous residue 298 
Skipped atom 1857 because residue number 231  < previous residue 298 
Skipped atom 1858 because residue number 231  < previous residue 298 
Skipped atom 1859 because residue number 231  < previous residue 298 
Skipped atom 1860 because residue number 231  < previous residue 298 
Skipped atom 1861 because residue number 231  < previous residue 298 
Skipped atom 1862 because residue number 231  < previous residue 298 
Skipped atom 1863 because residue number 231  < previous residue 298 
Skipped atom 1864 because residue number 232  < previous residue 298 
Skipped atom 1865 because residue number 232  < previous residue 298 
Skipped atom 1866 because residue number 232  < previous residue 298 
Skipped atom 1867 because residue number 232  < previous residue 298 
Skipped atom 1868 because residue number 232  < previous residue 298 
Skipped atom 1869 because residue number 233  < previous residue 298 
Skipped atom 1870 because residue number 233  < previous residue 298 
Skipped atom 1871 because residue number 233  < previous residue 298 
Skipped atom 1872 because residue number 233  < previous residue 298 
Skipped atom 1873 because residue number 233  < previous residue 298 
Skipped atom 1874 because residue number 233  < previous residue 298 
Skipped atom 1875 because residue number 233  < previous residue 298 
Skipped atom 1876 because residue number 233  < previous residue 298 
Skipped atom 1877 because residue number 234  < previous residue 298 
Skipped atom 1878 because residue number 234  < previous residue 298 
Skipped atom 1879 because residue number 234  < previous residue 298 
Skipped atom 1880 because residue number 234  < previous residue 298 
Skipped atom 1881 because residue number 234  < previous residue 298 
Skipped atom 1882 because residue number 234  < previous residue 298 
Skipped atom 1883 because residue number 234  < previous residue 298 
Skipped atom 1884 because residue number 234  < previous residue 298 
Skipped atom 1885 because residue number 234  < previous residue 298 
Skipped atom 1886 because residue number 235  < previous residue 298 
Skipped atom 1887 because residue number 235  < previous residue 298 
Skipped atom 1888 because residue number 235  < previous residue 298 
Skipped atom 1889 because residue number 235  < previous residue 298 
Skipped atom 1890 because residue number 235  < previous residue 298 
Skipped atom 1891 because residue number 235  < previous residue 298 
Skipped atom 1892 because residue number 236  < previous residue 298 
Skipped atom 1893 because residue number 236  < previous residue 298 
Skipped atom 1894 because residue number 236  < previous residue 298 
Skipped atom 1895 because residue number 236  < previous residue 298 
Skipped atom 1896 because residue number 237  < previous residue 298 
Skipped atom 1897 because residue number 237  < previous residue 298 
Skipped atom 1898 because residue number 237  < previous residue 298 
Skipped atom 1899 because residue number 237  < previous residue 298 
Skipped atom 1900 because residue number 237  < previous residue 298 
Skipped atom 1901 because residue number 237  < previous residue 298 
Skipped atom 1902 because residue number 237  < previous residue 298 
Skipped atom 1903 because residue number 237  < previous residue 298 
Skipped atom 1904 because residue number 237  < previous residue 298 
Skipped atom 1905 because residue number 238  < previous residue 298 
Skipped atom 1906 because residue number 238  < previous residue 298 
Skipped atom 1907 because residue number 238  < previous residue 298 
Skipped atom 1908 because residue number 238  < previous residue 298 
Skipped atom 1909 because residue number 238  < previous residue 298 
Skipped atom 1910 because residue number 239  < previous residue 298 
Skipped atom 1911 because residue number 239  < previous residue 298 
Skipped atom 1912 because residue number 239  < previous residue 298 
Skipped atom 1913 because residue number 239  < previous residue 298 
Skipped atom 1914 because residue number 239  < previous residue 298 
Skipped atom 1915 because residue number 239  < previous residue 298 
Skipped atom 1916 because residue number 239  < previous residue 298 
Skipped atom 1917 because residue number 239  < previous residue 298 
Skipped atom 1918 because residue number 240  < previous residue 298 
Skipped atom 1919 because residue number 240  < previous residue 298 
Skipped atom 1920 because residue number 240  < previous residue 298 
Skipped atom 1921 because residue number 240  < previous residue 298 
Skipped atom 1922 because residue number 240  < previous residue 298 
Skipped atom 1923 because residue number 240  < previous residue 298 
Skipped atom 1924 because residue number 240  < previous residue 298 
Skipped atom 1925 because residue number 241  < previous residue 298 
Skipped atom 1926 because residue number 241  < previous residue 298 
Skipped atom 1927 because residue number 241  < previous residue 298 
Skipped atom 1928 because residue number 241  < previous residue 298 
Skipped atom 1929 because residue number 241  < previous residue 298 
Skipped atom 1930 because residue number 241  < previous residue 298 
Skipped atom 1931 because residue number 241  < previous residue 298 
Skipped atom 1932 because residue number 241  < previous residue 298 
Skipped atom 1933 because residue number 241  < previous residue 298 
Skipped atom 1934 because residue number 241  < previous residue 298 
Skipped atom 1935 because residue number 241  < previous residue 298 
Skipped atom 1936 because residue number 241  < previous residue 298 
Skipped atom 1937 because residue number 242  < previous residue 298 
Skipped atom 1938 because residue number 242  < previous residue 298 
Skipped atom 1939 because residue number 242  < previous residue 298 
Skipped atom 1940 because residue number 242  < previous residue 298 
Skipped atom 1941 because residue number 242  < previous residue 298 
Skipped atom 1942 because residue number 243  < previous residue 298 
Skipped atom 1943 because residue number 243  < previous residue 298 
Skipped atom 1944 because residue number 243  < previous residue 298 
Skipped atom 1945 because residue number 243  < previous residue 298 
Skipped atom 1946 because residue number 243  < previous residue 298 
Skipped atom 1947 because residue number 243  < previous residue 298 
Skipped atom 1948 because residue number 244  < previous residue 298 
Skipped atom 1949 because residue number 244  < previous residue 298 
Skipped atom 1950 because residue number 244  < previous residue 298 
Skipped atom 1951 because residue number 244  < previous residue 298 
Skipped atom 1952 because residue number 244  < previous residue 298 
Skipped atom 1953 because residue number 244  < previous residue 298 
Skipped atom 1954 because residue number 244  < previous residue 298 
Skipped atom 1955 because residue number 244  < previous residue 298 
Skipped atom 1956 because residue number 244  < previous residue 298 
Skipped atom 1957 because residue number 244  < previous residue 298 
Skipped atom 1958 because residue number 244  < previous residue 298 
Skipped atom 1959 because residue number 245  < previous residue 298 
Skipped atom 1960 because residue number 245  < previous residue 298 
Skipped atom 1961 because residue number 245  < previous residue 298 
Skipped atom 1962 because residue number 245  < previous residue 298 
Skipped atom 1963 because residue number 245  < previous residue 298 
Skipped atom 1964 because residue number 245  < previous residue 298 
Skipped atom 1965 because residue number 245  < previous residue 298 
Skipped atom 1966 because residue number 245  < previous residue 298 
Skipped atom 1967 because residue number 246  < previous residue 298 
Skipped atom 1968 because residue number 246  < previous residue 298 
Skipped atom 1969 because residue number 246  < previous residue 298 
Skipped atom 1970 because residue number 246  < previous residue 298 
Skipped atom 1971 because residue number 246  < previous residue 298 
Skipped atom 1972 because residue number 246  < previous residue 298 
Skipped atom 1973 because residue number 246  < previous residue 298 
Skipped atom 1974 because residue number 246  < previous residue 298 
Skipped atom 1975 because residue number 247  < previous residue 298 
Skipped atom 1976 because residue number 247  < previous residue 298 
Skipped atom 1977 because residue number 247  < previous residue 298 
Skipped atom 1978 because residue number 247  < previous residue 298 
Skipped atom 1979 because residue number 247  < previous residue 298 
Skipped atom 1980 because residue number 247  < previous residue 298 
Skipped atom 1981 because residue number 247  < previous residue 298 
Skipped atom 1982 because residue number 248  < previous residue 298 
Skipped atom 1983 because residue number 248  < previous residue 298 
Skipped atom 1984 because residue number 248  < previous residue 298 
Skipped atom 1985 because residue number 248  < previous residue 298 
Skipped atom 1986 because residue number 248  < previous residue 298 
Skipped atom 1987 because residue number 249  < previous residue 298 
Skipped atom 1988 because residue number 249  < previous residue 298 
Skipped atom 1989 because residue number 249  < previous residue 298 
Skipped atom 1990 because residue number 249  < previous residue 298 
Skipped atom 1991 because residue number 249  < previous residue 298 
Skipped atom 1992 because residue number 249  < previous residue 298 
Skipped atom 1993 because residue number 249  < previous residue 298 
Skipped atom 1994 because residue number 249  < previous residue 298 
Skipped atom 1995 because residue number 249  < previous residue 298 
Skipped atom 1996 because residue number 249  < previous residue 298 
Skipped atom 1997 because residue number 249  < previous residue 298 
Skipped atom 1998 because residue number 250  < previous residue 298 
Skipped atom 1999 because residue number 250  < previous residue 298 
Skipped atom 2000 because residue number 250  < previous residue 298 
Skipped atom 2001 because residue number 250  < previous residue 298 
Skipped atom 2002 because residue number 250  < previous residue 298 
Skipped atom 2003 because residue number 250  < previous residue 298 
Skipped atom 2004 because residue number 250  < previous residue 298 
Skipped atom 2005 because residue number 251  < previous residue 298 
Skipped atom 2006 because residue number 251  < previous residue 298 
Skipped atom 2007 because residue number 251  < previous residue 298 
Skipped atom 2008 because residue number 251  < previous residue 298 
Skipped atom 2009 because residue number 251  < previous residue 298 
Skipped atom 2010 because residue number 251  < previous residue 298 
Skipped atom 2011 because residue number 251  < previous residue 298 
Skipped atom 2012 because residue number 251  < previous residue 298 
Skipped atom 2013 because residue number 251  < previous residue 298 
Skipped atom 2014 because residue number 251  < previous residue 298 
Skipped atom 2015 because residue number 251  < previous residue 298 
Skipped atom 2016 because residue number 251  < previous residue 298 
Skipped atom 2017 because residue number 252  < previous residue 298 
Skipped atom 2018 because residue number 252  < previous residue 298 
Skipped atom 2019 because residue number 252  < previous residue 298 
Skipped atom 2020 because residue number 252  < previous residue 298 
Skipped atom 2021 because residue number 252  < previous residue 298 
Skipped atom 2022 because residue number 252  < previous residue 298 
Skipped atom 2023 because residue number 252  < previous residue 298 
Skipped atom 2024 because residue number 253  < previous residue 298 
Skipped atom 2025 because residue number 253  < previous residue 298 
Skipped atom 2026 because residue number 253  < previous residue 298 
Skipped atom 2027 because residue number 253  < previous residue 298 
Skipped atom 2028 because residue number 253  < previous residue 298 
Skipped atom 2029 because residue number 253  < previous residue 298 
Skipped atom 2030 because residue number 253  < previous residue 298 
Skipped atom 2031 because residue number 253  < previous residue 298 
Skipped atom 2032 because residue number 253  < previous residue 298 
Skipped atom 2033 because residue number 253  < previous residue 298 
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1alq-orig.a2m
Writing a2m file: tmp/1alq-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-19882


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-19882/tmp -alignfile tmp/1alq-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1alq-orig.a2m (1 sequences, 266 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-19882/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-19882/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-19882/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19882/tmp.a2m (1 sequences, 266 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-19882/tmp.mod tmp/1alq-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-19882 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1alq-align.mod
tmp/1alq-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19882/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1alq-orig.a2m tmp/1alq-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1alq-align.mod
Running w0.5 tmp/1alq-orig.a2m tmp/1alq-align.mod
Running align2model tmp/1alq-align -i tmp/1alq-align.mod -db tmp/1alq-orig.a2m -db tmp/1alq-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1alq.94.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1alq.95.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1alq.95.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1alq.95.5.a2m \
	-target T0124 -template 1alq \
	-out T0124-1alq.95.5 -outdir und
Skipped atom 298 because residue number 31  < previous residue 298 
Skipped atom 299 because residue number 31  < previous residue 298 
Skipped atom 300 because residue number 31  < previous residue 298 
Skipped atom 301 because residue number 31  < previous residue 298 
Skipped atom 302 because residue number 31  < previous residue 298 
Skipped atom 303 because residue number 31  < previous residue 298 
Skipped atom 304 because residue number 31  < previous residue 298 
Skipped atom 305 because residue number 31  < previous residue 298 
Skipped atom 306 because residue number 31  < previous residue 298 
Skipped atom 307 because residue number 32  < previous residue 298 
Skipped atom 308 because residue number 32  < previous residue 298 
Skipped atom 309 because residue number 32  < previous residue 298 
Skipped atom 310 because residue number 32  < previous residue 298 
Skipped atom 311 because residue number 32  < previous residue 298 
Skipped atom 312 because residue number 32  < previous residue 298 
Skipped atom 313 because residue number 32  < previous residue 298 
Skipped atom 314 because residue number 32  < previous residue 298 
Skipped atom 315 because residue number 32  < previous residue 298 
Skipped atom 316 because residue number 33  < previous residue 298 
Skipped atom 317 because residue number 33  < previous residue 298 
Skipped atom 318 because residue number 33  < previous residue 298 
Skipped atom 319 because residue number 33  < previous residue 298 
Skipped atom 320 because residue number 33  < previous residue 298 
Skipped atom 321 because residue number 33  < previous residue 298 
Skipped atom 322 because residue number 33  < previous residue 298 
Skipped atom 323 because residue number 33  < previous residue 298 
Skipped atom 324 because residue number 34  < previous residue 298 
Skipped atom 325 because residue number 34  < previous residue 298 
Skipped atom 326 because residue number 34  < previous residue 298 
Skipped atom 327 because residue number 34  < previous residue 298 
Skipped atom 328 because residue number 34  < previous residue 298 
Skipped atom 329 because residue number 34  < previous residue 298 
Skipped atom 330 because residue number 34  < previous residue 298 
Skipped atom 331 because residue number 34  < previous residue 298 
Skipped atom 332 because residue number 35  < previous residue 298 
Skipped atom 333 because residue number 35  < previous residue 298 
Skipped atom 334 because residue number 35  < previous residue 298 
Skipped atom 335 because residue number 35  < previous residue 298 
Skipped atom 336 because residue number 35  < previous residue 298 
Skipped atom 337 because residue number 35  < previous residue 298 
Skipped atom 338 because residue number 35  < previous residue 298 
Skipped atom 339 because residue number 35  < previous residue 298 
Skipped atom 340 because residue number 36  < previous residue 298 
Skipped atom 341 because residue number 36  < previous residue 298 
Skipped atom 342 because residue number 36  < previous residue 298 
Skipped atom 343 because residue number 36  < previous residue 298 
Skipped atom 344 because residue number 36  < previous residue 298 
Skipped atom 345 because residue number 36  < previous residue 298 
Skipped atom 346 because residue number 36  < previous residue 298 
Skipped atom 347 because residue number 36  < previous residue 298 
Skipped atom 348 because residue number 37  < previous residue 298 
Skipped atom 349 because residue number 37  < previous residue 298 
Skipped atom 350 because residue number 37  < previous residue 298 
Skipped atom 351 because residue number 37  < previous residue 298 
Skipped atom 352 because residue number 37  < previous residue 298 
Skipped atom 353 because residue number 37  < previous residue 298 
Skipped atom 354 because residue number 37  < previous residue 298 
Skipped atom 355 because residue number 37  < previous residue 298 
Skipped atom 356 because residue number 37  < previous residue 298 
Skipped atom 357 because residue number 38  < previous residue 298 
Skipped atom 358 because residue number 38  < previous residue 298 
Skipped atom 359 because residue number 38  < previous residue 298 
Skipped atom 360 because residue number 38  < previous residue 298 
Skipped atom 361 because residue number 38  < previous residue 298 
Skipped atom 362 because residue number 38  < previous residue 298 
Skipped atom 363 because residue number 38  < previous residue 298 
Skipped atom 364 because residue number 38  < previous residue 298 
Skipped atom 365 because residue number 38  < previous residue 298 
Skipped atom 366 because residue number 39  < previous residue 298 
Skipped atom 367 because residue number 39  < previous residue 298 
Skipped atom 368 because residue number 39  < previous residue 298 
Skipped atom 369 because residue number 39  < previous residue 298 
Skipped atom 370 because residue number 39  < previous residue 298 
Skipped atom 371 because residue number 39  < previous residue 298 
Skipped atom 372 because residue number 39  < previous residue 298 
Skipped atom 373 because residue number 39  < previous residue 298 
Skipped atom 374 because residue number 39  < previous residue 298 
Skipped atom 375 because residue number 40  < previous residue 298 
Skipped atom 376 because residue number 40  < previous residue 298 
Skipped atom 377 because residue number 40  < previous residue 298 
Skipped atom 378 because residue number 40  < previous residue 298 
Skipped atom 379 because residue number 40  < previous residue 298 
Skipped atom 380 because residue number 40  < previous residue 298 
Skipped atom 381 because residue number 40  < previous residue 298 
Skipped atom 382 because residue number 40  < previous residue 298 
Skipped atom 383 because residue number 40  < previous residue 298 
Skipped atom 384 because residue number 40  < previous residue 298 
Skipped atom 385 because residue number 40  < previous residue 298 
Skipped atom 386 because residue number 40  < previous residue 298 
Skipped atom 387 because residue number 41  < previous residue 298 
Skipped atom 388 because residue number 41  < previous residue 298 
Skipped atom 389 because residue number 41  < previous residue 298 
Skipped atom 390 because residue number 41  < previous residue 298 
Skipped atom 391 because residue number 41  < previous residue 298 
Skipped atom 392 because residue number 41  < previous residue 298 
Skipped atom 393 because residue number 41  < previous residue 298 
Skipped atom 394 because residue number 41  < previous residue 298 
Skipped atom 395 because residue number 42  < previous residue 298 
Skipped atom 396 because residue number 42  < previous residue 298 
Skipped atom 397 because residue number 42  < previous residue 298 
Skipped atom 398 because residue number 42  < previous residue 298 
Skipped atom 399 because residue number 42  < previous residue 298 
Skipped atom 400 because residue number 43  < previous residue 298 
Skipped atom 401 because residue number 43  < previous residue 298 
Skipped atom 402 because residue number 43  < previous residue 298 
Skipped atom 403 because residue number 43  < previous residue 298 
Skipped atom 404 because residue number 43  < previous residue 298 
Skipped atom 405 because residue number 43  < previous residue 298 
Skipped atom 406 because residue number 43  < previous residue 298 
Skipped atom 407 because residue number 43  < previous residue 298 
Skipped atom 408 because residue number 43  < previous residue 298 
Skipped atom 409 because residue number 43  < previous residue 298 
Skipped atom 410 because residue number 44  < previous residue 298 
Skipped atom 411 because residue number 44  < previous residue 298 
Skipped atom 412 because residue number 44  < previous residue 298 
Skipped atom 413 because residue number 44  < previous residue 298 
Skipped atom 414 because residue number 44  < previous residue 298 
Skipped atom 415 because residue number 44  < previous residue 298 
Skipped atom 416 because residue number 44  < previous residue 298 
Skipped atom 417 because residue number 44  < previous residue 298 
Skipped atom 418 because residue number 45  < previous residue 298 
Skipped atom 419 because residue number 45  < previous residue 298 
Skipped atom 420 because residue number 45  < previous residue 298 
Skipped atom 421 because residue number 45  < previous residue 298 
Skipped atom 422 because residue number 46  < previous residue 298 
Skipped atom 423 because residue number 46  < previous residue 298 
Skipped atom 424 because residue number 46  < previous residue 298 
Skipped atom 425 because residue number 46  < previous residue 298 
Skipped atom 426 because residue number 46  < previous residue 298 
Skipped atom 427 because residue number 46  < previous residue 298 
Skipped atom 428 because residue number 46  < previous residue 298 
Skipped atom 429 because residue number 47  < previous residue 298 
Skipped atom 430 because residue number 47  < previous residue 298 
Skipped atom 431 because residue number 47  < previous residue 298 
Skipped atom 432 because residue number 47  < previous residue 298 
Skipped atom 433 because residue number 47  < previous residue 298 
Skipped atom 434 because residue number 47  < previous residue 298 
Skipped atom 435 because residue number 47  < previous residue 298 
Skipped atom 436 because residue number 47  < previous residue 298 
Skipped atom 437 because residue number 47  < previous residue 298 
Skipped atom 438 because residue number 47  < previous residue 298 
Skipped atom 439 because residue number 47  < previous residue 298 
Skipped atom 440 because residue number 47  < previous residue 298 
Skipped atom 441 because residue number 48  < previous residue 298 
Skipped atom 442 because residue number 48  < previous residue 298 
Skipped atom 443 because residue number 48  < previous residue 298 
Skipped atom 444 because residue number 48  < previous residue 298 
Skipped atom 445 because residue number 48  < previous residue 298 
Skipped atom 446 because residue number 49  < previous residue 298 
Skipped atom 447 because residue number 49  < previous residue 298 
Skipped atom 448 because residue number 49  < previous residue 298 
Skipped atom 449 because residue number 49  < previous residue 298 
Skipped atom 450 because residue number 49  < previous residue 298 
Skipped atom 451 because residue number 49  < previous residue 298 
Skipped atom 452 because residue number 49  < previous residue 298 
Skipped atom 453 because residue number 49  < previous residue 298 
Skipped atom 454 because residue number 50  < previous residue 298 
Skipped atom 455 because residue number 50  < previous residue 298 
Skipped atom 456 because residue number 50  < previous residue 298 
Skipped atom 457 because residue number 50  < previous residue 298 
Skipped atom 458 because residue number 50  < previous residue 298 
Skipped atom 459 because residue number 50  < previous residue 298 
Skipped atom 460 because residue number 50  < previous residue 298 
Skipped atom 461 because residue number 50  < previous residue 298 
Skipped atom 462 because residue number 51  < previous residue 298 
Skipped atom 463 because residue number 51  < previous residue 298 
Skipped atom 464 because residue number 51  < previous residue 298 
Skipped atom 465 because residue number 51  < previous residue 298 
Skipped atom 466 because residue number 51  < previous residue 298 
Skipped atom 467 because residue number 51  < previous residue 298 
Skipped atom 468 because residue number 51  < previous residue 298 
Skipped atom 469 because residue number 52  < previous residue 298 
Skipped atom 470 because residue number 52  < previous residue 298 
Skipped atom 471 because residue number 52  < previous residue 298 
Skipped atom 472 because residue number 52  < previous residue 298 
Skipped atom 473 because residue number 52  < previous residue 298 
Skipped atom 474 because residue number 52  < previous residue 298 
Skipped atom 475 because residue number 52  < previous residue 298 
Skipped atom 476 because residue number 52  < previous residue 298 
Skipped atom 477 because residue number 52  < previous residue 298 
Skipped atom 478 because residue number 53  < previous residue 298 
Skipped atom 479 because residue number 53  < previous residue 298 
Skipped atom 480 because residue number 53  < previous residue 298 
Skipped atom 481 because residue number 53  < previous residue 298 
Skipped atom 482 because residue number 53  < previous residue 298 
Skipped atom 483 because residue number 53  < previous residue 298 
Skipped atom 484 because residue number 54  < previous residue 298 
Skipped atom 485 because residue number 54  < previous residue 298 
Skipped atom 486 because residue number 54  < previous residue 298 
Skipped atom 487 because residue number 54  < previous residue 298 
Skipped atom 488 because residue number 55  < previous residue 298 
Skipped atom 489 because residue number 55  < previous residue 298 
Skipped atom 490 because residue number 55  < previous residue 298 
Skipped atom 491 because residue number 55  < previous residue 298 
Skipped atom 492 because residue number 55  < previous residue 298 
Skipped atom 493 because residue number 55  < previous residue 298 
Skipped atom 494 because residue number 55  < previous residue 298 
Skipped atom 495 because residue number 55  < previous residue 298 
Skipped atom 496 because residue number 55  < previous residue 298 
Skipped atom 497 because residue number 56  < previous residue 298 
Skipped atom 498 because residue number 56  < previous residue 298 
Skipped atom 499 because residue number 56  < previous residue 298 
Skipped atom 500 because residue number 56  < previous residue 298 
Skipped atom 501 because residue number 56  < previous residue 298 
Skipped atom 502 because residue number 56  < previous residue 298 
Skipped atom 503 because residue number 56  < previous residue 298 
Skipped atom 504 because residue number 56  < previous residue 298 
Skipped atom 505 because residue number 56  < previous residue 298 
Skipped atom 506 because residue number 57  < previous residue 298 
Skipped atom 507 because residue number 57  < previous residue 298 
Skipped atom 508 because residue number 57  < previous residue 298 
Skipped atom 509 because residue number 57  < previous residue 298 
Skipped atom 510 because residue number 57  < previous residue 298 
Skipped atom 511 because residue number 57  < previous residue 298 
Skipped atom 512 because residue number 57  < previous residue 298 
Skipped atom 513 because residue number 59  < previous residue 298 
Skipped atom 514 because residue number 59  < previous residue 298 
Skipped atom 515 because residue number 59  < previous residue 298 
Skipped atom 516 because residue number 59  < previous residue 298 
Skipped atom 517 because residue number 59  < previous residue 298 
Skipped atom 518 because residue number 59  < previous residue 298 
Skipped atom 519 because residue number 59  < previous residue 298 
Skipped atom 520 because residue number 59  < previous residue 298 
Skipped atom 521 because residue number 59  < previous residue 298 
Skipped atom 522 because residue number 60  < previous residue 298 
Skipped atom 523 because residue number 60  < previous residue 298 
Skipped atom 524 because residue number 60  < previous residue 298 
Skipped atom 525 because residue number 60  < previous residue 298 
Skipped atom 526 because residue number 60  < previous residue 298 
Skipped atom 527 because residue number 60  < previous residue 298 
Skipped atom 528 because residue number 60  < previous residue 298 
Skipped atom 529 because residue number 60  < previous residue 298 
Skipped atom 530 because residue number 60  < previous residue 298 
Skipped atom 531 because residue number 60  < previous residue 298 
Skipped atom 532 because residue number 60  < previous residue 298 
Skipped atom 533 because residue number 61  < previous residue 298 
Skipped atom 534 because residue number 61  < previous residue 298 
Skipped atom 535 because residue number 61  < previous residue 298 
Skipped atom 536 because residue number 61  < previous residue 298 
Skipped atom 537 because residue number 61  < previous residue 298 
Skipped atom 538 because residue number 61  < previous residue 298 
Skipped atom 539 because residue number 61  < previous residue 298 
Skipped atom 540 because residue number 61  < previous residue 298 
Skipped atom 541 because residue number 62  < previous residue 298 
Skipped atom 542 because residue number 62  < previous residue 298 
Skipped atom 543 because residue number 62  < previous residue 298 
Skipped atom 544 because residue number 62  < previous residue 298 
Skipped atom 545 because residue number 62  < previous residue 298 
Skipped atom 546 because residue number 62  < previous residue 298 
Skipped atom 547 because residue number 63  < previous residue 298 
Skipped atom 548 because residue number 63  < previous residue 298 
Skipped atom 549 because residue number 63  < previous residue 298 
Skipped atom 550 because residue number 63  < previous residue 298 
Skipped atom 551 because residue number 63  < previous residue 298 
Skipped atom 552 because residue number 63  < previous residue 298 
Skipped atom 553 because residue number 63  < previous residue 298 
Skipped atom 554 because residue number 63  < previous residue 298 
Skipped atom 555 because residue number 64  < previous residue 298 
Skipped atom 556 because residue number 64  < previous residue 298 
Skipped atom 557 because residue number 64  < previous residue 298 
Skipped atom 558 because residue number 64  < previous residue 298 
Skipped atom 559 because residue number 64  < previous residue 298 
Skipped atom 560 because residue number 64  < previous residue 298 
Skipped atom 561 because residue number 64  < previous residue 298 
Skipped atom 562 because residue number 64  < previous residue 298 
Skipped atom 563 because residue number 64  < previous residue 298 
Skipped atom 564 because residue number 65  < previous residue 298 
Skipped atom 565 because residue number 65  < previous residue 298 
Skipped atom 566 because residue number 65  < previous residue 298 
Skipped atom 567 because residue number 65  < previous residue 298 
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Skipped atom 569 because residue number 65  < previous residue 298 
Skipped atom 570 because residue number 65  < previous residue 298 
Skipped atom 571 because residue number 65  < previous residue 298 
Skipped atom 572 because residue number 65  < previous residue 298 
Skipped atom 573 because residue number 65  < previous residue 298 
Skipped atom 574 because residue number 65  < previous residue 298 
Skipped atom 575 because residue number 66  < previous residue 298 
Skipped atom 576 because residue number 66  < previous residue 298 
Skipped atom 577 because residue number 66  < previous residue 298 
Skipped atom 578 because residue number 66  < previous residue 298 
Skipped atom 579 because residue number 66  < previous residue 298 
Skipped atom 580 because residue number 66  < previous residue 298 
Skipped atom 581 because residue number 66  < previous residue 298 
Skipped atom 582 because residue number 66  < previous residue 298 
Skipped atom 583 because residue number 66  < previous residue 298 
Skipped atom 584 because residue number 66  < previous residue 298 
Skipped atom 585 because residue number 66  < previous residue 298 
Skipped atom 586 because residue number 67  < previous residue 298 
Skipped atom 587 because residue number 67  < previous residue 298 
Skipped atom 588 because residue number 67  < previous residue 298 
Skipped atom 589 because residue number 67  < previous residue 298 
Skipped atom 590 because residue number 67  < previous residue 298 
Skipped atom 591 because residue number 68  < previous residue 298 
Skipped atom 592 because residue number 68  < previous residue 298 
Skipped atom 593 because residue number 68  < previous residue 298 
Skipped atom 594 because residue number 68  < previous residue 298 
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Skipped atom 596 because residue number 68  < previous residue 298 
Skipped atom 597 because residue number 68  < previous residue 298 
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Skipped atom 599 because residue number 68  < previous residue 298 
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Skipped atom 602 because residue number 68  < previous residue 298 
Skipped atom 603 because residue number 69  < previous residue 298 
Skipped atom 604 because residue number 69  < previous residue 298 
Skipped atom 605 because residue number 69  < previous residue 298 
Skipped atom 606 because residue number 69  < previous residue 298 
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Skipped atom 608 because residue number 70  < previous residue 298 
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Skipped atom 619 because residue number 71  < previous residue 298 
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Skipped atom 621 because residue number 72  < previous residue 298 
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Skipped atom 624 because residue number 72  < previous residue 298 
Skipped atom 625 because residue number 72  < previous residue 298 
Skipped atom 626 because residue number 72  < previous residue 298 
Skipped atom 627 because residue number 73  < previous residue 298 
Skipped atom 628 because residue number 73  < previous residue 298 
Skipped atom 629 because residue number 73  < previous residue 298 
Skipped atom 630 because residue number 73  < previous residue 298 
Skipped atom 631 because residue number 73  < previous residue 298 
Skipped atom 632 because residue number 73  < previous residue 298 
Skipped atom 633 because residue number 73  < previous residue 298 
Skipped atom 634 because residue number 73  < previous residue 298 
Skipped atom 635 because residue number 73  < previous residue 298 
Skipped atom 636 because residue number 74  < previous residue 298 
Skipped atom 637 because residue number 74  < previous residue 298 
Skipped atom 638 because residue number 74  < previous residue 298 
Skipped atom 639 because residue number 74  < previous residue 298 
Skipped atom 640 because residue number 74  < previous residue 298 
Skipped atom 641 because residue number 75  < previous residue 298 
Skipped atom 642 because residue number 75  < previous residue 298 
Skipped atom 643 because residue number 75  < previous residue 298 
Skipped atom 644 because residue number 75  < previous residue 298 
Skipped atom 645 because residue number 75  < previous residue 298 
Skipped atom 646 because residue number 75  < previous residue 298 
Skipped atom 647 because residue number 75  < previous residue 298 
Skipped atom 648 because residue number 75  < previous residue 298 
Skipped atom 649 because residue number 76  < previous residue 298 
Skipped atom 650 because residue number 76  < previous residue 298 
Skipped atom 651 because residue number 76  < previous residue 298 
Skipped atom 652 because residue number 76  < previous residue 298 
Skipped atom 653 because residue number 76  < previous residue 298 
Skipped atom 654 because residue number 76  < previous residue 298 
Skipped atom 655 because residue number 76  < previous residue 298 
Skipped atom 656 because residue number 76  < previous residue 298 
Skipped atom 657 because residue number 77  < previous residue 298 
Skipped atom 658 because residue number 77  < previous residue 298 
Skipped atom 659 because residue number 77  < previous residue 298 
Skipped atom 660 because residue number 77  < previous residue 298 
Skipped atom 661 because residue number 77  < previous residue 298 
Skipped atom 662 because residue number 77  < previous residue 298 
Skipped atom 663 because residue number 78  < previous residue 298 
Skipped atom 664 because residue number 78  < previous residue 298 
Skipped atom 665 because residue number 78  < previous residue 298 
Skipped atom 666 because residue number 78  < previous residue 298 
Skipped atom 667 because residue number 78  < previous residue 298 
Skipped atom 668 because residue number 79  < previous residue 298 
Skipped atom 669 because residue number 79  < previous residue 298 
Skipped atom 670 because residue number 79  < previous residue 298 
Skipped atom 671 because residue number 79  < previous residue 298 
Skipped atom 672 because residue number 79  < previous residue 298 
Skipped atom 673 because residue number 79  < previous residue 298 
Skipped atom 674 because residue number 79  < previous residue 298 
Skipped atom 675 because residue number 79  < previous residue 298 
Skipped atom 676 because residue number 80  < previous residue 298 
Skipped atom 677 because residue number 80  < previous residue 298 
Skipped atom 678 because residue number 80  < previous residue 298 
Skipped atom 679 because residue number 80  < previous residue 298 
Skipped atom 680 because residue number 80  < previous residue 298 
Skipped atom 681 because residue number 80  < previous residue 298 
Skipped atom 682 because residue number 80  < previous residue 298 
Skipped atom 683 because residue number 80  < previous residue 298 
Skipped atom 684 because residue number 81  < previous residue 298 
Skipped atom 685 because residue number 81  < previous residue 298 
Skipped atom 686 because residue number 81  < previous residue 298 
Skipped atom 687 because residue number 81  < previous residue 298 
Skipped atom 688 because residue number 81  < previous residue 298 
Skipped atom 689 because residue number 81  < previous residue 298 
Skipped atom 690 because residue number 81  < previous residue 298 
Skipped atom 691 because residue number 81  < previous residue 298 
Skipped atom 692 because residue number 82  < previous residue 298 
Skipped atom 693 because residue number 82  < previous residue 298 
Skipped atom 694 because residue number 82  < previous residue 298 
Skipped atom 695 because residue number 82  < previous residue 298 
Skipped atom 696 because residue number 82  < previous residue 298 
Skipped atom 697 because residue number 82  < previous residue 298 
Skipped atom 698 because residue number 82  < previous residue 298 
Skipped atom 699 because residue number 82  < previous residue 298 
Skipped atom 700 because residue number 82  < previous residue 298 
Skipped atom 701 because residue number 83  < previous residue 298 
Skipped atom 702 because residue number 83  < previous residue 298 
Skipped atom 703 because residue number 83  < previous residue 298 
Skipped atom 704 because residue number 83  < previous residue 298 
Skipped atom 705 because residue number 83  < previous residue 298 
Skipped atom 706 because residue number 83  < previous residue 298 
Skipped atom 707 because residue number 83  < previous residue 298 
Skipped atom 708 because residue number 83  < previous residue 298 
Skipped atom 709 because residue number 83  < previous residue 298 
Skipped atom 710 because residue number 84  < previous residue 298 
Skipped atom 711 because residue number 84  < previous residue 298 
Skipped atom 712 because residue number 84  < previous residue 298 
Skipped atom 713 because residue number 84  < previous residue 298 
Skipped atom 714 because residue number 84  < previous residue 298 
Skipped atom 715 because residue number 84  < previous residue 298 
Skipped atom 716 because residue number 84  < previous residue 298 
Skipped atom 717 because residue number 87  < previous residue 298 
Skipped atom 718 because residue number 87  < previous residue 298 
Skipped atom 719 because residue number 87  < previous residue 298 
Skipped atom 720 because residue number 87  < previous residue 298 
Skipped atom 721 because residue number 87  < previous residue 298 
Skipped atom 722 because residue number 87  < previous residue 298 
Skipped atom 723 because residue number 87  < previous residue 298 
Skipped atom 724 because residue number 88  < previous residue 298 
Skipped atom 725 because residue number 88  < previous residue 298 
Skipped atom 726 because residue number 88  < previous residue 298 
Skipped atom 727 because residue number 88  < previous residue 298 
Skipped atom 728 because residue number 88  < previous residue 298 
Skipped atom 729 because residue number 88  < previous residue 298 
Skipped atom 730 because residue number 88  < previous residue 298 
Skipped atom 731 because residue number 88  < previous residue 298 
Skipped atom 732 because residue number 88  < previous residue 298 
Skipped atom 733 because residue number 88  < previous residue 298 
Skipped atom 734 because residue number 88  < previous residue 298 
Skipped atom 735 because residue number 88  < previous residue 298 
Skipped atom 736 because residue number 89  < previous residue 298 
Skipped atom 737 because residue number 89  < previous residue 298 
Skipped atom 738 because residue number 89  < previous residue 298 
Skipped atom 739 because residue number 89  < previous residue 298 
Skipped atom 740 because residue number 89  < previous residue 298 
Skipped atom 741 because residue number 89  < previous residue 298 
Skipped atom 742 because residue number 89  < previous residue 298 
Skipped atom 743 because residue number 89  < previous residue 298 
Skipped atom 744 because residue number 90  < previous residue 298 
Skipped atom 745 because residue number 90  < previous residue 298 
Skipped atom 746 because residue number 90  < previous residue 298 
Skipped atom 747 because residue number 90  < previous residue 298 
Skipped atom 748 because residue number 90  < previous residue 298 
Skipped atom 749 because residue number 90  < previous residue 298 
Skipped atom 750 because residue number 90  < previous residue 298 
Skipped atom 751 because residue number 90  < previous residue 298 
Skipped atom 752 because residue number 90  < previous residue 298 
Skipped atom 753 because residue number 91  < previous residue 298 
Skipped atom 754 because residue number 91  < previous residue 298 
Skipped atom 755 because residue number 91  < previous residue 298 
Skipped atom 756 because residue number 91  < previous residue 298 
Skipped atom 757 because residue number 91  < previous residue 298 
Skipped atom 758 because residue number 91  < previous residue 298 
Skipped atom 759 because residue number 91  < previous residue 298 
Skipped atom 760 because residue number 91  < previous residue 298 
Skipped atom 761 because residue number 92  < previous residue 298 
Skipped atom 762 because residue number 92  < previous residue 298 
Skipped atom 763 because residue number 92  < previous residue 298 
Skipped atom 764 because residue number 92  < previous residue 298 
Skipped atom 765 because residue number 92  < previous residue 298 
Skipped atom 766 because residue number 92  < previous residue 298 
Skipped atom 767 because residue number 92  < previous residue 298 
Skipped atom 768 because residue number 92  < previous residue 298 
Skipped atom 769 because residue number 93  < previous residue 298 
Skipped atom 770 because residue number 93  < previous residue 298 
Skipped atom 771 because residue number 93  < previous residue 298 
Skipped atom 772 because residue number 93  < previous residue 298 
Skipped atom 773 because residue number 93  < previous residue 298 
Skipped atom 774 because residue number 93  < previous residue 298 
Skipped atom 775 because residue number 93  < previous residue 298 
Skipped atom 776 because residue number 93  < previous residue 298 
Skipped atom 777 because residue number 93  < previous residue 298 
Skipped atom 778 because residue number 94  < previous residue 298 
Skipped atom 779 because residue number 94  < previous residue 298 
Skipped atom 780 because residue number 94  < previous residue 298 
Skipped atom 781 because residue number 94  < previous residue 298 
Skipped atom 782 because residue number 94  < previous residue 298 
Skipped atom 783 because residue number 94  < previous residue 298 
Skipped atom 784 because residue number 94  < previous residue 298 
Skipped atom 785 because residue number 94  < previous residue 298 
Skipped atom 786 because residue number 94  < previous residue 298 
Skipped atom 787 because residue number 95  < previous residue 298 
Skipped atom 788 because residue number 95  < previous residue 298 
Skipped atom 789 because residue number 95  < previous residue 298 
Skipped atom 790 because residue number 95  < previous residue 298 
Skipped atom 791 because residue number 95  < previous residue 298 
Skipped atom 792 because residue number 95  < previous residue 298 
Skipped atom 793 because residue number 95  < previous residue 298 
Skipped atom 794 because residue number 96  < previous residue 298 
Skipped atom 795 because residue number 96  < previous residue 298 
Skipped atom 796 because residue number 96  < previous residue 298 
Skipped atom 797 because residue number 96  < previous residue 298 
Skipped atom 798 because residue number 96  < previous residue 298 
Skipped atom 799 because residue number 96  < previous residue 298 
Skipped atom 800 because residue number 96  < previous residue 298 
Skipped atom 801 because residue number 96  < previous residue 298 
Skipped atom 802 because residue number 96  < previous residue 298 
Skipped atom 803 because residue number 96  < previous residue 298 
Skipped atom 804 because residue number 97  < previous residue 298 
Skipped atom 805 because residue number 97  < previous residue 298 
Skipped atom 806 because residue number 97  < previous residue 298 
Skipped atom 807 because residue number 97  < previous residue 298 
Skipped atom 808 because residue number 97  < previous residue 298 
Skipped atom 809 because residue number 97  < previous residue 298 
Skipped atom 810 because residue number 97  < previous residue 298 
Skipped atom 811 because residue number 97  < previous residue 298 
Skipped atom 812 because residue number 98  < previous residue 298 
Skipped atom 813 because residue number 98  < previous residue 298 
Skipped atom 814 because residue number 98  < previous residue 298 
Skipped atom 815 because residue number 98  < previous residue 298 
Skipped atom 816 because residue number 98  < previous residue 298 
Skipped atom 817 because residue number 98  < previous residue 298 
Skipped atom 818 because residue number 98  < previous residue 298 
Skipped atom 819 because residue number 98  < previous residue 298 
Skipped atom 820 because residue number 99  < previous residue 298 
Skipped atom 821 because residue number 99  < previous residue 298 
Skipped atom 822 because residue number 99  < previous residue 298 
Skipped atom 823 because residue number 99  < previous residue 298 
Skipped atom 824 because residue number 99  < previous residue 298 
Skipped atom 825 because residue number 99  < previous residue 298 
Skipped atom 826 because residue number 99  < previous residue 298 
Skipped atom 827 because residue number 99  < previous residue 298 
Skipped atom 828 because residue number 99  < previous residue 298 
Skipped atom 829 because residue number 100  < previous residue 298 
Skipped atom 830 because residue number 100  < previous residue 298 
Skipped atom 831 because residue number 100  < previous residue 298 
Skipped atom 832 because residue number 100  < previous residue 298 
Skipped atom 833 because residue number 100  < previous residue 298 
Skipped atom 834 because residue number 100  < previous residue 298 
Skipped atom 835 because residue number 100  < previous residue 298 
Skipped atom 836 because residue number 100  < previous residue 298 
Skipped atom 837 because residue number 101  < previous residue 298 
Skipped atom 838 because residue number 101  < previous residue 298 
Skipped atom 839 because residue number 101  < previous residue 298 
Skipped atom 840 because residue number 101  < previous residue 298 
Skipped atom 841 because residue number 101  < previous residue 298 
Skipped atom 842 because residue number 101  < previous residue 298 
Skipped atom 843 because residue number 101  < previous residue 298 
Skipped atom 844 because residue number 101  < previous residue 298 
Skipped atom 845 because residue number 102  < previous residue 298 
Skipped atom 846 because residue number 102  < previous residue 298 
Skipped atom 847 because residue number 102  < previous residue 298 
Skipped atom 848 because residue number 102  < previous residue 298 
Skipped atom 849 because residue number 102  < previous residue 298 
Skipped atom 850 because residue number 102  < previous residue 298 
Skipped atom 851 because residue number 102  < previous residue 298 
Skipped atom 852 because residue number 102  < previous residue 298 
Skipped atom 853 because residue number 103  < previous residue 298 
Skipped atom 854 because residue number 103  < previous residue 298 
Skipped atom 855 because residue number 103  < previous residue 298 
Skipped atom 856 because residue number 103  < previous residue 298 
Skipped atom 857 because residue number 103  < previous residue 298 
Skipped atom 858 because residue number 103  < previous residue 298 
Skipped atom 859 because residue number 103  < previous residue 298 
Skipped atom 860 because residue number 104  < previous residue 298 
Skipped atom 861 because residue number 104  < previous residue 298 
Skipped atom 862 because residue number 104  < previous residue 298 
Skipped atom 863 because residue number 104  < previous residue 298 
Skipped atom 864 because residue number 104  < previous residue 298 
Skipped atom 865 because residue number 105  < previous residue 298 
Skipped atom 866 because residue number 105  < previous residue 298 
Skipped atom 867 because residue number 105  < previous residue 298 
Skipped atom 868 because residue number 105  < previous residue 298 
Skipped atom 869 because residue number 105  < previous residue 298 
Skipped atom 870 because residue number 105  < previous residue 298 
Skipped atom 871 because residue number 105  < previous residue 298 
Skipped atom 872 because residue number 105  < previous residue 298 
Skipped atom 873 because residue number 105  < previous residue 298 
Skipped atom 874 because residue number 105  < previous residue 298 
Skipped atom 875 because residue number 105  < previous residue 298 
Skipped atom 876 because residue number 105  < previous residue 298 
Skipped atom 877 because residue number 106  < previous residue 298 
Skipped atom 878 because residue number 106  < previous residue 298 
Skipped atom 879 because residue number 106  < previous residue 298 
Skipped atom 880 because residue number 106  < previous residue 298 
Skipped atom 881 because residue number 106  < previous residue 298 
Skipped atom 882 because residue number 106  < previous residue 298 
Skipped atom 883 because residue number 107  < previous residue 298 
Skipped atom 884 because residue number 107  < previous residue 298 
Skipped atom 885 because residue number 107  < previous residue 298 
Skipped atom 886 because residue number 107  < previous residue 298 
Skipped atom 887 because residue number 107  < previous residue 298 
Skipped atom 888 because residue number 107  < previous residue 298 
Skipped atom 889 because residue number 107  < previous residue 298 
Skipped atom 890 because residue number 108  < previous residue 298 
Skipped atom 891 because residue number 108  < previous residue 298 
Skipped atom 892 because residue number 108  < previous residue 298 
Skipped atom 893 because residue number 108  < previous residue 298 
Skipped atom 894 because residue number 108  < previous residue 298 
Skipped atom 895 because residue number 108  < previous residue 298 
Skipped atom 896 because residue number 108  < previous residue 298 
Skipped atom 897 because residue number 108  < previous residue 298 
Skipped atom 898 because residue number 109  < previous residue 298 
Skipped atom 899 because residue number 109  < previous residue 298 
Skipped atom 900 because residue number 109  < previous residue 298 
Skipped atom 901 because residue number 109  < previous residue 298 
Skipped atom 902 because residue number 109  < previous residue 298 
Skipped atom 903 because residue number 109  < previous residue 298 
Skipped atom 904 because residue number 109  < previous residue 298 
Skipped atom 905 because residue number 109  < previous residue 298 
Skipped atom 906 because residue number 110  < previous residue 298 
Skipped atom 907 because residue number 110  < previous residue 298 
Skipped atom 908 because residue number 110  < previous residue 298 
Skipped atom 909 because residue number 110  < previous residue 298 
Skipped atom 910 because residue number 110  < previous residue 298 
Skipped atom 911 because residue number 110  < previous residue 298 
Skipped atom 912 because residue number 110  < previous residue 298 
Skipped atom 913 because residue number 110  < previous residue 298 
Skipped atom 914 because residue number 110  < previous residue 298 
Skipped atom 915 because residue number 111  < previous residue 298 
Skipped atom 916 because residue number 111  < previous residue 298 
Skipped atom 917 because residue number 111  < previous residue 298 
Skipped atom 918 because residue number 111  < previous residue 298 
Skipped atom 919 because residue number 111  < previous residue 298 
Skipped atom 920 because residue number 111  < previous residue 298 
Skipped atom 921 because residue number 111  < previous residue 298 
Skipped atom 922 because residue number 111  < previous residue 298 
Skipped atom 923 because residue number 111  < previous residue 298 
Skipped atom 924 because residue number 112  < previous residue 298 
Skipped atom 925 because residue number 112  < previous residue 298 
Skipped atom 926 because residue number 112  < previous residue 298 
Skipped atom 927 because residue number 112  < previous residue 298 
Skipped atom 928 because residue number 112  < previous residue 298 
Skipped atom 929 because residue number 112  < previous residue 298 
Skipped atom 930 because residue number 112  < previous residue 298 
Skipped atom 931 because residue number 112  < previous residue 298 
Skipped atom 932 because residue number 112  < previous residue 298 
Skipped atom 933 because residue number 112  < previous residue 298 
Skipped atom 934 because residue number 112  < previous residue 298 
Skipped atom 935 because residue number 112  < previous residue 298 
Skipped atom 936 because residue number 113  < previous residue 298 
Skipped atom 937 because residue number 113  < previous residue 298 
Skipped atom 938 because residue number 113  < previous residue 298 
Skipped atom 939 because residue number 113  < previous residue 298 
Skipped atom 940 because residue number 113  < previous residue 298 
Skipped atom 941 because residue number 113  < previous residue 298 
Skipped atom 942 because residue number 113  < previous residue 298 
Skipped atom 943 because residue number 114  < previous residue 298 
Skipped atom 944 because residue number 114  < previous residue 298 
Skipped atom 945 because residue number 114  < previous residue 298 
Skipped atom 946 because residue number 114  < previous residue 298 
Skipped atom 947 because residue number 115  < previous residue 298 
Skipped atom 948 because residue number 115  < previous residue 298 
Skipped atom 949 because residue number 115  < previous residue 298 
Skipped atom 950 because residue number 115  < previous residue 298 
Skipped atom 951 because residue number 115  < previous residue 298 
Skipped atom 952 because residue number 115  < previous residue 298 
Skipped atom 953 because residue number 115  < previous residue 298 
Skipped atom 954 because residue number 115  < previous residue 298 
Skipped atom 955 because residue number 115  < previous residue 298 
Skipped atom 956 because residue number 116  < previous residue 298 
Skipped atom 957 because residue number 116  < previous residue 298 
Skipped atom 958 because residue number 116  < previous residue 298 
Skipped atom 959 because residue number 116  < previous residue 298 
Skipped atom 960 because residue number 116  < previous residue 298 
Skipped atom 961 because residue number 116  < previous residue 298 
Skipped atom 962 because residue number 116  < previous residue 298 
Skipped atom 963 because residue number 116  < previous residue 298 
Skipped atom 964 because residue number 117  < previous residue 298 
Skipped atom 965 because residue number 117  < previous residue 298 
Skipped atom 966 because residue number 117  < previous residue 298 
Skipped atom 967 because residue number 117  < previous residue 298 
Skipped atom 968 because residue number 117  < previous residue 298 
Skipped atom 969 because residue number 117  < previous residue 298 
Skipped atom 970 because residue number 117  < previous residue 298 
Skipped atom 971 because residue number 117  < previous residue 298 
Skipped atom 972 because residue number 118  < previous residue 298 
Skipped atom 973 because residue number 118  < previous residue 298 
Skipped atom 974 because residue number 118  < previous residue 298 
Skipped atom 975 because residue number 118  < previous residue 298 
Skipped atom 976 because residue number 118  < previous residue 298 
Skipped atom 977 because residue number 118  < previous residue 298 
Skipped atom 978 because residue number 118  < previous residue 298 
Skipped atom 979 because residue number 119  < previous residue 298 
Skipped atom 980 because residue number 119  < previous residue 298 
Skipped atom 981 because residue number 119  < previous residue 298 
Skipped atom 982 because residue number 119  < previous residue 298 
Skipped atom 983 because residue number 119  < previous residue 298 
Skipped atom 984 because residue number 119  < previous residue 298 
Skipped atom 985 because residue number 119  < previous residue 298 
Skipped atom 986 because residue number 119  < previous residue 298 
Skipped atom 987 because residue number 120  < previous residue 298 
Skipped atom 988 because residue number 120  < previous residue 298 
Skipped atom 989 because residue number 120  < previous residue 298 
Skipped atom 990 because residue number 120  < previous residue 298 
Skipped atom 991 because residue number 120  < previous residue 298 
Skipped atom 992 because residue number 120  < previous residue 298 
Skipped atom 993 because residue number 120  < previous residue 298 
Skipped atom 994 because residue number 120  < previous residue 298 
Skipped atom 995 because residue number 120  < previous residue 298 
Skipped atom 996 because residue number 121  < previous residue 298 
Skipped atom 997 because residue number 121  < previous residue 298 
Skipped atom 998 because residue number 121  < previous residue 298 
Skipped atom 999 because residue number 121  < previous residue 298 
Skipped atom 1000 because residue number 121  < previous residue 298 
Skipped atom 1001 because residue number 122  < previous residue 298 
Skipped atom 1002 because residue number 122  < previous residue 298 
Skipped atom 1003 because residue number 122  < previous residue 298 
Skipped atom 1004 because residue number 122  < previous residue 298 
Skipped atom 1005 because residue number 122  < previous residue 298 
Skipped atom 1006 because residue number 122  < previous residue 298 
Skipped atom 1007 because residue number 122  < previous residue 298 
Skipped atom 1008 because residue number 122  < previous residue 298 
Skipped atom 1009 because residue number 123  < previous residue 298 
Skipped atom 1010 because residue number 123  < previous residue 298 
Skipped atom 1011 because residue number 123  < previous residue 298 
Skipped atom 1012 because residue number 123  < previous residue 298 
Skipped atom 1013 because residue number 123  < previous residue 298 
Skipped atom 1014 because residue number 123  < previous residue 298 
Skipped atom 1015 because residue number 123  < previous residue 298 
Skipped atom 1016 because residue number 123  < previous residue 298 
Skipped atom 1017 because residue number 124  < previous residue 298 
Skipped atom 1018 because residue number 124  < previous residue 298 
Skipped atom 1019 because residue number 124  < previous residue 298 
Skipped atom 1020 because residue number 124  < previous residue 298 
Skipped atom 1021 because residue number 124  < previous residue 298 
Skipped atom 1022 because residue number 124  < previous residue 298 
Skipped atom 1023 because residue number 124  < previous residue 298 
Skipped atom 1024 because residue number 124  < previous residue 298 
Skipped atom 1025 because residue number 124  < previous residue 298 
Skipped atom 1026 because residue number 125  < previous residue 298 
Skipped atom 1027 because residue number 125  < previous residue 298 
Skipped atom 1028 because residue number 125  < previous residue 298 
Skipped atom 1029 because residue number 125  < previous residue 298 
Skipped atom 1030 because residue number 125  < previous residue 298 
Skipped atom 1031 because residue number 126  < previous residue 298 
Skipped atom 1032 because residue number 126  < previous residue 298 
Skipped atom 1033 because residue number 126  < previous residue 298 
Skipped atom 1034 because residue number 126  < previous residue 298 
Skipped atom 1035 because residue number 126  < previous residue 298 
Skipped atom 1036 because residue number 126  < previous residue 298 
Skipped atom 1037 because residue number 127  < previous residue 298 
Skipped atom 1038 because residue number 127  < previous residue 298 
Skipped atom 1039 because residue number 127  < previous residue 298 
Skipped atom 1040 because residue number 127  < previous residue 298 
Skipped atom 1041 because residue number 127  < previous residue 298 
Skipped atom 1042 because residue number 127  < previous residue 298 
Skipped atom 1043 because residue number 127  < previous residue 298 
Skipped atom 1044 because residue number 127  < previous residue 298 
Skipped atom 1045 because residue number 128  < previous residue 298 
Skipped atom 1046 because residue number 128  < previous residue 298 
Skipped atom 1047 because residue number 128  < previous residue 298 
Skipped atom 1048 because residue number 128  < previous residue 298 
Skipped atom 1049 because residue number 128  < previous residue 298 
Skipped atom 1050 because residue number 128  < previous residue 298 
Skipped atom 1051 because residue number 128  < previous residue 298 
Skipped atom 1052 because residue number 129  < previous residue 298 
Skipped atom 1053 because residue number 129  < previous residue 298 
Skipped atom 1054 because residue number 129  < previous residue 298 
Skipped atom 1055 because residue number 129  < previous residue 298 
Skipped atom 1056 because residue number 129  < previous residue 298 
Skipped atom 1057 because residue number 129  < previous residue 298 
Skipped atom 1058 because residue number 129  < previous residue 298 
Skipped atom 1059 because residue number 129  < previous residue 298 
Skipped atom 1060 because residue number 129  < previous residue 298 
Skipped atom 1061 because residue number 129  < previous residue 298 
Skipped atom 1062 because residue number 129  < previous residue 298 
Skipped atom 1063 because residue number 129  < previous residue 298 
Skipped atom 1064 because residue number 130  < previous residue 298 
Skipped atom 1065 because residue number 130  < previous residue 298 
Skipped atom 1066 because residue number 130  < previous residue 298 
Skipped atom 1067 because residue number 130  < previous residue 298 
Skipped atom 1068 because residue number 130  < previous residue 298 
Skipped atom 1069 because residue number 130  < previous residue 298 
Skipped atom 1070 because residue number 131  < previous residue 298 
Skipped atom 1071 because residue number 131  < previous residue 298 
Skipped atom 1072 because residue number 131  < previous residue 298 
Skipped atom 1073 because residue number 131  < previous residue 298 
Skipped atom 1074 because residue number 131  < previous residue 298 
Skipped atom 1075 because residue number 131  < previous residue 298 
Skipped atom 1076 because residue number 131  < previous residue 298 
Skipped atom 1077 because residue number 131  < previous residue 298 
Skipped atom 1078 because residue number 132  < previous residue 298 
Skipped atom 1079 because residue number 132  < previous residue 298 
Skipped atom 1080 because residue number 132  < previous residue 298 
Skipped atom 1081 because residue number 132  < previous residue 298 
Skipped atom 1082 because residue number 132  < previous residue 298 
Skipped atom 1083 because residue number 132  < previous residue 298 
Skipped atom 1084 because residue number 132  < previous residue 298 
Skipped atom 1085 because residue number 132  < previous residue 298 
Skipped atom 1086 because residue number 133  < previous residue 298 
Skipped atom 1087 because residue number 133  < previous residue 298 
Skipped atom 1088 because residue number 133  < previous residue 298 
Skipped atom 1089 because residue number 133  < previous residue 298 
Skipped atom 1090 because residue number 133  < previous residue 298 
Skipped atom 1091 because residue number 133  < previous residue 298 
Skipped atom 1092 because residue number 133  < previous residue 298 
Skipped atom 1093 because residue number 134  < previous residue 298 
Skipped atom 1094 because residue number 134  < previous residue 298 
Skipped atom 1095 because residue number 134  < previous residue 298 
Skipped atom 1096 because residue number 134  < previous residue 298 
Skipped atom 1097 because residue number 134  < previous residue 298 
Skipped atom 1098 because residue number 135  < previous residue 298 
Skipped atom 1099 because residue number 135  < previous residue 298 
Skipped atom 1100 because residue number 135  < previous residue 298 
Skipped atom 1101 because residue number 135  < previous residue 298 
Skipped atom 1102 because residue number 135  < previous residue 298 
Skipped atom 1103 because residue number 135  < previous residue 298 
Skipped atom 1104 because residue number 135  < previous residue 298 
Skipped atom 1105 because residue number 135  < previous residue 298 
Skipped atom 1106 because residue number 136  < previous residue 298 
Skipped atom 1107 because residue number 136  < previous residue 298 
Skipped atom 1108 because residue number 136  < previous residue 298 
Skipped atom 1109 because residue number 136  < previous residue 298 
Skipped atom 1110 because residue number 136  < previous residue 298 
Skipped atom 1111 because residue number 136  < previous residue 298 
Skipped atom 1112 because residue number 136  < previous residue 298 
Skipped atom 1113 because residue number 136  < previous residue 298 
Skipped atom 1114 because residue number 137  < previous residue 298 
Skipped atom 1115 because residue number 137  < previous residue 298 
Skipped atom 1116 because residue number 137  < previous residue 298 
Skipped atom 1117 because residue number 137  < previous residue 298 
Skipped atom 1118 because residue number 137  < previous residue 298 
Skipped atom 1119 because residue number 137  < previous residue 298 
Skipped atom 1120 because residue number 137  < previous residue 298 
Skipped atom 1121 because residue number 137  < previous residue 298 
Skipped atom 1122 because residue number 137  < previous residue 298 
Skipped atom 1123 because residue number 138  < previous residue 298 
Skipped atom 1124 because residue number 138  < previous residue 298 
Skipped atom 1125 because residue number 138  < previous residue 298 
Skipped atom 1126 because residue number 138  < previous residue 298 
Skipped atom 1127 because residue number 138  < previous residue 298 
Skipped atom 1128 because residue number 138  < previous residue 298 
Skipped atom 1129 because residue number 138  < previous residue 298 
Skipped atom 1130 because residue number 138  < previous residue 298 
Skipped atom 1131 because residue number 139  < previous residue 298 
Skipped atom 1132 because residue number 139  < previous residue 298 
Skipped atom 1133 because residue number 139  < previous residue 298 
Skipped atom 1134 because residue number 139  < previous residue 298 
Skipped atom 1135 because residue number 139  < previous residue 298 
Skipped atom 1136 because residue number 139  < previous residue 298 
Skipped atom 1137 because residue number 139  < previous residue 298 
Skipped atom 1138 because residue number 139  < previous residue 298 
Skipped atom 1139 because residue number 140  < previous residue 298 
Skipped atom 1140 because residue number 140  < previous residue 298 
Skipped atom 1141 because residue number 140  < previous residue 298 
Skipped atom 1142 because residue number 140  < previous residue 298 
Skipped atom 1143 because residue number 140  < previous residue 298 
Skipped atom 1144 because residue number 140  < previous residue 298 
Skipped atom 1145 because residue number 140  < previous residue 298 
Skipped atom 1146 because residue number 140  < previous residue 298 
Skipped atom 1147 because residue number 140  < previous residue 298 
Skipped atom 1148 because residue number 141  < previous residue 298 
Skipped atom 1149 because residue number 141  < previous residue 298 
Skipped atom 1150 because residue number 141  < previous residue 298 
Skipped atom 1151 because residue number 141  < previous residue 298 
Skipped atom 1152 because residue number 141  < previous residue 298 
Skipped atom 1153 because residue number 141  < previous residue 298 
Skipped atom 1154 because residue number 141  < previous residue 298 
Skipped atom 1155 because residue number 141  < previous residue 298 
Skipped atom 1156 because residue number 141  < previous residue 298 
Skipped atom 1157 because residue number 142  < previous residue 298 
Skipped atom 1158 because residue number 142  < previous residue 298 
Skipped atom 1159 because residue number 142  < previous residue 298 
Skipped atom 1160 because residue number 142  < previous residue 298 
Skipped atom 1161 because residue number 142  < previous residue 298 
Skipped atom 1162 because residue number 142  < previous residue 298 
Skipped atom 1163 because residue number 142  < previous residue 298 
Skipped atom 1164 because residue number 142  < previous residue 298 
Skipped atom 1165 because residue number 143  < previous residue 298 
Skipped atom 1166 because residue number 143  < previous residue 298 
Skipped atom 1167 because residue number 143  < previous residue 298 
Skipped atom 1168 because residue number 143  < previous residue 298 
Skipped atom 1169 because residue number 144  < previous residue 298 
Skipped atom 1170 because residue number 144  < previous residue 298 
Skipped atom 1171 because residue number 144  < previous residue 298 
Skipped atom 1172 because residue number 144  < previous residue 298 
Skipped atom 1173 because residue number 145  < previous residue 298 
Skipped atom 1174 because residue number 145  < previous residue 298 
Skipped atom 1175 because residue number 145  < previous residue 298 
Skipped atom 1176 because residue number 145  < previous residue 298 
Skipped atom 1177 because residue number 145  < previous residue 298 
Skipped atom 1178 because residue number 145  < previous residue 298 
Skipped atom 1179 because residue number 145  < previous residue 298 
Skipped atom 1180 because residue number 145  < previous residue 298 
Skipped atom 1181 because residue number 146  < previous residue 298 
Skipped atom 1182 because residue number 146  < previous residue 298 
Skipped atom 1183 because residue number 146  < previous residue 298 
Skipped atom 1184 because residue number 146  < previous residue 298 
Skipped atom 1185 because residue number 146  < previous residue 298 
Skipped atom 1186 because residue number 146  < previous residue 298 
Skipped atom 1187 because residue number 146  < previous residue 298 
Skipped atom 1188 because residue number 146  < previous residue 298 
Skipped atom 1189 because residue number 146  < previous residue 298 
Skipped atom 1190 because residue number 147  < previous residue 298 
Skipped atom 1191 because residue number 147  < previous residue 298 
Skipped atom 1192 because residue number 147  < previous residue 298 
Skipped atom 1193 because residue number 147  < previous residue 298 
Skipped atom 1194 because residue number 147  < previous residue 298 
Skipped atom 1195 because residue number 147  < previous residue 298 
Skipped atom 1196 because residue number 147  < previous residue 298 
Skipped atom 1197 because residue number 147  < previous residue 298 
Skipped atom 1198 because residue number 147  < previous residue 298 
Skipped atom 1199 because residue number 148  < previous residue 298 
Skipped atom 1200 because residue number 148  < previous residue 298 
Skipped atom 1201 because residue number 148  < previous residue 298 
Skipped atom 1202 because residue number 148  < previous residue 298 
Skipped atom 1203 because residue number 148  < previous residue 298 
Skipped atom 1204 because residue number 148  < previous residue 298 
Skipped atom 1205 because residue number 148  < previous residue 298 
Skipped atom 1206 because residue number 149  < previous residue 298 
Skipped atom 1207 because residue number 149  < previous residue 298 
Skipped atom 1208 because residue number 149  < previous residue 298 
Skipped atom 1209 because residue number 149  < previous residue 298 
Skipped atom 1210 because residue number 149  < previous residue 298 
Skipped atom 1211 because residue number 149  < previous residue 298 
Skipped atom 1212 because residue number 149  < previous residue 298 
Skipped atom 1213 because residue number 149  < previous residue 298 
Skipped atom 1214 because residue number 149  < previous residue 298 
Skipped atom 1215 because residue number 150  < previous residue 298 
Skipped atom 1216 because residue number 150  < previous residue 298 
Skipped atom 1217 because residue number 150  < previous residue 298 
Skipped atom 1218 because residue number 150  < previous residue 298 
Skipped atom 1219 because residue number 150  < previous residue 298 
Skipped atom 1220 because residue number 150  < previous residue 298 
Skipped atom 1221 because residue number 150  < previous residue 298 
Skipped atom 1222 because residue number 150  < previous residue 298 
Skipped atom 1223 because residue number 150  < previous residue 298 
Skipped atom 1224 because residue number 151  < previous residue 298 
Skipped atom 1225 because residue number 151  < previous residue 298 
Skipped atom 1226 because residue number 151  < previous residue 298 
Skipped atom 1227 because residue number 151  < previous residue 298 
Skipped atom 1228 because residue number 151  < previous residue 298 
Skipped atom 1229 because residue number 151  < previous residue 298 
Skipped atom 1230 because residue number 151  < previous residue 298 
Skipped atom 1231 because residue number 151  < previous residue 298 
Skipped atom 1232 because residue number 151  < previous residue 298 
Skipped atom 1233 because residue number 151  < previous residue 298 
Skipped atom 1234 because residue number 151  < previous residue 298 
Skipped atom 1235 because residue number 152  < previous residue 298 
Skipped atom 1236 because residue number 152  < previous residue 298 
Skipped atom 1237 because residue number 152  < previous residue 298 
Skipped atom 1238 because residue number 152  < previous residue 298 
Skipped atom 1239 because residue number 152  < previous residue 298 
Skipped atom 1240 because residue number 152  < previous residue 298 
Skipped atom 1241 because residue number 152  < previous residue 298 
Skipped atom 1242 because residue number 152  < previous residue 298 
Skipped atom 1243 because residue number 153  < previous residue 298 
Skipped atom 1244 because residue number 153  < previous residue 298 
Skipped atom 1245 because residue number 153  < previous residue 298 
Skipped atom 1246 because residue number 153  < previous residue 298 
Skipped atom 1247 because residue number 153  < previous residue 298 
Skipped atom 1248 because residue number 153  < previous residue 298 
Skipped atom 1249 because residue number 153  < previous residue 298 
Skipped atom 1250 because residue number 153  < previous residue 298 
Skipped atom 1251 because residue number 153  < previous residue 298 
Skipped atom 1252 because residue number 154  < previous residue 298 
Skipped atom 1253 because residue number 154  < previous residue 298 
Skipped atom 1254 because residue number 154  < previous residue 298 
Skipped atom 1255 because residue number 154  < previous residue 298 
Skipped atom 1256 because residue number 154  < previous residue 298 
Skipped atom 1257 because residue number 154  < previous residue 298 
Skipped atom 1258 because residue number 154  < previous residue 298 
Skipped atom 1259 because residue number 154  < previous residue 298 
Skipped atom 1260 because residue number 154  < previous residue 298 
Skipped atom 1261 because residue number 155  < previous residue 298 
Skipped atom 1262 because residue number 155  < previous residue 298 
Skipped atom 1263 because residue number 155  < previous residue 298 
Skipped atom 1264 because residue number 155  < previous residue 298 
Skipped atom 1265 because residue number 155  < previous residue 298 
Skipped atom 1266 because residue number 155  < previous residue 298 
Skipped atom 1267 because residue number 155  < previous residue 298 
Skipped atom 1268 because residue number 155  < previous residue 298 
Skipped atom 1269 because residue number 156  < previous residue 298 
Skipped atom 1270 because residue number 156  < previous residue 298 
Skipped atom 1271 because residue number 156  < previous residue 298 
Skipped atom 1272 because residue number 156  < previous residue 298 
Skipped atom 1273 because residue number 157  < previous residue 298 
Skipped atom 1274 because residue number 157  < previous residue 298 
Skipped atom 1275 because residue number 157  < previous residue 298 
Skipped atom 1276 because residue number 157  < previous residue 298 
Skipped atom 1277 because residue number 157  < previous residue 298 
Skipped atom 1278 because residue number 157  < previous residue 298 
Skipped atom 1279 because residue number 157  < previous residue 298 
Skipped atom 1280 because residue number 157  < previous residue 298 
Skipped atom 1281 because residue number 158  < previous residue 298 
Skipped atom 1282 because residue number 158  < previous residue 298 
Skipped atom 1283 because residue number 158  < previous residue 298 
Skipped atom 1284 because residue number 158  < previous residue 298 
Skipped atom 1285 because residue number 158  < previous residue 298 
Skipped atom 1286 because residue number 158  < previous residue 298 
Skipped atom 1287 because residue number 158  < previous residue 298 
Skipped atom 1288 because residue number 158  < previous residue 298 
Skipped atom 1289 because residue number 158  < previous residue 298 
Skipped atom 1290 because residue number 159  < previous residue 298 
Skipped atom 1291 because residue number 159  < previous residue 298 
Skipped atom 1292 because residue number 159  < previous residue 298 
Skipped atom 1293 because residue number 159  < previous residue 298 
Skipped atom 1294 because residue number 159  < previous residue 298 
Skipped atom 1295 because residue number 159  < previous residue 298 
Skipped atom 1296 because residue number 159  < previous residue 298 
Skipped atom 1297 because residue number 160  < previous residue 298 
Skipped atom 1298 because residue number 160  < previous residue 298 
Skipped atom 1299 because residue number 160  < previous residue 298 
Skipped atom 1300 because residue number 160  < previous residue 298 
Skipped atom 1301 because residue number 160  < previous residue 298 
Skipped atom 1302 because residue number 160  < previous residue 298 
Skipped atom 1303 because residue number 160  < previous residue 298 
Skipped atom 1304 because residue number 161  < previous residue 298 
Skipped atom 1305 because residue number 161  < previous residue 298 
Skipped atom 1306 because residue number 161  < previous residue 298 
Skipped atom 1307 because residue number 161  < previous residue 298 
Skipped atom 1308 because residue number 161  < previous residue 298 
Skipped atom 1309 because residue number 161  < previous residue 298 
Skipped atom 1310 because residue number 161  < previous residue 298 
Skipped atom 1311 because residue number 161  < previous residue 298 
Skipped atom 1312 because residue number 162  < previous residue 298 
Skipped atom 1313 because residue number 162  < previous residue 298 
Skipped atom 1314 because residue number 162  < previous residue 298 
Skipped atom 1315 because residue number 162  < previous residue 298 
Skipped atom 1316 because residue number 162  < previous residue 298 
Skipped atom 1317 because residue number 162  < previous residue 298 
Skipped atom 1318 because residue number 162  < previous residue 298 
Skipped atom 1319 because residue number 163  < previous residue 298 
Skipped atom 1320 because residue number 163  < previous residue 298 
Skipped atom 1321 because residue number 163  < previous residue 298 
Skipped atom 1322 because residue number 163  < previous residue 298 
Skipped atom 1323 because residue number 163  < previous residue 298 
Skipped atom 1324 because residue number 163  < previous residue 298 
Skipped atom 1325 because residue number 163  < previous residue 298 
Skipped atom 1326 because residue number 164  < previous residue 298 
Skipped atom 1327 because residue number 164  < previous residue 298 
Skipped atom 1328 because residue number 164  < previous residue 298 
Skipped atom 1329 because residue number 164  < previous residue 298 
Skipped atom 1330 because residue number 164  < previous residue 298 
Skipped atom 1331 because residue number 164  < previous residue 298 
Skipped atom 1332 because residue number 164  < previous residue 298 
Skipped atom 1333 because residue number 164  < previous residue 298 
Skipped atom 1334 because residue number 164  < previous residue 298 
Skipped atom 1335 because residue number 164  < previous residue 298 
Skipped atom 1336 because residue number 164  < previous residue 298 
Skipped atom 1337 because residue number 165  < previous residue 298 
Skipped atom 1338 because residue number 165  < previous residue 298 
Skipped atom 1339 because residue number 165  < previous residue 298 
Skipped atom 1340 because residue number 165  < previous residue 298 
Skipped atom 1341 because residue number 165  < previous residue 298 
Skipped atom 1342 because residue number 165  < previous residue 298 
Skipped atom 1343 because residue number 165  < previous residue 298 
Skipped atom 1344 because residue number 165  < previous residue 298 
Skipped atom 1345 because residue number 165  < previous residue 298 
Skipped atom 1346 because residue number 165  < previous residue 298 
Skipped atom 1347 because residue number 165  < previous residue 298 
Skipped atom 1348 because residue number 165  < previous residue 298 
Skipped atom 1349 because residue number 166  < previous residue 298 
Skipped atom 1350 because residue number 166  < previous residue 298 
Skipped atom 1351 because residue number 166  < previous residue 298 
Skipped atom 1352 because residue number 166  < previous residue 298 
Skipped atom 1353 because residue number 166  < previous residue 298 
Skipped atom 1354 because residue number 166  < previous residue 298 
Skipped atom 1355 because residue number 166  < previous residue 298 
Skipped atom 1356 because residue number 166  < previous residue 298 
Skipped atom 1357 because residue number 166  < previous residue 298 
Skipped atom 1358 because residue number 167  < previous residue 298 
Skipped atom 1359 because residue number 167  < previous residue 298 
Skipped atom 1360 because residue number 167  < previous residue 298 
Skipped atom 1361 because residue number 167  < previous residue 298 
Skipped atom 1362 because residue number 167  < previous residue 298 
Skipped atom 1363 because residue number 167  < previous residue 298 
Skipped atom 1364 because residue number 167  < previous residue 298 
Skipped atom 1365 because residue number 167  < previous residue 298 
Skipped atom 1366 because residue number 168  < previous residue 298 
Skipped atom 1367 because residue number 168  < previous residue 298 
Skipped atom 1368 because residue number 168  < previous residue 298 
Skipped atom 1369 because residue number 168  < previous residue 298 
Skipped atom 1370 because residue number 168  < previous residue 298 
Skipped atom 1371 because residue number 168  < previous residue 298 
Skipped atom 1372 because residue number 168  < previous residue 298 
Skipped atom 1373 because residue number 168  < previous residue 298 
Skipped atom 1374 because residue number 168  < previous residue 298 
Skipped atom 1375 because residue number 169  < previous residue 298 
Skipped atom 1376 because residue number 169  < previous residue 298 
Skipped atom 1377 because residue number 169  < previous residue 298 
Skipped atom 1378 because residue number 169  < previous residue 298 
Skipped atom 1379 because residue number 169  < previous residue 298 
Skipped atom 1380 because residue number 169  < previous residue 298 
Skipped atom 1381 because residue number 169  < previous residue 298 
Skipped atom 1382 because residue number 169  < previous residue 298 
Skipped atom 1383 because residue number 170  < previous residue 298 
Skipped atom 1384 because residue number 170  < previous residue 298 
Skipped atom 1385 because residue number 170  < previous residue 298 
Skipped atom 1386 because residue number 170  < previous residue 298 
Skipped atom 1387 because residue number 170  < previous residue 298 
Skipped atom 1388 because residue number 170  < previous residue 298 
Skipped atom 1389 because residue number 170  < previous residue 298 
Skipped atom 1390 because residue number 170  < previous residue 298 
Skipped atom 1391 because residue number 171  < previous residue 298 
Skipped atom 1392 because residue number 171  < previous residue 298 
Skipped atom 1393 because residue number 171  < previous residue 298 
Skipped atom 1394 because residue number 171  < previous residue 298 
Skipped atom 1395 because residue number 171  < previous residue 298 
Skipped atom 1396 because residue number 171  < previous residue 298 
Skipped atom 1397 because residue number 171  < previous residue 298 
Skipped atom 1398 because residue number 171  < previous residue 298 
Skipped atom 1399 because residue number 171  < previous residue 298 
Skipped atom 1400 because residue number 171  < previous residue 298 
Skipped atom 1401 because residue number 171  < previous residue 298 
Skipped atom 1402 because residue number 171  < previous residue 298 
Skipped atom 1403 because residue number 172  < previous residue 298 
Skipped atom 1404 because residue number 172  < previous residue 298 
Skipped atom 1405 because residue number 172  < previous residue 298 
Skipped atom 1406 because residue number 172  < previous residue 298 
Skipped atom 1407 because residue number 172  < previous residue 298 
Skipped atom 1408 because residue number 172  < previous residue 298 
Skipped atom 1409 because residue number 172  < previous residue 298 
Skipped atom 1410 because residue number 172  < previous residue 298 
Skipped atom 1411 because residue number 172  < previous residue 298 
Skipped atom 1412 because residue number 172  < previous residue 298 
Skipped atom 1413 because residue number 172  < previous residue 298 
Skipped atom 1414 because residue number 172  < previous residue 298 
Skipped atom 1415 because residue number 173  < previous residue 298 
Skipped atom 1416 because residue number 173  < previous residue 298 
Skipped atom 1417 because residue number 173  < previous residue 298 
Skipped atom 1418 because residue number 173  < previous residue 298 
Skipped atom 1419 because residue number 173  < previous residue 298 
Skipped atom 1420 because residue number 173  < previous residue 298 
Skipped atom 1421 because residue number 174  < previous residue 298 
Skipped atom 1422 because residue number 174  < previous residue 298 
Skipped atom 1423 because residue number 174  < previous residue 298 
Skipped atom 1424 because residue number 174  < previous residue 298 
Skipped atom 1425 because residue number 174  < previous residue 298 
Skipped atom 1426 because residue number 174  < previous residue 298 
Skipped atom 1427 because residue number 174  < previous residue 298 
Skipped atom 1428 because residue number 175  < previous residue 298 
Skipped atom 1429 because residue number 175  < previous residue 298 
Skipped atom 1430 because residue number 175  < previous residue 298 
Skipped atom 1431 because residue number 175  < previous residue 298 
Skipped atom 1432 because residue number 175  < previous residue 298 
Skipped atom 1433 because residue number 175  < previous residue 298 
Skipped atom 1434 because residue number 175  < previous residue 298 
Skipped atom 1435 because residue number 175  < previous residue 298 
Skipped atom 1436 because residue number 175  < previous residue 298 
Skipped atom 1437 because residue number 176  < previous residue 298 
Skipped atom 1438 because residue number 176  < previous residue 298 
Skipped atom 1439 because residue number 176  < previous residue 298 
Skipped atom 1440 because residue number 176  < previous residue 298 
Skipped atom 1441 because residue number 176  < previous residue 298 
Skipped atom 1442 because residue number 176  < previous residue 298 
Skipped atom 1443 because residue number 177  < previous residue 298 
Skipped atom 1444 because residue number 177  < previous residue 298 
Skipped atom 1445 because residue number 177  < previous residue 298 
Skipped atom 1446 because residue number 177  < previous residue 298 
Skipped atom 1447 because residue number 177  < previous residue 298 
Skipped atom 1448 because residue number 177  < previous residue 298 
Skipped atom 1449 because residue number 177  < previous residue 298 
Skipped atom 1450 because residue number 177  < previous residue 298 
Skipped atom 1451 because residue number 177  < previous residue 298 
Skipped atom 1452 because residue number 178  < previous residue 298 
Skipped atom 1453 because residue number 178  < previous residue 298 
Skipped atom 1454 because residue number 178  < previous residue 298 
Skipped atom 1455 because residue number 178  < previous residue 298 
Skipped atom 1456 because residue number 178  < previous residue 298 
Skipped atom 1457 because residue number 178  < previous residue 298 
Skipped atom 1458 because residue number 178  < previous residue 298 
Skipped atom 1459 because residue number 178  < previous residue 298 
Skipped atom 1460 because residue number 178  < previous residue 298 
Skipped atom 1461 because residue number 179  < previous residue 298 
Skipped atom 1462 because residue number 179  < previous residue 298 
Skipped atom 1463 because residue number 179  < previous residue 298 
Skipped atom 1464 because residue number 179  < previous residue 298 
Skipped atom 1465 because residue number 179  < previous residue 298 
Skipped atom 1466 because residue number 179  < previous residue 298 
Skipped atom 1467 because residue number 179  < previous residue 298 
Skipped atom 1468 because residue number 179  < previous residue 298 
Skipped atom 1469 because residue number 180  < previous residue 298 
Skipped atom 1470 because residue number 180  < previous residue 298 
Skipped atom 1471 because residue number 180  < previous residue 298 
Skipped atom 1472 because residue number 180  < previous residue 298 
Skipped atom 1473 because residue number 180  < previous residue 298 
Skipped atom 1474 because residue number 180  < previous residue 298 
Skipped atom 1475 because residue number 180  < previous residue 298 
Skipped atom 1476 because residue number 181  < previous residue 298 
Skipped atom 1477 because residue number 181  < previous residue 298 
Skipped atom 1478 because residue number 181  < previous residue 298 
Skipped atom 1479 because residue number 181  < previous residue 298 
Skipped atom 1480 because residue number 181  < previous residue 298 
Skipped atom 1481 because residue number 181  < previous residue 298 
Skipped atom 1482 because residue number 182  < previous residue 298 
Skipped atom 1483 because residue number 182  < previous residue 298 
Skipped atom 1484 because residue number 182  < previous residue 298 
Skipped atom 1485 because residue number 182  < previous residue 298 
Skipped atom 1486 because residue number 182  < previous residue 298 
Skipped atom 1487 because residue number 182  < previous residue 298 
Skipped atom 1488 because residue number 182  < previous residue 298 
Skipped atom 1489 because residue number 183  < previous residue 298 
Skipped atom 1490 because residue number 183  < previous residue 298 
Skipped atom 1491 because residue number 183  < previous residue 298 
Skipped atom 1492 because residue number 183  < previous residue 298 
Skipped atom 1493 because residue number 183  < previous residue 298 
Skipped atom 1494 because residue number 183  < previous residue 298 
Skipped atom 1495 because residue number 183  < previous residue 298 
Skipped atom 1496 because residue number 184  < previous residue 298 
Skipped atom 1497 because residue number 184  < previous residue 298 
Skipped atom 1498 because residue number 184  < previous residue 298 
Skipped atom 1499 because residue number 184  < previous residue 298 
Skipped atom 1500 because residue number 184  < previous residue 298 
Skipped atom 1501 because residue number 185  < previous residue 298 
Skipped atom 1502 because residue number 185  < previous residue 298 
Skipped atom 1503 because residue number 185  < previous residue 298 
Skipped atom 1504 because residue number 185  < previous residue 298 
Skipped atom 1505 because residue number 185  < previous residue 298 
Skipped atom 1506 because residue number 186  < previous residue 298 
Skipped atom 1507 because residue number 186  < previous residue 298 
Skipped atom 1508 because residue number 186  < previous residue 298 
Skipped atom 1509 because residue number 186  < previous residue 298 
Skipped atom 1510 because residue number 186  < previous residue 298 
Skipped atom 1511 because residue number 186  < previous residue 298 
Skipped atom 1512 because residue number 186  < previous residue 298 
Skipped atom 1513 because residue number 186  < previous residue 298 
Skipped atom 1514 because residue number 186  < previous residue 298 
Skipped atom 1515 because residue number 186  < previous residue 298 
Skipped atom 1516 because residue number 186  < previous residue 298 
Skipped atom 1517 because residue number 187  < previous residue 298 
Skipped atom 1518 because residue number 187  < previous residue 298 
Skipped atom 1519 because residue number 187  < previous residue 298 
Skipped atom 1520 because residue number 187  < previous residue 298 
Skipped atom 1521 because residue number 188  < previous residue 298 
Skipped atom 1522 because residue number 188  < previous residue 298 
Skipped atom 1523 because residue number 188  < previous residue 298 
Skipped atom 1524 because residue number 188  < previous residue 298 
Skipped atom 1525 because residue number 188  < previous residue 298 
Skipped atom 1526 because residue number 188  < previous residue 298 
Skipped atom 1527 because residue number 188  < previous residue 298 
Skipped atom 1528 because residue number 188  < previous residue 298 
Skipped atom 1529 because residue number 188  < previous residue 298 
Skipped atom 1530 because residue number 189  < previous residue 298 
Skipped atom 1531 because residue number 189  < previous residue 298 
Skipped atom 1532 because residue number 189  < previous residue 298 
Skipped atom 1533 because residue number 189  < previous residue 298 
Skipped atom 1534 because residue number 189  < previous residue 298 
Skipped atom 1535 because residue number 189  < previous residue 298 
Skipped atom 1536 because residue number 189  < previous residue 298 
Skipped atom 1537 because residue number 190  < previous residue 298 
Skipped atom 1538 because residue number 190  < previous residue 298 
Skipped atom 1539 because residue number 190  < previous residue 298 
Skipped atom 1540 because residue number 190  < previous residue 298 
Skipped atom 1541 because residue number 190  < previous residue 298 
Skipped atom 1542 because residue number 190  < previous residue 298 
Skipped atom 1543 because residue number 190  < previous residue 298 
Skipped atom 1544 because residue number 190  < previous residue 298 
Skipped atom 1545 because residue number 191  < previous residue 298 
Skipped atom 1546 because residue number 191  < previous residue 298 
Skipped atom 1547 because residue number 191  < previous residue 298 
Skipped atom 1548 because residue number 191  < previous residue 298 
Skipped atom 1549 because residue number 191  < previous residue 298 
Skipped atom 1550 because residue number 191  < previous residue 298 
Skipped atom 1551 because residue number 191  < previous residue 298 
Skipped atom 1552 because residue number 191  < previous residue 298 
Skipped atom 1553 because residue number 192  < previous residue 298 
Skipped atom 1554 because residue number 192  < previous residue 298 
Skipped atom 1555 because residue number 192  < previous residue 298 
Skipped atom 1556 because residue number 192  < previous residue 298 
Skipped atom 1557 because residue number 192  < previous residue 298 
Skipped atom 1558 because residue number 192  < previous residue 298 
Skipped atom 1559 because residue number 192  < previous residue 298 
Skipped atom 1560 because residue number 192  < previous residue 298 
Skipped atom 1561 because residue number 192  < previous residue 298 
Skipped atom 1562 because residue number 193  < previous residue 298 
Skipped atom 1563 because residue number 193  < previous residue 298 
Skipped atom 1564 because residue number 193  < previous residue 298 
Skipped atom 1565 because residue number 193  < previous residue 298 
Skipped atom 1566 because residue number 193  < previous residue 298 
Skipped atom 1567 because residue number 193  < previous residue 298 
Skipped atom 1568 because residue number 193  < previous residue 298 
Skipped atom 1569 because residue number 193  < previous residue 298 
Skipped atom 1570 because residue number 194  < previous residue 298 
Skipped atom 1571 because residue number 194  < previous residue 298 
Skipped atom 1572 because residue number 194  < previous residue 298 
Skipped atom 1573 because residue number 194  < previous residue 298 
Skipped atom 1574 because residue number 194  < previous residue 298 
Skipped atom 1575 because residue number 194  < previous residue 298 
Skipped atom 1576 because residue number 194  < previous residue 298 
Skipped atom 1577 because residue number 194  < previous residue 298 
Skipped atom 1578 because residue number 195  < previous residue 298 
Skipped atom 1579 because residue number 195  < previous residue 298 
Skipped atom 1580 because residue number 195  < previous residue 298 
Skipped atom 1581 because residue number 195  < previous residue 298 
Skipped atom 1582 because residue number 195  < previous residue 298 
Skipped atom 1583 because residue number 196  < previous residue 298 
Skipped atom 1584 because residue number 196  < previous residue 298 
Skipped atom 1585 because residue number 196  < previous residue 298 
Skipped atom 1586 because residue number 196  < previous residue 298 
Skipped atom 1587 because residue number 196  < previous residue 298 
Skipped atom 1588 because residue number 196  < previous residue 298 
Skipped atom 1589 because residue number 196  < previous residue 298 
Skipped atom 1590 because residue number 196  < previous residue 298 
Skipped atom 1591 because residue number 197  < previous residue 298 
Skipped atom 1592 because residue number 197  < previous residue 298 
Skipped atom 1593 because residue number 197  < previous residue 298 
Skipped atom 1594 because residue number 197  < previous residue 298 
Skipped atom 1595 because residue number 198  < previous residue 298 
Skipped atom 1596 because residue number 198  < previous residue 298 
Skipped atom 1597 because residue number 198  < previous residue 298 
Skipped atom 1598 because residue number 198  < previous residue 298 
Skipped atom 1599 because residue number 198  < previous residue 298 
Skipped atom 1600 because residue number 198  < previous residue 298 
Skipped atom 1601 because residue number 198  < previous residue 298 
Skipped atom 1602 because residue number 198  < previous residue 298 
Skipped atom 1603 because residue number 198  < previous residue 298 
Skipped atom 1604 because residue number 199  < previous residue 298 
Skipped atom 1605 because residue number 199  < previous residue 298 
Skipped atom 1606 because residue number 199  < previous residue 298 
Skipped atom 1607 because residue number 199  < previous residue 298 
Skipped atom 1608 because residue number 199  < previous residue 298 
Skipped atom 1609 because residue number 199  < previous residue 298 
Skipped atom 1610 because residue number 199  < previous residue 298 
Skipped atom 1611 because residue number 199  < previous residue 298 
Skipped atom 1612 because residue number 200  < previous residue 298 
Skipped atom 1613 because residue number 200  < previous residue 298 
Skipped atom 1614 because residue number 200  < previous residue 298 
Skipped atom 1615 because residue number 200  < previous residue 298 
Skipped atom 1616 because residue number 200  < previous residue 298 
Skipped atom 1617 because residue number 200  < previous residue 298 
Skipped atom 1618 because residue number 201  < previous residue 298 
Skipped atom 1619 because residue number 201  < previous residue 298 
Skipped atom 1620 because residue number 201  < previous residue 298 
Skipped atom 1621 because residue number 201  < previous residue 298 
Skipped atom 1622 because residue number 201  < previous residue 298 
Skipped atom 1623 because residue number 201  < previous residue 298 
Skipped atom 1624 because residue number 201  < previous residue 298 
Skipped atom 1625 because residue number 201  < previous residue 298 
Skipped atom 1626 because residue number 201  < previous residue 298 
Skipped atom 1627 because residue number 202  < previous residue 298 
Skipped atom 1628 because residue number 202  < previous residue 298 
Skipped atom 1629 because residue number 202  < previous residue 298 
Skipped atom 1630 because residue number 202  < previous residue 298 
Skipped atom 1631 because residue number 202  < previous residue 298 
Skipped atom 1632 because residue number 202  < previous residue 298 
Skipped atom 1633 because residue number 202  < previous residue 298 
Skipped atom 1634 because residue number 202  < previous residue 298 
Skipped atom 1635 because residue number 202  < previous residue 298 
Skipped atom 1636 because residue number 203  < previous residue 298 
Skipped atom 1637 because residue number 203  < previous residue 298 
Skipped atom 1638 because residue number 203  < previous residue 298 
Skipped atom 1639 because residue number 203  < previous residue 298 
Skipped atom 1640 because residue number 203  < previous residue 298 
Skipped atom 1641 because residue number 203  < previous residue 298 
Skipped atom 1642 because residue number 203  < previous residue 298 
Skipped atom 1643 because residue number 203  < previous residue 298 
Skipped atom 1644 because residue number 204  < previous residue 298 
Skipped atom 1645 because residue number 204  < previous residue 298 
Skipped atom 1646 because residue number 204  < previous residue 298 
Skipped atom 1647 because residue number 204  < previous residue 298 
Skipped atom 1648 because residue number 204  < previous residue 298 
Skipped atom 1649 because residue number 204  < previous residue 298 
Skipped atom 1650 because residue number 204  < previous residue 298 
Skipped atom 1651 because residue number 204  < previous residue 298 
Skipped atom 1652 because residue number 204  < previous residue 298 
Skipped atom 1653 because residue number 205  < previous residue 298 
Skipped atom 1654 because residue number 205  < previous residue 298 
Skipped atom 1655 because residue number 205  < previous residue 298 
Skipped atom 1656 because residue number 205  < previous residue 298 
Skipped atom 1657 because residue number 205  < previous residue 298 
Skipped atom 1658 because residue number 205  < previous residue 298 
Skipped atom 1659 because residue number 205  < previous residue 298 
Skipped atom 1660 because residue number 205  < previous residue 298 
Skipped atom 1661 because residue number 205  < previous residue 298 
Skipped atom 1662 because residue number 206  < previous residue 298 
Skipped atom 1663 because residue number 206  < previous residue 298 
Skipped atom 1664 because residue number 206  < previous residue 298 
Skipped atom 1665 because residue number 206  < previous residue 298 
Skipped atom 1666 because residue number 206  < previous residue 298 
Skipped atom 1667 because residue number 206  < previous residue 298 
Skipped atom 1668 because residue number 206  < previous residue 298 
Skipped atom 1669 because residue number 206  < previous residue 298 
Skipped atom 1670 because residue number 206  < previous residue 298 
Skipped atom 1671 because residue number 206  < previous residue 298 
Skipped atom 1672 because residue number 206  < previous residue 298 
Skipped atom 1673 because residue number 207  < previous residue 298 
Skipped atom 1674 because residue number 207  < previous residue 298 
Skipped atom 1675 because residue number 207  < previous residue 298 
Skipped atom 1676 because residue number 207  < previous residue 298 
Skipped atom 1677 because residue number 207  < previous residue 298 
Skipped atom 1678 because residue number 207  < previous residue 298 
Skipped atom 1679 because residue number 207  < previous residue 298 
Skipped atom 1680 because residue number 207  < previous residue 298 
Skipped atom 1681 because residue number 208  < previous residue 298 
Skipped atom 1682 because residue number 208  < previous residue 298 
Skipped atom 1683 because residue number 208  < previous residue 298 
Skipped atom 1684 because residue number 208  < previous residue 298 
Skipped atom 1685 because residue number 208  < previous residue 298 
Skipped atom 1686 because residue number 208  < previous residue 298 
Skipped atom 1687 because residue number 208  < previous residue 298 
Skipped atom 1688 because residue number 208  < previous residue 298 
Skipped atom 1689 because residue number 209  < previous residue 298 
Skipped atom 1690 because residue number 209  < previous residue 298 
Skipped atom 1691 because residue number 209  < previous residue 298 
Skipped atom 1692 because residue number 209  < previous residue 298 
Skipped atom 1693 because residue number 209  < previous residue 298 
Skipped atom 1694 because residue number 209  < previous residue 298 
Skipped atom 1695 because residue number 209  < previous residue 298 
Skipped atom 1696 because residue number 209  < previous residue 298 
Skipped atom 1697 because residue number 210  < previous residue 298 
Skipped atom 1698 because residue number 210  < previous residue 298 
Skipped atom 1699 because residue number 210  < previous residue 298 
Skipped atom 1700 because residue number 210  < previous residue 298 
Skipped atom 1701 because residue number 210  < previous residue 298 
Skipped atom 1702 because residue number 210  < previous residue 298 
Skipped atom 1703 because residue number 210  < previous residue 298 
Skipped atom 1704 because residue number 210  < previous residue 298 
Skipped atom 1705 because residue number 211  < previous residue 298 
Skipped atom 1706 because residue number 211  < previous residue 298 
Skipped atom 1707 because residue number 211  < previous residue 298 
Skipped atom 1708 because residue number 211  < previous residue 298 
Skipped atom 1709 because residue number 211  < previous residue 298 
Skipped atom 1710 because residue number 211  < previous residue 298 
Skipped atom 1711 because residue number 211  < previous residue 298 
Skipped atom 1712 because residue number 211  < previous residue 298 
Skipped atom 1713 because residue number 212  < previous residue 298 
Skipped atom 1714 because residue number 212  < previous residue 298 
Skipped atom 1715 because residue number 212  < previous residue 298 
Skipped atom 1716 because residue number 212  < previous residue 298 
Skipped atom 1717 because residue number 212  < previous residue 298 
Skipped atom 1718 because residue number 212  < previous residue 298 
Skipped atom 1719 because residue number 212  < previous residue 298 
Skipped atom 1720 because residue number 212  < previous residue 298 
Skipped atom 1721 because residue number 213  < previous residue 298 
Skipped atom 1722 because residue number 213  < previous residue 298 
Skipped atom 1723 because residue number 213  < previous residue 298 
Skipped atom 1724 because residue number 213  < previous residue 298 
Skipped atom 1725 because residue number 213  < previous residue 298 
Skipped atom 1726 because residue number 213  < previous residue 298 
Skipped atom 1727 because residue number 213  < previous residue 298 
Skipped atom 1728 because residue number 213  < previous residue 298 
Skipped atom 1729 because residue number 214  < previous residue 298 
Skipped atom 1730 because residue number 214  < previous residue 298 
Skipped atom 1731 because residue number 214  < previous residue 298 
Skipped atom 1732 because residue number 214  < previous residue 298 
Skipped atom 1733 because residue number 214  < previous residue 298 
Skipped atom 1734 because residue number 214  < previous residue 298 
Skipped atom 1735 because residue number 214  < previous residue 298 
Skipped atom 1736 because residue number 214  < previous residue 298 
Skipped atom 1737 because residue number 215  < previous residue 298 
Skipped atom 1738 because residue number 215  < previous residue 298 
Skipped atom 1739 because residue number 215  < previous residue 298 
Skipped atom 1740 because residue number 215  < previous residue 298 
Skipped atom 1741 because residue number 215  < previous residue 298 
Skipped atom 1742 because residue number 215  < previous residue 298 
Skipped atom 1743 because residue number 215  < previous residue 298 
Skipped atom 1744 because residue number 215  < previous residue 298 
Skipped atom 1745 because residue number 215  < previous residue 298 
Skipped atom 1746 because residue number 216  < previous residue 298 
Skipped atom 1747 because residue number 216  < previous residue 298 
Skipped atom 1748 because residue number 216  < previous residue 298 
Skipped atom 1749 because residue number 216  < previous residue 298 
Skipped atom 1750 because residue number 216  < previous residue 298 
Skipped atom 1751 because residue number 216  < previous residue 298 
Skipped atom 1752 because residue number 217  < previous residue 298 
Skipped atom 1753 because residue number 217  < previous residue 298 
Skipped atom 1754 because residue number 217  < previous residue 298 
Skipped atom 1755 because residue number 217  < previous residue 298 
Skipped atom 1756 because residue number 218  < previous residue 298 
Skipped atom 1757 because residue number 218  < previous residue 298 
Skipped atom 1758 because residue number 218  < previous residue 298 
Skipped atom 1759 because residue number 218  < previous residue 298 
Skipped atom 1760 because residue number 218  < previous residue 298 
Skipped atom 1761 because residue number 218  < previous residue 298 
Skipped atom 1762 because residue number 218  < previous residue 298 
Skipped atom 1763 because residue number 218  < previous residue 298 
Skipped atom 1764 because residue number 219  < previous residue 298 
Skipped atom 1765 because residue number 219  < previous residue 298 
Skipped atom 1766 because residue number 219  < previous residue 298 
Skipped atom 1767 because residue number 219  < previous residue 298 
Skipped atom 1768 because residue number 219  < previous residue 298 
Skipped atom 1769 because residue number 219  < previous residue 298 
Skipped atom 1770 because residue number 219  < previous residue 298 
Skipped atom 1771 because residue number 220  < previous residue 298 
Skipped atom 1772 because residue number 220  < previous residue 298 
Skipped atom 1773 because residue number 220  < previous residue 298 
Skipped atom 1774 because residue number 220  < previous residue 298 
Skipped atom 1775 because residue number 220  < previous residue 298 
Skipped atom 1776 because residue number 220  < previous residue 298 
Skipped atom 1777 because residue number 220  < previous residue 298 
Skipped atom 1778 because residue number 220  < previous residue 298 
Skipped atom 1779 because residue number 221  < previous residue 298 
Skipped atom 1780 because residue number 221  < previous residue 298 
Skipped atom 1781 because residue number 221  < previous residue 298 
Skipped atom 1782 because residue number 221  < previous residue 298 
Skipped atom 1783 because residue number 221  < previous residue 298 
Skipped atom 1784 because residue number 221  < previous residue 298 
Skipped atom 1785 because residue number 221  < previous residue 298 
Skipped atom 1786 because residue number 221  < previous residue 298 
Skipped atom 1787 because residue number 222  < previous residue 298 
Skipped atom 1788 because residue number 222  < previous residue 298 
Skipped atom 1789 because residue number 222  < previous residue 298 
Skipped atom 1790 because residue number 222  < previous residue 298 
Skipped atom 1791 because residue number 222  < previous residue 298 
Skipped atom 1792 because residue number 222  < previous residue 298 
Skipped atom 1793 because residue number 222  < previous residue 298 
Skipped atom 1794 because residue number 222  < previous residue 298 
Skipped atom 1795 because residue number 222  < previous residue 298 
Skipped atom 1796 because residue number 223  < previous residue 298 
Skipped atom 1797 because residue number 223  < previous residue 298 
Skipped atom 1798 because residue number 223  < previous residue 298 
Skipped atom 1799 because residue number 223  < previous residue 298 
Skipped atom 1800 because residue number 223  < previous residue 298 
Skipped atom 1801 because residue number 223  < previous residue 298 
Skipped atom 1802 because residue number 223  < previous residue 298 
Skipped atom 1803 because residue number 223  < previous residue 298 
Skipped atom 1804 because residue number 224  < previous residue 298 
Skipped atom 1805 because residue number 224  < previous residue 298 
Skipped atom 1806 because residue number 224  < previous residue 298 
Skipped atom 1807 because residue number 224  < previous residue 298 
Skipped atom 1808 because residue number 225  < previous residue 298 
Skipped atom 1809 because residue number 225  < previous residue 298 
Skipped atom 1810 because residue number 225  < previous residue 298 
Skipped atom 1811 because residue number 225  < previous residue 298 
Skipped atom 1812 because residue number 225  < previous residue 298 
Skipped atom 1813 because residue number 225  < previous residue 298 
Skipped atom 1814 because residue number 225  < previous residue 298 
Skipped atom 1815 because residue number 226  < previous residue 298 
Skipped atom 1816 because residue number 226  < previous residue 298 
Skipped atom 1817 because residue number 226  < previous residue 298 
Skipped atom 1818 because residue number 226  < previous residue 298 
Skipped atom 1819 because residue number 226  < previous residue 298 
Skipped atom 1820 because residue number 226  < previous residue 298 
Skipped atom 1821 because residue number 226  < previous residue 298 
Skipped atom 1822 because residue number 227  < previous residue 298 
Skipped atom 1823 because residue number 227  < previous residue 298 
Skipped atom 1824 because residue number 227  < previous residue 298 
Skipped atom 1825 because residue number 227  < previous residue 298 
Skipped atom 1826 because residue number 227  < previous residue 298 
Skipped atom 1827 because residue number 227  < previous residue 298 
Skipped atom 1828 because residue number 228  < previous residue 298 
Skipped atom 1829 because residue number 228  < previous residue 298 
Skipped atom 1830 because residue number 228  < previous residue 298 
Skipped atom 1831 because residue number 228  < previous residue 298 
Skipped atom 1832 because residue number 228  < previous residue 298 
Skipped atom 1833 because residue number 228  < previous residue 298 
Skipped atom 1834 because residue number 228  < previous residue 298 
Skipped atom 1835 because residue number 228  < previous residue 298 
Skipped atom 1836 because residue number 229  < previous residue 298 
Skipped atom 1837 because residue number 229  < previous residue 298 
Skipped atom 1838 because residue number 229  < previous residue 298 
Skipped atom 1839 because residue number 229  < previous residue 298 
Skipped atom 1840 because residue number 229  < previous residue 298 
Skipped atom 1841 because residue number 229  < previous residue 298 
Skipped atom 1842 because residue number 229  < previous residue 298 
Skipped atom 1843 because residue number 229  < previous residue 298 
Skipped atom 1844 because residue number 229  < previous residue 298 
Skipped atom 1845 because residue number 229  < previous residue 298 
Skipped atom 1846 because residue number 229  < previous residue 298 
Skipped atom 1847 because residue number 229  < previous residue 298 
Skipped atom 1848 because residue number 230  < previous residue 298 
Skipped atom 1849 because residue number 230  < previous residue 298 
Skipped atom 1850 because residue number 230  < previous residue 298 
Skipped atom 1851 because residue number 230  < previous residue 298 
Skipped atom 1852 because residue number 230  < previous residue 298 
Skipped atom 1853 because residue number 230  < previous residue 298 
Skipped atom 1854 because residue number 230  < previous residue 298 
Skipped atom 1855 because residue number 230  < previous residue 298 
Skipped atom 1856 because residue number 230  < previous residue 298 
Skipped atom 1857 because residue number 231  < previous residue 298 
Skipped atom 1858 because residue number 231  < previous residue 298 
Skipped atom 1859 because residue number 231  < previous residue 298 
Skipped atom 1860 because residue number 231  < previous residue 298 
Skipped atom 1861 because residue number 231  < previous residue 298 
Skipped atom 1862 because residue number 231  < previous residue 298 
Skipped atom 1863 because residue number 231  < previous residue 298 
Skipped atom 1864 because residue number 232  < previous residue 298 
Skipped atom 1865 because residue number 232  < previous residue 298 
Skipped atom 1866 because residue number 232  < previous residue 298 
Skipped atom 1867 because residue number 232  < previous residue 298 
Skipped atom 1868 because residue number 232  < previous residue 298 
Skipped atom 1869 because residue number 233  < previous residue 298 
Skipped atom 1870 because residue number 233  < previous residue 298 
Skipped atom 1871 because residue number 233  < previous residue 298 
Skipped atom 1872 because residue number 233  < previous residue 298 
Skipped atom 1873 because residue number 233  < previous residue 298 
Skipped atom 1874 because residue number 233  < previous residue 298 
Skipped atom 1875 because residue number 233  < previous residue 298 
Skipped atom 1876 because residue number 233  < previous residue 298 
Skipped atom 1877 because residue number 234  < previous residue 298 
Skipped atom 1878 because residue number 234  < previous residue 298 
Skipped atom 1879 because residue number 234  < previous residue 298 
Skipped atom 1880 because residue number 234  < previous residue 298 
Skipped atom 1881 because residue number 234  < previous residue 298 
Skipped atom 1882 because residue number 234  < previous residue 298 
Skipped atom 1883 because residue number 234  < previous residue 298 
Skipped atom 1884 because residue number 234  < previous residue 298 
Skipped atom 1885 because residue number 234  < previous residue 298 
Skipped atom 1886 because residue number 235  < previous residue 298 
Skipped atom 1887 because residue number 235  < previous residue 298 
Skipped atom 1888 because residue number 235  < previous residue 298 
Skipped atom 1889 because residue number 235  < previous residue 298 
Skipped atom 1890 because residue number 235  < previous residue 298 
Skipped atom 1891 because residue number 235  < previous residue 298 
Skipped atom 1892 because residue number 236  < previous residue 298 
Skipped atom 1893 because residue number 236  < previous residue 298 
Skipped atom 1894 because residue number 236  < previous residue 298 
Skipped atom 1895 because residue number 236  < previous residue 298 
Skipped atom 1896 because residue number 237  < previous residue 298 
Skipped atom 1897 because residue number 237  < previous residue 298 
Skipped atom 1898 because residue number 237  < previous residue 298 
Skipped atom 1899 because residue number 237  < previous residue 298 
Skipped atom 1900 because residue number 237  < previous residue 298 
Skipped atom 1901 because residue number 237  < previous residue 298 
Skipped atom 1902 because residue number 237  < previous residue 298 
Skipped atom 1903 because residue number 237  < previous residue 298 
Skipped atom 1904 because residue number 237  < previous residue 298 
Skipped atom 1905 because residue number 238  < previous residue 298 
Skipped atom 1906 because residue number 238  < previous residue 298 
Skipped atom 1907 because residue number 238  < previous residue 298 
Skipped atom 1908 because residue number 238  < previous residue 298 
Skipped atom 1909 because residue number 238  < previous residue 298 
Skipped atom 1910 because residue number 239  < previous residue 298 
Skipped atom 1911 because residue number 239  < previous residue 298 
Skipped atom 1912 because residue number 239  < previous residue 298 
Skipped atom 1913 because residue number 239  < previous residue 298 
Skipped atom 1914 because residue number 239  < previous residue 298 
Skipped atom 1915 because residue number 239  < previous residue 298 
Skipped atom 1916 because residue number 239  < previous residue 298 
Skipped atom 1917 because residue number 239  < previous residue 298 
Skipped atom 1918 because residue number 240  < previous residue 298 
Skipped atom 1919 because residue number 240  < previous residue 298 
Skipped atom 1920 because residue number 240  < previous residue 298 
Skipped atom 1921 because residue number 240  < previous residue 298 
Skipped atom 1922 because residue number 240  < previous residue 298 
Skipped atom 1923 because residue number 240  < previous residue 298 
Skipped atom 1924 because residue number 240  < previous residue 298 
Skipped atom 1925 because residue number 241  < previous residue 298 
Skipped atom 1926 because residue number 241  < previous residue 298 
Skipped atom 1927 because residue number 241  < previous residue 298 
Skipped atom 1928 because residue number 241  < previous residue 298 
Skipped atom 1929 because residue number 241  < previous residue 298 
Skipped atom 1930 because residue number 241  < previous residue 298 
Skipped atom 1931 because residue number 241  < previous residue 298 
Skipped atom 1932 because residue number 241  < previous residue 298 
Skipped atom 1933 because residue number 241  < previous residue 298 
Skipped atom 1934 because residue number 241  < previous residue 298 
Skipped atom 1935 because residue number 241  < previous residue 298 
Skipped atom 1936 because residue number 241  < previous residue 298 
Skipped atom 1937 because residue number 242  < previous residue 298 
Skipped atom 1938 because residue number 242  < previous residue 298 
Skipped atom 1939 because residue number 242  < previous residue 298 
Skipped atom 1940 because residue number 242  < previous residue 298 
Skipped atom 1941 because residue number 242  < previous residue 298 
Skipped atom 1942 because residue number 243  < previous residue 298 
Skipped atom 1943 because residue number 243  < previous residue 298 
Skipped atom 1944 because residue number 243  < previous residue 298 
Skipped atom 1945 because residue number 243  < previous residue 298 
Skipped atom 1946 because residue number 243  < previous residue 298 
Skipped atom 1947 because residue number 243  < previous residue 298 
Skipped atom 1948 because residue number 244  < previous residue 298 
Skipped atom 1949 because residue number 244  < previous residue 298 
Skipped atom 1950 because residue number 244  < previous residue 298 
Skipped atom 1951 because residue number 244  < previous residue 298 
Skipped atom 1952 because residue number 244  < previous residue 298 
Skipped atom 1953 because residue number 244  < previous residue 298 
Skipped atom 1954 because residue number 244  < previous residue 298 
Skipped atom 1955 because residue number 244  < previous residue 298 
Skipped atom 1956 because residue number 244  < previous residue 298 
Skipped atom 1957 because residue number 244  < previous residue 298 
Skipped atom 1958 because residue number 244  < previous residue 298 
Skipped atom 1959 because residue number 245  < previous residue 298 
Skipped atom 1960 because residue number 245  < previous residue 298 
Skipped atom 1961 because residue number 245  < previous residue 298 
Skipped atom 1962 because residue number 245  < previous residue 298 
Skipped atom 1963 because residue number 245  < previous residue 298 
Skipped atom 1964 because residue number 245  < previous residue 298 
Skipped atom 1965 because residue number 245  < previous residue 298 
Skipped atom 1966 because residue number 245  < previous residue 298 
Skipped atom 1967 because residue number 246  < previous residue 298 
Skipped atom 1968 because residue number 246  < previous residue 298 
Skipped atom 1969 because residue number 246  < previous residue 298 
Skipped atom 1970 because residue number 246  < previous residue 298 
Skipped atom 1971 because residue number 246  < previous residue 298 
Skipped atom 1972 because residue number 246  < previous residue 298 
Skipped atom 1973 because residue number 246  < previous residue 298 
Skipped atom 1974 because residue number 246  < previous residue 298 
Skipped atom 1975 because residue number 247  < previous residue 298 
Skipped atom 1976 because residue number 247  < previous residue 298 
Skipped atom 1977 because residue number 247  < previous residue 298 
Skipped atom 1978 because residue number 247  < previous residue 298 
Skipped atom 1979 because residue number 247  < previous residue 298 
Skipped atom 1980 because residue number 247  < previous residue 298 
Skipped atom 1981 because residue number 247  < previous residue 298 
Skipped atom 1982 because residue number 248  < previous residue 298 
Skipped atom 1983 because residue number 248  < previous residue 298 
Skipped atom 1984 because residue number 248  < previous residue 298 
Skipped atom 1985 because residue number 248  < previous residue 298 
Skipped atom 1986 because residue number 248  < previous residue 298 
Skipped atom 1987 because residue number 249  < previous residue 298 
Skipped atom 1988 because residue number 249  < previous residue 298 
Skipped atom 1989 because residue number 249  < previous residue 298 
Skipped atom 1990 because residue number 249  < previous residue 298 
Skipped atom 1991 because residue number 249  < previous residue 298 
Skipped atom 1992 because residue number 249  < previous residue 298 
Skipped atom 1993 because residue number 249  < previous residue 298 
Skipped atom 1994 because residue number 249  < previous residue 298 
Skipped atom 1995 because residue number 249  < previous residue 298 
Skipped atom 1996 because residue number 249  < previous residue 298 
Skipped atom 1997 because residue number 249  < previous residue 298 
Skipped atom 1998 because residue number 250  < previous residue 298 
Skipped atom 1999 because residue number 250  < previous residue 298 
Skipped atom 2000 because residue number 250  < previous residue 298 
Skipped atom 2001 because residue number 250  < previous residue 298 
Skipped atom 2002 because residue number 250  < previous residue 298 
Skipped atom 2003 because residue number 250  < previous residue 298 
Skipped atom 2004 because residue number 250  < previous residue 298 
Skipped atom 2005 because residue number 251  < previous residue 298 
Skipped atom 2006 because residue number 251  < previous residue 298 
Skipped atom 2007 because residue number 251  < previous residue 298 
Skipped atom 2008 because residue number 251  < previous residue 298 
Skipped atom 2009 because residue number 251  < previous residue 298 
Skipped atom 2010 because residue number 251  < previous residue 298 
Skipped atom 2011 because residue number 251  < previous residue 298 
Skipped atom 2012 because residue number 251  < previous residue 298 
Skipped atom 2013 because residue number 251  < previous residue 298 
Skipped atom 2014 because residue number 251  < previous residue 298 
Skipped atom 2015 because residue number 251  < previous residue 298 
Skipped atom 2016 because residue number 251  < previous residue 298 
Skipped atom 2017 because residue number 252  < previous residue 298 
Skipped atom 2018 because residue number 252  < previous residue 298 
Skipped atom 2019 because residue number 252  < previous residue 298 
Skipped atom 2020 because residue number 252  < previous residue 298 
Skipped atom 2021 because residue number 252  < previous residue 298 
Skipped atom 2022 because residue number 252  < previous residue 298 
Skipped atom 2023 because residue number 252  < previous residue 298 
Skipped atom 2024 because residue number 253  < previous residue 298 
Skipped atom 2025 because residue number 253  < previous residue 298 
Skipped atom 2026 because residue number 253  < previous residue 298 
Skipped atom 2027 because residue number 253  < previous residue 298 
Skipped atom 2028 because residue number 253  < previous residue 298 
Skipped atom 2029 because residue number 253  < previous residue 298 
Skipped atom 2030 because residue number 253  < previous residue 298 
Skipped atom 2031 because residue number 253  < previous residue 298 
Skipped atom 2032 because residue number 253  < previous residue 298 
Skipped atom 2033 because residue number 253  < previous residue 298 
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1alq-orig.a2m
Writing a2m file: tmp/1alq-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26473


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26473/tmp -alignfile tmp/1alq-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1alq-orig.a2m (1 sequences, 266 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26473/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26473/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26473/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26473/tmp.a2m (1 sequences, 266 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26473/tmp.mod tmp/1alq-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26473 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1alq-align.mod
tmp/1alq-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26473/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1alq-orig.a2m tmp/1alq-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1alq-align.mod
Running w0.5 tmp/1alq-orig.a2m tmp/1alq-align.mod
Running align2model tmp/1alq-align -i tmp/1alq-align.mod -db tmp/1alq-orig.a2m -db tmp/1alq-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1alq.95.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1amp.4.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1amp.4.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1amp.4.1.a2m \
	-target T0124 -template 1amp \
	-out T0124-1amp.4.1 -outdir und
partial PDB gets fragment 280 through 289 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
THR    2    1
GLN    3   12
LEU    4    3
PRO    5    2
GLU    6   15
PRO    7    2
GLN    8   10
THR    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 10 rotamers of residue Q 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1amp.4.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1amp.5.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1amp.5.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1amp.5.1.a2m \
	-target T0124 -template 1amp \
	-out T0124-1amp.5.1 -outdir und
partial PDB gets fragment 279 through 288 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
GLN    2   12
LEU    3    3
PRO    4    2
GLU    5   12
PRO    6    2
GLN    7   14
THR    8    2
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.18770
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1amp.5.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1amp.6.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1amp.6.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1amp.6.0.a2m \
	-target T0124 -template 1amp \
	-out T0124-1amp.6.0 -outdir und
partial PDB gets fragment 278 through 287 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
PRO    3    2
GLU    4   12
PRO    5    2
GLN    6   11
THR    7    1
SER    9    2
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue S 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    8.86497
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1amp.6.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1amp.7.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1amp.7.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1amp.7.1.a2m \
	-target T0124 -template 1amp \
	-out T0124-1amp.7.1 -outdir und
partial PDB gets fragment 277 through 286 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    2    2
GLU    3   12
PRO    4    2
GLN    5   11
THR    6    2
SER    8    3
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.20636
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1amp.7.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1amp.8.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1amp.8.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1amp.8.5.a2m \
	-target T0124 -template 1amp \
	-out T0124-1amp.8.5 -outdir und
partial PDB gets fragment 276 through 285 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
GLU    2   12
PRO    3    2
GLN    4   11
THR    5    2
SER    7    3
LEU    8    3
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1amp.8.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1aocA.166.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1aocA.166.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1aocA.166.4.a2m \
	-target T0124 -template 1aocA \
	-out T0124-1aocA.166.4 -outdir und
partial PDB gets fragment 37 through 46 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
ASN    2    4
SER    3    2
HIS    4    3
ILE    5    2
GLN    6   15
GLU    7    7
VAL    8    1
VAL    9    3
GLN   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue H 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 1 rotamers of residue V 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1aocA.166.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1aocA.167.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1aocA.167.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1aocA.167.3.a2m \
	-target T0124 -template 1aocA \
	-out T0124-1aocA.167.3 -outdir und
partial PDB gets fragment 36 through 45 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
SER    2    3
HIS    3    3
ILE    4    4
GLN    5   13
GLU    6   12
VAL    8    2
GLN    9   11
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8    9     14.3665
Cluster     1 =   8   9
2 clashing residues after turn 
Residue clashes:
8-9
cluster 1 has 2 members and 0.000e+00 combinations:
 8  9 
Energy     14.3665
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
0.000000 < 14.366461: keeping 
Solved cluster 1: residual clashing  0.74
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1aocA.167.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1aoeA.52.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1aoeA.52.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1aoeA.52.5.a2m \
	-target T0124 -template 1aoeA \
	-out T0124-1aoeA.52.5 -outdir und
Skipped atom 225, because occupancy 0.5 <= existing 0.500001
Skipped atom 227, because occupancy 0.5 <= existing 0.500001
Skipped atom 229, because occupancy 0.5 <= existing 0.500001
Skipped atom 231, because occupancy 0.5 <= existing 0.500001
Skipped atom 258, because occupancy 0.5 <= existing 0.500001
Skipped atom 329, because occupancy 0.5 <= existing 0.500001
Skipped atom 331, because occupancy 0.5 <= existing 0.500001
Skipped atom 333, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 342, because occupancy 0.5 <= existing 0.500001
Skipped atom 344, because occupancy 0.5 <= existing 0.500001
Skipped atom 346, because occupancy 0.5 <= existing 0.500001
Skipped atom 348, because occupancy 0.5 <= existing 0.500001
Skipped atom 350, because occupancy 0.5 <= existing 0.500001
Skipped atom 428, because occupancy 0.5 <= existing 0.500001
Skipped atom 430, because occupancy 0.5 <= existing 0.500001
Skipped atom 432, because occupancy 0.5 <= existing 0.500001
Skipped atom 434, because occupancy 0.5 <= existing 0.500001
Skipped atom 652, because occupancy 0.5 <= existing 0.500001
Skipped atom 654, because occupancy 0.5 <= existing 0.500001
Skipped atom 656, because occupancy 0.5 <= existing 0.500001
Skipped atom 658, because occupancy 0.5 <= existing 0.500001
Skipped atom 660, because occupancy 0.5 <= existing 0.500001
Skipped atom 667, because occupancy 0.5 <= existing 0.500001
Skipped atom 703, because occupancy 0.5 <= existing 0.500001
Skipped atom 705, because occupancy 0.5 <= existing 0.500001
Skipped atom 707, because occupancy 0.5 <= existing 0.500001
Skipped atom 709, because occupancy 0.5 <= existing 0.500001
Skipped atom 896, because occupancy 0.5 <= existing 0.500001
Skipped atom 898, because occupancy 0.5 <= existing 0.500001
Skipped atom 900, because occupancy 0.5 <= existing 0.500001
Skipped atom 993, because occupancy 0.5 <= existing 0.500001
Skipped atom 995, because occupancy 0.5 <= existing 0.500001
Skipped atom 997, because occupancy 0.5 <= existing 0.500001
Skipped atom 1073, because occupancy 0.5 <= existing 0.500001
Skipped atom 1075, because occupancy 0.5 <= existing 0.500001
Skipped atom 1077, because occupancy 0.5 <= existing 0.500001
Skipped atom 1116, because occupancy 0.5 <= existing 0.500001
Skipped atom 1118, because occupancy 0.5 <= existing 0.500001
Skipped atom 1120, because occupancy 0.5 <= existing 0.500001
Skipped atom 1122, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 142 through 151 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
TYR    2    2
SER    3    3
VAL    4    2
LEU    5    3
GLU    8   11
PRO    9    2
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.98682
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1aoeA.52.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1aq0A.135.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1aq0A.135.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1aq0A.135.4.a2m \
	-target T0124 -template 1aq0A \
	-out T0124-1aq0A.135.4 -outdir und
Skipped atom 1309, because occupancy 0.41 <= existing 0.590001
Skipped atom 1311, because occupancy 0.41 <= existing 0.590001
Skipped atom 1313, because occupancy 0.41 <= existing 0.590001
Skipped atom 1315, because occupancy 0.41 <= existing 0.590001
Skipped atom 2246, because occupancy 0.36 <= existing 0.640001
Skipped atom 2248, because occupancy 0.36 <= existing 0.640001
Skipped atom 2250, because occupancy 0.36 <= existing 0.640001
Skipped atom 2252, because occupancy 0.36 <= existing 0.640001
partial PDB gets fragment 61 through 71 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LYS    2   26
LEU    3    3
GLU    4   13
LYS    6   26
ARG    7   27
LEU    8    3
ASP    9    4
ARG   10   27
ILE   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    8.56094
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1aq0A.135.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1aq0A.136.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1aq0A.136.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1aq0A.136.4.a2m \
	-target T0124 -template 1aq0A \
	-out T0124-1aq0A.136.4 -outdir und
Skipped atom 1309, because occupancy 0.41 <= existing 0.590001
Skipped atom 1311, because occupancy 0.41 <= existing 0.590001
Skipped atom 1313, because occupancy 0.41 <= existing 0.590001
Skipped atom 1315, because occupancy 0.41 <= existing 0.590001
Skipped atom 2246, because occupancy 0.36 <= existing 0.640001
Skipped atom 2248, because occupancy 0.36 <= existing 0.640001
Skipped atom 2250, because occupancy 0.36 <= existing 0.640001
Skipped atom 2252, because occupancy 0.36 <= existing 0.640001
partial PDB gets fragment 60 through 70 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
GLU    3   13
LYS    5   20
ARG    6   32
LEU    7    3
ASP    8    4
ARG    9   27
ILE   10    5
GLN   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    9     11.7780
Cluster     1 =   6   9
2 clashing residues after turn 
Residue clashes:
6-9
cluster 1 has 2 members and 2.200e+01 combinations:
 9  6 
Energy     11.7780
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 2.200e+01 - Sending to search
0.000000 < 11.777960: keeping 
Solved cluster 1: residual clashing  1.32
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1aq0A.136.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1aq0A.138.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1aq0A.138.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1aq0A.138.4.a2m \
	-target T0124 -template 1aq0A \
	-out T0124-1aq0A.138.4 -outdir und
Skipped atom 1309, because occupancy 0.41 <= existing 0.590001
Skipped atom 1311, because occupancy 0.41 <= existing 0.590001
Skipped atom 1313, because occupancy 0.41 <= existing 0.590001
Skipped atom 1315, because occupancy 0.41 <= existing 0.590001
Skipped atom 2246, because occupancy 0.36 <= existing 0.640001
Skipped atom 2248, because occupancy 0.36 <= existing 0.640001
Skipped atom 2250, because occupancy 0.36 <= existing 0.640001
Skipped atom 2252, because occupancy 0.36 <= existing 0.640001
partial PDB gets fragment 60 through 69 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    3   26
ARG    4   32
LEU    5    3
ASP    6    4
ARG    7   27
ILE    8    3
GLN    9   12
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    6.98802
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1aq0A.138.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1aq0A.138.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1aq0A.138.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1aq0A.138.5.a2m \
	-target T0124 -template 1aq0A \
	-out T0124-1aq0A.138.5 -outdir und
Skipped atom 1309, because occupancy 0.41 <= existing 0.590001
Skipped atom 1311, because occupancy 0.41 <= existing 0.590001
Skipped atom 1313, because occupancy 0.41 <= existing 0.590001
Skipped atom 1315, because occupancy 0.41 <= existing 0.590001
Skipped atom 2246, because occupancy 0.36 <= existing 0.640001
Skipped atom 2248, because occupancy 0.36 <= existing 0.640001
Skipped atom 2250, because occupancy 0.36 <= existing 0.640001
Skipped atom 2252, because occupancy 0.36 <= existing 0.640001
partial PDB gets fragment 58 through 68 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    3   26
ARG    4   27
LEU    5    3
ASP    6    4
ARG    7   28
ILE    8    5
GLN    9   12
VAL   10    2
MET   11   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.59593
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1aq0A.138.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1aq0A.140.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1aq0A.140.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1aq0A.140.4.a2m \
	-target T0124 -template 1aq0A \
	-out T0124-1aq0A.140.4 -outdir und
Skipped atom 1309, because occupancy 0.41 <= existing 0.590001
Skipped atom 1311, because occupancy 0.41 <= existing 0.590001
Skipped atom 1313, because occupancy 0.41 <= existing 0.590001
Skipped atom 1315, because occupancy 0.41 <= existing 0.590001
Skipped atom 2246, because occupancy 0.36 <= existing 0.640001
Skipped atom 2248, because occupancy 0.36 <= existing 0.640001
Skipped atom 2250, because occupancy 0.36 <= existing 0.640001
Skipped atom 2252, because occupancy 0.36 <= existing 0.640001
partial PDB gets fragment 58 through 67 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
ARG    2   32
LEU    3    3
ASP    4    4
ARG    5   27
ILE    6    5
GLN    7   13
VAL    8    3
MET    9   10
MET   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    6     19.8522
Cluster     1 =   2   6
2 clashing residues after turn 
Residue clashes:
2-6
cluster 1 has 2 members and 6.480e+02 combinations:
 2  6 
Energy     19.8522
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 6.480e+02 - Sending to search
0.000000 < 19.852188: keeping 
Solved cluster 1: residual clashing  0.33
Still clashes at these sidechain pairs:
Residual clashes =    2.32833
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1aq0A.140.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1aq0A.141.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1aq0A.141.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1aq0A.141.4.a2m \
	-target T0124 -template 1aq0A \
	-out T0124-1aq0A.141.4 -outdir und
Skipped atom 1309, because occupancy 0.41 <= existing 0.590001
Skipped atom 1311, because occupancy 0.41 <= existing 0.590001
Skipped atom 1313, because occupancy 0.41 <= existing 0.590001
Skipped atom 1315, because occupancy 0.41 <= existing 0.590001
Skipped atom 2246, because occupancy 0.36 <= existing 0.640001
Skipped atom 2248, because occupancy 0.36 <= existing 0.640001
Skipped atom 2250, because occupancy 0.36 <= existing 0.640001
Skipped atom 2252, because occupancy 0.36 <= existing 0.640001
partial PDB gets fragment 57 through 66 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   22
ASP    3    5
ARG    4   27
ILE    5    3
GLN    6   12
VAL    7    3
MET    8   12
MET    9   10
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1aq0A.141.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1atzA.10.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1atzA.10.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1atzA.10.1.a2m \
	-target T0124 -template 1atzA \
	-out T0124-1atzA.10.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1atzA-orig.a2m
Writing a2m file: tmp/1atzA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28862


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28862/tmp -alignfile tmp/1atzA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1atzA-orig.a2m (1 sequences, 189 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28862/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28862/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28862/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28862/tmp.a2m (1 sequences, 189 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28862/tmp.mod tmp/1atzA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28862 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1atzA-align.mod
tmp/1atzA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28862/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1atzA-orig.a2m tmp/1atzA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1atzA-align.mod
Running w0.5 tmp/1atzA-orig.a2m tmp/1atzA-align.mod
Running align2model tmp/1atzA-align -i tmp/1atzA-align.mod -db tmp/1atzA-orig.a2m -db tmp/1atzA-pdb.a2m
partial PDB gets fragment 167 through 176 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
GLN    2   14
THR    3    2
SER    5    2
LEU    6    3
GLU    8   15
GLN   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    3.16005
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1atzA.10.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1atzA.7.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1atzA.7.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1atzA.7.5.a2m \
	-target T0124 -template 1atzA \
	-out T0124-1atzA.7.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1atzA-orig.a2m
Writing a2m file: tmp/1atzA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28320


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28320/tmp -alignfile tmp/1atzA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1atzA-orig.a2m (1 sequences, 189 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28320/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28320/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28320/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28320/tmp.a2m (1 sequences, 189 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28320/tmp.mod tmp/1atzA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28320 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1atzA-align.mod
tmp/1atzA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28320/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1atzA-orig.a2m tmp/1atzA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1atzA-align.mod
Running w0.5 tmp/1atzA-orig.a2m tmp/1atzA-align.mod
Running align2model tmp/1atzA-align -i tmp/1atzA-align.mod -db tmp/1atzA-orig.a2m -db tmp/1atzA-pdb.a2m
partial PDB gets fragment 170 through 179 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
PRO    2    2
GLU    3   15
PRO    4    2
GLN    5   13
THR    6    2
SER    8    2
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1atzA.7.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1atzA.8.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1atzA.8.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1atzA.8.0.a2m \
	-target T0124 -template 1atzA \
	-out T0124-1atzA.8.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1atzA-orig.a2m
Writing a2m file: tmp/1atzA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15296


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15296/tmp -alignfile tmp/1atzA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1atzA-orig.a2m (1 sequences, 189 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15296/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15296/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15296/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15296/tmp.a2m (1 sequences, 189 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15296/tmp.mod tmp/1atzA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15296 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1atzA-align.mod
tmp/1atzA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15296/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1atzA-orig.a2m tmp/1atzA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1atzA-align.mod
Running w0.5 tmp/1atzA-orig.a2m tmp/1atzA-align.mod
Running align2model tmp/1atzA-align -i tmp/1atzA-align.mod -db tmp/1atzA-orig.a2m -db tmp/1atzA-pdb.a2m
partial PDB gets fragment 169 through 178 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
GLU    2   15
PRO    3    2
GLN    4   15
THR    5    2
SER    7    2
LEU    8    4
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.46343
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1atzA.8.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1atzA.9.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1atzA.9.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1atzA.9.0.a2m \
	-target T0124 -template 1atzA \
	-out T0124-1atzA.9.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1atzA-orig.a2m
Writing a2m file: tmp/1atzA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27224


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27224/tmp -alignfile tmp/1atzA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1atzA-orig.a2m (1 sequences, 189 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27224/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27224/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27224/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27224/tmp.a2m (1 sequences, 189 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27224/tmp.mod tmp/1atzA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27224 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1atzA-align.mod
tmp/1atzA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27224/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1atzA-orig.a2m tmp/1atzA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1atzA-align.mod
Running w0.5 tmp/1atzA-orig.a2m tmp/1atzA-align.mod
Running align2model tmp/1atzA-align -i tmp/1atzA-align.mod -db tmp/1atzA-orig.a2m -db tmp/1atzA-pdb.a2m
partial PDB gets fragment 168 through 177 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
PRO    2    2
GLN    3   14
SER    6    2
LEU    7    3
GLU    9   11
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 3 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1atzA.9.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1axn.0.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1axn.0.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1axn.0.4.a2m \
	-target T0124 -template 1axn \
	-out T0124-1axn.0.4 -outdir und
Skipped atom 223, because occupancy 0.4 <= existing 0.600001
Skipped atom 225, because occupancy 0.4 <= existing 0.600001
Skipped atom 227, because occupancy 0.4 <= existing 0.600001
Skipped atom 229, because occupancy 0.4 <= existing 0.600001
partial PDB gets fragment 307 through 316 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
MET    2    6
LYS    3   30
GLU    4   12
VAL    5    1
THR    6    2
GLN    7   12
PRO    9    2
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue V 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.17408
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1axn.0.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0b.52.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0b.52.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0b.52.3.a2m \
	-target T0124 -template 1b0b \
	-out T0124-1b0b.52.3 -outdir und
Skipped atom 80, because occupancy 0.5 <= existing 0.500001
Skipped atom 82, because occupancy 0.5 <= existing 0.500001
Skipped atom 84, because occupancy 0.5 <= existing 0.500001
Skipped atom 86, because occupancy 0.5 <= existing 0.500001
Skipped atom 88, because occupancy 0.5 <= existing 0.500001
Skipped atom 94, because occupancy 0.5 <= existing 0.500001
Skipped atom 96, because occupancy 0.5 <= existing 0.500001
Skipped atom 102, because occupancy 0.5 <= existing 0.500001
Skipped atom 104, because occupancy 0.5 <= existing 0.500001
Skipped atom 132, because occupancy 0.5 <= existing 0.500001
Skipped atom 134, because occupancy 0.5 <= existing 0.500001
Skipped atom 145, because occupancy 0.5 <= existing 0.500001
Skipped atom 147, because occupancy 0.5 <= existing 0.500001
Skipped atom 332, because occupancy 0.5 <= existing 0.500001
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 581, because occupancy 0.5 <= existing 0.500001
Skipped atom 583, because occupancy 0.5 <= existing 0.500001
Skipped atom 585, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0b-orig.a2m
Writing a2m file: tmp/1b0b-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27531


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27531/tmp -alignfile tmp/1b0b-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0b-orig.a2m (1 sequences, 143 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27531/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27531/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27531/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27531/tmp.a2m (1 sequences, 143 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27531/tmp.mod tmp/1b0b-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27531 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0b-align.mod
tmp/1b0b-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27531/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0b-orig.a2m tmp/1b0b-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0b-align.mod
Running w0.5 tmp/1b0b-orig.a2m tmp/1b0b-align.mod
Running align2model tmp/1b0b-align -i tmp/1b0b-align.mod -db tmp/1b0b-orig.a2m -db tmp/1b0b-pdb.a2m
partial PDB gets fragment 117 through 126 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
SER    3    2
VAL    4    3
LEU    5    3
PHE    6    3
LEU    7    3
GLU    8   12
PRO    9    2
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0b.52.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.133.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.133.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.133.2.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.133.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27799


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27799/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27799/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27799/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27799/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27799/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27799/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27799 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27799/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 103 through 112 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    5
LYS    2   24
LYS    3   25
LYS    4   24
LEU    5    3
GLU    6   12
LYS    8   27
ARG    9   26
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 5 rotamers of residue I 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    7     20.0000
Cluster     1 =   2   7
2 clashing residues after turn 
Residue clashes:
2-7
cluster 1 has 2 members and 5.000e+01 combinations:
 2  7 
Energy     31.4737
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 5.000e+01 - Sending to search
0.000000 < 31.473680: keeping 
Solved cluster 1: residual clashing 11.68
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.133.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.134.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.134.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.134.2.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.134.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15807


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15807/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15807/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15807/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15807/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15807/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15807/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15807 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15807/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 102 through 111 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   17
LYS    2   26
LYS    3   24
LEU    4    3
GLU    5   12
LYS    7   26
ARG    8   32
LEU    9    3
ASP   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.134.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.136.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.136.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.136.5.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.136.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32645


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32645/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32645/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32645/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32645/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32645/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32645/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32645 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32645/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 100 through 109 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
LEU    2    3
GLU    3   13
LYS    5   24
ARG    6   26
ASP    8    5
ARG    9   27
ILE   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.136.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.147.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.147.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.147.0.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.147.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28081


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28081/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28081/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28081/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28081/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28081/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28081/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28081 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28081/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 89 through 98 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
MET    2   11
MET    3    9
ARG    4   31
SER    5    3
THR    6    2
SER    7    3
ASP    8    5
LYS    9   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue T 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.147.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.149.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.149.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.149.3.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.149.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26898


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26898/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26898/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26898/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26898/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26898/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26898/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26898 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26898/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 85 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
ARG    2   25
SER    3    2
SER    5    3
ASP    6    5
LYS    7   25
GLN   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.149.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.150.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.150.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.150.2.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.150.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-24276


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-24276/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-24276/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-24276/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-24276/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24276/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-24276/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-24276 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24276/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 84 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    2    3
THR    3    1
SER    4    2
ASP    5    5
LYS    6   24
GLN    9   14
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.150.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.151.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.151.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.151.3.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.151.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21289


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21289/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21289/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21289/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21289/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21289/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21289/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21289 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21289/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 83 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
THR    2    2
SER    3    3
ASP    4    5
LYS    5   28
GLN    8   13
GLU    9   14
ARG   10   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.151.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.94.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.94.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.94.3.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.94.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28445


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28445/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28445/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28445/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28445/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28445/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28445/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28445 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28445/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 146 through 156 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   29
ARG    2   32
LYS    3   25
GLU    4   15
GLN    5   15
HIS    6    4
THR    8    2
GLU    9   12
THR   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.26360
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.94.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.95.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.95.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.95.2.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.95.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11508


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11508/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11508/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11508/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11508/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11508/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11508/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-11508 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11508/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 145 through 155 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
LYS    2   27
GLU    3   15
GLN    4   14
HIS    5    3
THR    7    2
GLU    8   12
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.95.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.96.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.96.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.96.5.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.96.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9588


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9588/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9588/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9588/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9588/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9588/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9588/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9588 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9588/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 144 through 154 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   16
GLN    3   13
HIS    4    4
THR    6    2
GLU    7   15
GLN    8   12
THR    9    1
LYS   11   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.94876
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.96.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.97.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.97.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.97.5.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.97.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-16896


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-16896/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-16896/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16896/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16896/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16896/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16896/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16896 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16896/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 143 through 153 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
GLN    2   10
HIS    3    3
THR    5    2
GLU    6   14
GLN    7   13
THR    8    1
LYS   10   24
ILE   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.42776
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.97.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b0uA.98.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b0uA.98.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b0uA.98.5.a2m \
	-target T0124 -template 1b0uA \
	-out T0124-1b0uA.98.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b0uA-orig.a2m
Writing a2m file: tmp/1b0uA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13038


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13038/tmp -alignfile tmp/1b0uA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b0uA-orig.a2m (1 sequences, 262 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13038/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13038/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13038/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13038/tmp.a2m (1 sequences, 262 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13038/tmp.mod tmp/1b0uA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13038 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b0uA-align.mod
tmp/1b0uA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13038/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b0uA-orig.a2m tmp/1b0uA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b0uA-align.mod
Running w0.5 tmp/1b0uA-orig.a2m tmp/1b0uA-align.mod
Running align2model tmp/1b0uA-align -i tmp/1b0uA-align.mod -db tmp/1b0uA-orig.a2m -db tmp/1b0uA-pdb.a2m
partial PDB gets fragment 142 through 152 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
HIS    2    3
THR    4    2
GLU    5   13
GLN    6   15
THR    7    1
LYS    9   24
ILE   10    3
THR   11    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b0uA.98.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b5qA.192.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b5qA.192.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b5qA.192.2.a2m \
	-target T0124 -template 1b5qA \
	-out T0124-1b5qA.192.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b5qA-orig.a2m
Writing a2m file: tmp/1b5qA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14561


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14561/tmp -alignfile tmp/1b5qA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b5qA-orig.a2m (1 sequences, 472 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14561/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14561/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14561/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14561/tmp.a2m (1 sequences, 472 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14561/tmp.mod tmp/1b5qA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14561 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b5qA-align.mod
tmp/1b5qA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14561/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b5qA-orig.a2m tmp/1b5qA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b5qA-align.mod
Running w0.5 tmp/1b5qA-orig.a2m tmp/1b5qA-align.mod
Running align2model tmp/1b5qA-align -i tmp/1b5qA-align.mod -db tmp/1b5qA-orig.a2m -db tmp/1b5qA-pdb.a2m
partial PDB gets fragment 32 through 42 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
GLU    2   11
LYS    3   24
GLN    4   10
GLU    6    8
ASN    7    5
LEU    8    3
ARG    9   25
ILE   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.79363
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b5qA.192.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b5qA.192.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b5qA.192.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b5qA.192.4.a2m \
	-target T0124 -template 1b5qA \
	-out T0124-1b5qA.192.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b5qA-orig.a2m
Writing a2m file: tmp/1b5qA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20220


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20220/tmp -alignfile tmp/1b5qA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b5qA-orig.a2m (1 sequences, 472 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20220/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20220/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20220/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20220/tmp.a2m (1 sequences, 472 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20220/tmp.mod tmp/1b5qA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20220 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b5qA-align.mod
tmp/1b5qA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20220/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b5qA-orig.a2m tmp/1b5qA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b5qA-align.mod
Running w0.5 tmp/1b5qA-orig.a2m tmp/1b5qA-align.mod
Running align2model tmp/1b5qA-align -i tmp/1b5qA-align.mod -db tmp/1b5qA-orig.a2m -db tmp/1b5qA-pdb.a2m
partial PDB gets fragment 34 through 43 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
GLU    2   13
LYS    3   30
GLN    4   14
GLU    6   12
ASN    7    3
LEU    8    2
ARG    9   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b5qA.192.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b5qA.193.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b5qA.193.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b5qA.193.3.a2m \
	-target T0124 -template 1b5qA \
	-out T0124-1b5qA.193.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b5qA-orig.a2m
Writing a2m file: tmp/1b5qA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31565


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31565/tmp -alignfile tmp/1b5qA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b5qA-orig.a2m (1 sequences, 472 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31565/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31565/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31565/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31565/tmp.a2m (1 sequences, 472 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31565/tmp.mod tmp/1b5qA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31565 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b5qA-align.mod
tmp/1b5qA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31565/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b5qA-orig.a2m tmp/1b5qA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b5qA-align.mod
Running w0.5 tmp/1b5qA-orig.a2m tmp/1b5qA-align.mod
Running align2model tmp/1b5qA-align -i tmp/1b5qA-align.mod -db tmp/1b5qA-orig.a2m -db tmp/1b5qA-pdb.a2m
partial PDB gets fragment 31 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    2   19
GLN    3   10
GLU    5   13
ASN    6    4
LEU    7    3
ILE   10    4
GLN   11   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b5qA.193.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b5qA.194.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b5qA.194.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b5qA.194.5.a2m \
	-target T0124 -template 1b5qA \
	-out T0124-1b5qA.194.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b5qA-orig.a2m
Writing a2m file: tmp/1b5qA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25092


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25092/tmp -alignfile tmp/1b5qA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b5qA-orig.a2m (1 sequences, 472 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25092/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25092/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25092/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25092/tmp.a2m (1 sequences, 472 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25092/tmp.mod tmp/1b5qA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25092 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b5qA-align.mod
tmp/1b5qA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25092/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b5qA-orig.a2m tmp/1b5qA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b5qA-align.mod
Running w0.5 tmp/1b5qA-orig.a2m tmp/1b5qA-align.mod
Running align2model tmp/1b5qA-align -i tmp/1b5qA-align.mod -db tmp/1b5qA-orig.a2m -db tmp/1b5qA-pdb.a2m
partial PDB gets fragment 30 through 40 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
GLN    2   12
GLU    4   11
ASN    5    5
LEU    6    2
ARG    7   32
ILE    9    3
GLN   10   12
GLU   11   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    7     46.8822
Cluster     1 =   2   7
2 clashing residues after turn 
Residue clashes:
2-7
cluster 1 has 2 members and 3.600e+01 combinations:
 7  2 
Energy     49.3729
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 3.600e+01 - Sending to search
46.882183 < 49.372868: keeping 
0.000000 < 49.372864: keeping 
Solved cluster 1: residual clashing  0.98
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b5qA.194.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b5qA.196.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b5qA.196.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b5qA.196.3.a2m \
	-target T0124 -template 1b5qA \
	-out T0124-1b5qA.196.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b5qA-orig.a2m
Writing a2m file: tmp/1b5qA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8236


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8236/tmp -alignfile tmp/1b5qA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b5qA-orig.a2m (1 sequences, 472 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8236/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8236/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8236/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8236/tmp.a2m (1 sequences, 472 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8236/tmp.mod tmp/1b5qA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8236 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b5qA-align.mod
tmp/1b5qA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8236/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b5qA-orig.a2m tmp/1b5qA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b5qA-align.mod
Running w0.5 tmp/1b5qA-orig.a2m tmp/1b5qA-align.mod
Running align2model tmp/1b5qA-align -i tmp/1b5qA-align.mod -db tmp/1b5qA-orig.a2m -db tmp/1b5qA-pdb.a2m
partial PDB gets fragment 30 through 39 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   12
ASN    3    5
LEU    4    2
ARG    5   27
ILE    7    5
GLN    8   14
GLU    9   14
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b5qA.196.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b6a.23.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b6a.23.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b6a.23.5.a2m \
	-target T0124 -template 1b6a \
	-out T0124-1b6a.23.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b6a-orig.a2m
Writing a2m file: tmp/1b6a-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32716


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32716/tmp -alignfile tmp/1b6a-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b6a-orig.a2m (1 sequences, 478 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32716/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32716/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32716/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32716/tmp.a2m (1 sequences, 478 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32716/tmp.mod tmp/1b6a-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32716 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b6a-align.mod
tmp/1b6a-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32716/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b6a-orig.a2m tmp/1b6a-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b6a-align.mod
Running w0.5 tmp/1b6a-orig.a2m tmp/1b6a-align.mod
Running align2model tmp/1b6a-align -i tmp/1b6a-align.mod -db tmp/1b6a-orig.a2m -db tmp/1b6a-pdb.a2m
partial PDB gets fragment 324 through 333 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
PHE    2    3
LEU    3    2
LEU    5    4
LEU    6    2
LYS    7   27
LYS    8   27
GLN    9   15
GLU   10   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    9     76.9711
turnclash      3    2    7    0     60.7322
Cluster     1 =   3   7   9
3 clashing residues after turn 
Residue clashes:
3-9
3-7
cluster 1 has 3 members and 1.560e+02 combinations:
 7  3  9 
Energy     81.5853
Searching cluster 3
Combinations for 3 members in cluster 1 OK: 1.560e+02 - Sending to search
51.445244 < 81.585251: keeping 
35.077026 < 52.425945: keeping 
0.000000 < 36.556114: keeping 
Solved cluster 1: residual clashing  1.83
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b6a.23.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b6a.24.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b6a.24.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b6a.24.4.a2m \
	-target T0124 -template 1b6a \
	-out T0124-1b6a.24.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b6a-orig.a2m
Writing a2m file: tmp/1b6a-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6285


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6285/tmp -alignfile tmp/1b6a-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b6a-orig.a2m (1 sequences, 478 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6285/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6285/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6285/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6285/tmp.a2m (1 sequences, 478 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6285/tmp.mod tmp/1b6a-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6285 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b6a-align.mod
tmp/1b6a-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6285/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b6a-orig.a2m tmp/1b6a-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b6a-align.mod
Running w0.5 tmp/1b6a-orig.a2m tmp/1b6a-align.mod
Running align2model tmp/1b6a-align -i tmp/1b6a-align.mod -db tmp/1b6a-orig.a2m -db tmp/1b6a-pdb.a2m
partial PDB gets fragment 330 through 339 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PHE    1    3
LEU    2    3
LYS    3   29
LEU    4    4
LEU    5    3
LYS    6   31
LYS    7   25
GLN    8   12
GLU    9   14
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b6a.24.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b6a.24.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b6a.24.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b6a.24.5.a2m \
	-target T0124 -template 1b6a \
	-out T0124-1b6a.24.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b6a-orig.a2m
Writing a2m file: tmp/1b6a-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26078


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26078/tmp -alignfile tmp/1b6a-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b6a-orig.a2m (1 sequences, 478 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26078/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26078/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26078/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26078/tmp.a2m (1 sequences, 478 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26078/tmp.mod tmp/1b6a-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26078 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b6a-align.mod
tmp/1b6a-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26078/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b6a-orig.a2m tmp/1b6a-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b6a-align.mod
Running w0.5 tmp/1b6a-orig.a2m tmp/1b6a-align.mod
Running align2model tmp/1b6a-align -i tmp/1b6a-align.mod -db tmp/1b6a-orig.a2m -db tmp/1b6a-pdb.a2m
partial PDB gets fragment 323 through 332 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PHE    1    3
LEU    2    3
LYS    3   20
LEU    4    2
LEU    5    3
LYS    6   27
LYS    7   21
GLN    8   13
GLU    9   15
LYS   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.29418
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b6a.24.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b6a.25.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b6a.25.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b6a.25.2.a2m \
	-target T0124 -template 1b6a \
	-out T0124-1b6a.25.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b6a-orig.a2m
Writing a2m file: tmp/1b6a-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28156


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28156/tmp -alignfile tmp/1b6a-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b6a-orig.a2m (1 sequences, 478 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28156/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28156/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28156/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28156/tmp.a2m (1 sequences, 478 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28156/tmp.mod tmp/1b6a-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28156 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b6a-align.mod
tmp/1b6a-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28156/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b6a-orig.a2m tmp/1b6a-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b6a-align.mod
Running w0.5 tmp/1b6a-orig.a2m tmp/1b6a-align.mod
Running align2model tmp/1b6a-align -i tmp/1b6a-align.mod -db tmp/1b6a-orig.a2m -db tmp/1b6a-pdb.a2m
partial PDB gets fragment 329 through 338 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
LYS    2   27
LEU    3    3
LEU    4    5
LYS    5   31
LYS    6   27
GLN    7   15
GLU    8   14
LYS    9   27
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b6a.25.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b6a.26.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b6a.26.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b6a.26.1.a2m \
	-target T0124 -template 1b6a \
	-out T0124-1b6a.26.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b6a-orig.a2m
Writing a2m file: tmp/1b6a-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15704


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15704/tmp -alignfile tmp/1b6a-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b6a-orig.a2m (1 sequences, 478 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15704/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15704/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15704/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15704/tmp.a2m (1 sequences, 478 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15704/tmp.mod tmp/1b6a-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15704 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b6a-align.mod
tmp/1b6a-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15704/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b6a-orig.a2m tmp/1b6a-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b6a-align.mod
Running w0.5 tmp/1b6a-orig.a2m tmp/1b6a-align.mod
Running align2model tmp/1b6a-align -i tmp/1b6a-align.mod -db tmp/1b6a-orig.a2m -db tmp/1b6a-pdb.a2m
partial PDB gets fragment 328 through 337 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
LEU    2    2
LEU    3    3
LYS    4   27
LYS    5   29
GLU    7   15
LYS    8   31
GLU    9   14
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b6a.26.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b6a.27.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b6a.27.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b6a.27.1.a2m \
	-target T0124 -template 1b6a \
	-out T0124-1b6a.27.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b6a-orig.a2m
Writing a2m file: tmp/1b6a-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28116


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28116/tmp -alignfile tmp/1b6a-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b6a-orig.a2m (1 sequences, 478 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28116/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28116/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28116/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28116/tmp.a2m (1 sequences, 478 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28116/tmp.mod tmp/1b6a-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28116 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b6a-align.mod
tmp/1b6a-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28116/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b6a-orig.a2m tmp/1b6a-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b6a-align.mod
Running w0.5 tmp/1b6a-orig.a2m tmp/1b6a-align.mod
Running align2model tmp/1b6a-align -i tmp/1b6a-align.mod -db tmp/1b6a-orig.a2m -db tmp/1b6a-pdb.a2m
partial PDB gets fragment 327 through 336 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LEU    2    3
LYS    3   21
LYS    4   27
GLN    5   14
GLU    6   15
LYS    7   31
GLU    8   15
LEU    9    4
LYS   10   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b6a.27.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b6a.28.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b6a.28.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b6a.28.5.a2m \
	-target T0124 -template 1b6a \
	-out T0124-1b6a.28.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b6a-orig.a2m
Writing a2m file: tmp/1b6a-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7516


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7516/tmp -alignfile tmp/1b6a-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b6a-orig.a2m (1 sequences, 478 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7516/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7516/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7516/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7516/tmp.a2m (1 sequences, 478 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7516/tmp.mod tmp/1b6a-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7516 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b6a-align.mod
tmp/1b6a-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7516/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b6a-orig.a2m tmp/1b6a-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b6a-align.mod
Running w0.5 tmp/1b6a-orig.a2m tmp/1b6a-align.mod
Running align2model tmp/1b6a-align -i tmp/1b6a-align.mod -db tmp/1b6a-orig.a2m -db tmp/1b6a-pdb.a2m
partial PDB gets fragment 326 through 335 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
LYS    3   31
GLN    4   11
GLU    5   12
LYS    6   27
GLU    7   15
LEU    8    4
LYS    9   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b6a.28.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b71A.229.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b71A.229.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b71A.229.5.a2m \
	-target T0124 -template 1b71A \
	-out T0124-1b71A.229.5 -outdir und
Skipped atom 57, because occupancy 0.3 <= existing 0.700001
Skipped atom 59, because occupancy 0.3 <= existing 0.700001
Skipped atom 61, because occupancy 0.3 <= existing 0.700001
Skipped atom 63, because occupancy 0.3 <= existing 0.700001
Skipped atom 65, because occupancy 0.3 <= existing 0.700001
Skipped atom 67, because occupancy 0.3 <= existing 0.700001
Skipped atom 156, because occupancy 0.4 <= existing 0.600001
Skipped atom 158, because occupancy 0.4 <= existing 0.600001
Skipped atom 160, because occupancy 0.4 <= existing 0.600001
Skipped atom 653, because occupancy 0.4 <= existing 0.600001
Skipped atom 655, because occupancy 0.4 <= existing 0.600001
Skipped atom 657, because occupancy 0.4 <= existing 0.600001
Skipped atom 919, because occupancy 0.5 <= existing 0.500001
Skipped atom 921, because occupancy 0.5 <= existing 0.500001
Skipped atom 923, because occupancy 0.5 <= existing 0.500001
Skipped atom 925, because occupancy 0.5 <= existing 0.500001
Skipped atom 1068, because occupancy 0.5 <= existing 0.500001
Skipped atom 1070, because occupancy 0.5 <= existing 0.500001
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1134, because occupancy 0.5 <= existing 0.500001
Skipped atom 1136, because occupancy 0.5 <= existing 0.500001
Skipped atom 1138, because occupancy 0.5 <= existing 0.500001
Skipped atom 1140, because occupancy 0.5 <= existing 0.500001
Skipped atom 1142, because occupancy 0.5 <= existing 0.500001
Skipped atom 1363, because occupancy 0.4 <= existing 0.600001
Skipped atom 1365, because occupancy 0.4 <= existing 0.600001
Skipped atom 1367, because occupancy 0.4 <= existing 0.600001
Skipped atom 1369, because occupancy 0.4 <= existing 0.600001
Skipped atom 1403, because occupancy 0.5 <= existing 0.500001
Skipped atom 1405, because occupancy 0.5 <= existing 0.500001
Skipped atom 1407, because occupancy 0.5 <= existing 0.500001
Skipped atom 1409, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 4 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   11
GLU    2   13
MET    3    8
VAL    4    3
LYS    5   26
ASN    6    4
TYR    7    4
MET    8   10
LYS    9   24
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b71A.229.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.115.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.115.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.115.3.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.115.3 -outdir und
partial PDB gets fragment 132 through 141 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   11
ILE    2    4
GLU    4   13
LEU    5    3
LEU    8    3
LYS    9   26
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.115.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.118.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.118.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.118.1.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.118.1 -outdir und
partial PDB gets fragment 135 through 144 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    2    3
LEU    5    3
LYS    6   26
GLU    7   12
SER    8    3
SER    9    3
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.118.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.119.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.119.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.119.5.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.119.5 -outdir und
partial PDB gets fragment 134 through 143 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   26
LEU    4    3
LYS    5   26
GLU    6   12
GLU    9   13
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.119.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.121.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.121.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.121.3.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.121.3 -outdir und
partial PDB gets fragment 132 through 141 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    3
LYS    3   26
GLU    4   12
SER    5    2
SER    6    3
GLU    7   12
SER    8    3
ASN    9    4
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.121.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.122.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.122.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.122.5.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.122.5 -outdir und
partial PDB gets fragment 129 through 138 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   27
SER    4    3
SER    5    3
GLU    6   12
SER    7    3
ASN    8    5
ILE    9    3
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.122.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.123.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.123.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.123.5.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.123.5 -outdir und
partial PDB gets fragment 128 through 137 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   28
GLU    2   12
SER    3    3
SER    4    2
GLU    5   12
SER    6    3
ASN    7    4
LYS    9   26
ASP   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.123.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.185.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.185.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.185.4.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.185.4 -outdir und
partial PDB gets fragment 51 through 60 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   32
TYR    3    2
GLN    4   11
GLN    5   12
LYS    6   31
LEU    7    3
GLU    8   12
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.185.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.186.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.186.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.186.1.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.186.1 -outdir und
partial PDB gets fragment 50 through 59 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   30
TYR    2    3
GLN    3   15
GLN    4   12
LYS    5   23
LEU    6    3
GLU    7   15
LYS    9   29
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    3.69012
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.186.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.187.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.187.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.187.0.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.187.0 -outdir und
partial PDB gets fragment 49 through 58 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
GLN    2   13
GLN    3   12
LEU    5    4
GLU    6   14
GLU    7   13
LYS    8   31
GLN    9   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.15389
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.187.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.188.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.188.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.188.3.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.188.3 -outdir und
partial PDB gets fragment 48 through 57 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLN    2   12
LYS    3   29
LEU    4    3
GLU    5   15
GLU    6   12
LYS    7   23
GLN    8   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.188.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.189.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.189.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.189.1.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.189.1 -outdir und
partial PDB gets fragment 47 through 56 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
LYS    2   27
LEU    3    3
GLU    4   14
GLU    5   12
GLN    7   17
GLU    9   13
ASN   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.189.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.190.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.190.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.190.4.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.190.4 -outdir und
partial PDB gets fragment 46 through 55 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
LEU    2    3
GLU    3   13
GLU    4   13
LYS    5   29
GLN    6   12
GLU    8   12
ASN    9    6
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.190.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8aA.191.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8aA.191.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8aA.191.3.a2m \
	-target T0124 -template 1b8aA \
	-out T0124-1b8aA.191.3 -outdir und
partial PDB gets fragment 45 through 54 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   12
GLU    3   13
LYS    4   27
GLN    5   12
GLU    7   12
ASN    8    5
LEU    9    2
ARG   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8aA.191.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.148.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.148.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.148.3.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.148.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5694


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5694/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5694/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5694/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5694/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5694/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5694/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5694 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5694/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 68 through 77 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1    7
MET    2    6
ARG    3   25
SER    4    2
THR    5    2
SER    6    3
ASP    7    4
LYS    8   21
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.148.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.149.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.149.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.149.5.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.149.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9089


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9089/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9089/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9089/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9089/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9089/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9089/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9089 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9089/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 67 through 76 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
ARG    2   20
SER    3    3
THR    4    2
SER    5    2
ASP    6    5
LYS    7   26
GLN   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 10 rotamers of residue Q 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.149.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.150.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.150.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.150.5.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.150.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14193


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14193/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14193/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14193/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14193/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14193/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14193/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14193 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14193/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 66 through 75 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
SER    2    2
THR    3    1
SER    4    3
ASP    5    3
LYS    6   24
GLN    9   14
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    6.81189
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.150.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.151.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.151.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.151.4.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.151.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-526


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-526/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-526/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-526/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-526/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-526/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-526/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-526 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-526/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 65 through 74 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
THR    2    2
SER    3    2
ASP    4    4
LYS    5   21
GLN    8   15
GLU    9   12
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 21 rotamers of residue K 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    6     15.6911
Cluster     1 =   3   6
2 clashing residues after turn 
Residue clashes:
3-6
cluster 1 has 2 members and 4.200e+01 combinations:
 3  6 
Energy     84.5902
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 4.200e+01 - Sending to search
12.703336 < 84.590233: keeping 
0.000000 < 46.430508: keeping 
0.000000 < 41.969692: keeping 
Solved cluster 1: residual clashing 35.98
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.151.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.152.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.152.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.152.3.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.152.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27495


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27495/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27495/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27495/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27495/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27495/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27495/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27495 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27495/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 64 through 73 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
SER    2    2
ASP    3    6
LYS    4   30
GLN    7   14
GLU    8   12
ARG    9   32
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.152.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.153.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.153.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.153.4.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.153.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28874


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28874/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28874/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28874/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28874/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28874/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28874/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28874 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28874/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 63 through 72 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
ASP    2    5
LYS    3   25
GLN    6   16
GLU    7   14
ARG    8   25
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 14 rotamers of residue E 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.153.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.154.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.154.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.154.4.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.154.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26184


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26184/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26184/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26184/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26184/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26184/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26184/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26184 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26184/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 62 through 71 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
LYS    2   25
GLN    5   14
GLU    6   15
ARG    7   20
LEU    8    2
LYS    9   27
LYS   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue L 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.154.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.155.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.155.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.155.2.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.155.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29354


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29354/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29354/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29354/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29354/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29354/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29354/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29354 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29354/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 60 through 70 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
GLN    4   11
GLU    5   14
ARG    6   26
LEU    7    3
LYS    8   30
LYS    9   18
GLU   10   14
ILE   11    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 14 rotamers of residue E 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.155.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.155.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.155.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.155.4.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.155.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-24949


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-24949/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-24949/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-24949/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-24949/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24949/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-24949/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-24949 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24949/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 59 through 68 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
GLN    4   12
GLU    5   12
ARG    6   28
LEU    7    2
LYS    8   26
LYS    9   30
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.155.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.155.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.155.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.155.5.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.155.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29816


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29816/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29816/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29816/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29816/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29816/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29816/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29816 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29816/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 61 through 70 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
GLN    4   13
ARG    6   26
LEU    7    3
LYS    8   18
LYS    9   21
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   10     26.7150
Cluster     1 =   6  10
2 clashing residues after turn 
Residue clashes:
6-10
cluster 1 has 2 members and 0.000e+00 combinations:
 6  10 
Energy     28.7997
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
26.714977 < 28.799667: keeping 
Solved cluster 1: residual clashing 28.80
Still clashes at these sidechain pairs:
ires=    6 irot=    1 jres=   10 jrot=    2      26.7150
Residual clashes =   26.71498
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.155.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.156.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.156.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.156.2.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.156.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27556


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27556/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27556/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27556/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27556/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27556/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27556/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27556 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27556/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 59 through 69 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    3   12
GLU    4   12
ARG    5   26
LEU    6    2
LYS    7   25
LYS    8   26
GLU    9   15
ILE   10    2
ASN   11    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 5 rotamers of residue N 12 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.156.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.157.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.157.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.157.3.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.157.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27927


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27927/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27927/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27927/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27927/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27927/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27927/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27927 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27927/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 58 through 68 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    2   12
GLU    3   12
LEU    5    3
LYS    6   25
LYS    7   24
ILE    9    5
ASN   10    4
ASN   11    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   11     20.0000
keepclash     9   10     14.8119
Cluster     1 =   6  11
Cluster     2 =   9  10
4 clashing residues after turn 
Residue clashes:
6-11
9-10
cluster 1 has 2 members and 8.000e+00 combinations:
 6  11 
Energy     20.0000
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 8.000e+00 - Sending to search
2.405997 < 20.000000: keeping 
0.000000 < 3.509064: keeping 
Solved cluster 1: residual clashing  2.14
cluster 2 has 2 members and 0.000e+00 combinations:
 9  10 
Energy     14.8119
Searching cluster 9
Combinations for 2 members in cluster 2 OK: 0.000e+00 - Sending to search
0.000000 < 14.811918: keeping 
Solved cluster 2: residual clashing  0.99
Still clashes at these sidechain pairs:
Residual clashes =    3.06518
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.157.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.158.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.158.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.158.4.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.158.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28712


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28712/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28712/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28712/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28712/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28712/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28712/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28712 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28712/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 57 through 67 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLU    2   12
ARG    3   27
LEU    4    3
LYS    5   25
LYS    6   25
GLU    7   12
ILE    8    5
ASN    9    4
ASN   10    6
SER   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.158.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.159.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.159.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.159.2.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.159.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29608


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29608/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29608/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29608/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29608/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29608/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29608/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29608 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29608/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 56 through 66 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   28
LEU    3    3
LYS    4   26
LYS    5   26
GLU    6   12
ILE    7    3
ASN    8    4
ASN    9    5
SER   10    2
HIS   11    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.159.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.160.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.160.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.160.1.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.160.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28856


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28856/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28856/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28856/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28856/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28856/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28856/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28856 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28856/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 55 through 65 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
LEU    2    3
LYS    3   26
LYS    4   26
GLU    5   12
ILE    6    3
ASN    7    4
SER    9    3
HIS   10    3
ILE   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.160.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.161.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.161.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.161.1.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.161.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-330


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-330/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-330/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-330/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-330/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-330/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-330/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-330 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-330/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 54 through 65 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   26
LYS    3   26
GLU    4   12
ILE    5    3
ASN    6    4
ASN    7    4
SER    8    3
HIS    9    3
ILE   10    2
GLN   11   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.161.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.162.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.162.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.162.1.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.162.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7801


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7801/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7801/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7801/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7801/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7801/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7801/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7801 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7801/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 53 through 64 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   20
LYS    2   26
GLU    3   12
ILE    4    3
ASN    5    4
ASN    6    4
SER    7    3
HIS    8    4
ILE    9    2
GLN   10   12
GLU   11   12
VAL   12    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    9     10.0541
Cluster     1 =   5   9
2 clashing residues after turn 
Residue clashes:
5-9
cluster 1 has 2 members and 8.000e+00 combinations:
 5  9 
Energy     14.4059
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 8.000e+00 - Sending to search
0.000000 < 14.405939: keeping 
Solved cluster 1: residual clashing  0.14
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.162.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.165.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.165.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.165.4.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.165.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22856


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22856/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22856/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22856/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22856/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22856/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22856/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22856 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22856/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 54 through 63 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
ASN    2    4
ASN    3    4
SER    4    3
HIS    5    4
ILE    6    3
GLN    7   12
GLU    8   12
VAL    9    1
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    6     12.5843
Cluster     1 =   2   6
2 clashing residues after turn 
Residue clashes:
2-6
cluster 1 has 2 members and 1.200e+01 combinations:
 2  6 
Energy     14.7964
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 1.200e+01 - Sending to search
0.000000 < 14.796396: keeping 
Solved cluster 1: residual clashing  0.14
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.165.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.186.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.186.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.186.4.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.186.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12563


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12563/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12563/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12563/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12563/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12563/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12563/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12563 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12563/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 37 through 46 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   32
TYR    2    2
GLN    3   15
GLN    4   14
LYS    5   27
LEU    6    3
GLU    7   14
GLU    8   15
LYS    9   27
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    4     71.6677
Cluster     1 =   2   4
2 clashing residues after turn 
Residue clashes:
2-4
cluster 1 has 2 members and 4.500e+02 combinations:
 4  2 
Energy     71.6677
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 4.500e+02 - Sending to search
6.475317 < 71.667717: keeping 
0.000000 < 6.681117: keeping 
Solved cluster 1: residual clashing  0.21
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.186.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.187.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.187.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.187.1.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.187.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17469


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17469/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17469/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17469/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17469/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17469/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17469/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17469 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17469/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 36 through 45 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
GLN    2   15
GLN    3    8
LEU    5    4
GLU    6   13
GLU    7   13
LYS    8   25
GLN    9   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.187.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b8jA.188.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b8jA.188.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b8jA.188.4.a2m \
	-target T0124 -template 1b8jA \
	-out T0124-1b8jA.188.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1b8jA-orig.a2m
Writing a2m file: tmp/1b8jA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29865


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29865/tmp -alignfile tmp/1b8jA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1b8jA-orig.a2m (1 sequences, 449 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29865/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29865/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29865/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29865/tmp.a2m (1 sequences, 449 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29865/tmp.mod tmp/1b8jA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29865 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1b8jA-align.mod
tmp/1b8jA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29865/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1b8jA-orig.a2m tmp/1b8jA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1b8jA-align.mod
Running w0.5 tmp/1b8jA-orig.a2m tmp/1b8jA-align.mod
Running align2model tmp/1b8jA-align -i tmp/1b8jA-align.mod -db tmp/1b8jA-orig.a2m -db tmp/1b8jA-pdb.a2m
partial PDB gets fragment 35 through 44 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLN    2   12
LYS    3   31
LEU    4    2
GLU    5   15
GLU    6   15
LYS    7   27
GLN    8   12
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    6     54.7065
Cluster     1 =   4   6
2 clashing residues after turn 
Residue clashes:
4-6
cluster 1 has 2 members and 4.050e+02 combinations:
 6  4 
Energy     54.7065
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 4.050e+02 - Sending to search
0.000000 < 54.706474: keeping 
Solved cluster 1: residual clashing  0.49
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b8jA.188.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1b9oA.60.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1b9oA.60.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1b9oA.60.5.a2m \
	-target T0124 -template 1b9oA \
	-out T0124-1b9oA.60.5 -outdir und
Skipped atom 15, because occupancy 0.5 <= existing 0.500001
Skipped atom 17, because occupancy 0.5 <= existing 0.500001
Skipped atom 19, because occupancy 0.5 <= existing 0.500001
Skipped atom 21, because occupancy 0.5 <= existing 0.500001
Skipped atom 23, because occupancy 0.5 <= existing 0.500001
Skipped atom 62, because occupancy 0.5 <= existing 0.500001
Skipped atom 64, because occupancy 0.5 <= existing 0.500001
Skipped atom 66, because occupancy 0.5 <= existing 0.500001
Skipped atom 68, because occupancy 0.5 <= existing 0.500001
Skipped atom 70, because occupancy 0.5 <= existing 0.500001
Skipped atom 84, because occupancy 0.4 <= existing 0.600001
Skipped atom 86, because occupancy 0.4 <= existing 0.600001
Skipped atom 219, because occupancy 0.45 <= existing 0.550001
Skipped atom 221, because occupancy 0.45 <= existing 0.550001
Skipped atom 223, because occupancy 0.45 <= existing 0.550001
Skipped atom 225, because occupancy 0.45 <= existing 0.550001
Skipped atom 321, because occupancy 0.5 <= existing 0.500001
Skipped atom 323, because occupancy 0.5 <= existing 0.500001
Skipped atom 325, because occupancy 0.5 <= existing 0.500001
Skipped atom 327, because occupancy 0.5 <= existing 0.500001
Skipped atom 329, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 516, because occupancy 0.5 <= existing 0.500001
Skipped atom 518, because occupancy 0.5 <= existing 0.500001
Skipped atom 520, because occupancy 0.5 <= existing 0.500001
Skipped atom 522, because occupancy 0.5 <= existing 0.500001
Skipped atom 528, because occupancy 0.5 <= existing 0.500001
Skipped atom 530, because occupancy 0.5 <= existing 0.500001
Skipped atom 599, because occupancy 0.5 <= existing 0.500001
Skipped atom 601, because occupancy 0.5 <= existing 0.500001
Skipped atom 603, because occupancy 0.5 <= existing 0.500001
Skipped atom 605, because occupancy 0.5 <= existing 0.500001
Skipped atom 1004, because occupancy 0.5 <= existing 0.500001
Skipped atom 1006, because occupancy 0.5 <= existing 0.500001
Skipped atom 1008, because occupancy 0.5 <= existing 0.500001
Skipped atom 1010, because occupancy 0.5 <= existing 0.500001
Skipped atom 1012, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 79 through 88 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
VAL    2    1
TYR    3    2
PRO    4    2
ARG    5   26
LEU    7    3
SER    9    3
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1b9oA.60.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bdmA.79.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bdmA.79.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bdmA.79.5.a2m \
	-target T0124 -template 1bdmA \
	-out T0124-1bdmA.79.5 -outdir und
Skipped atom 196, because occupancy 0.5 <= existing 0.500001
Skipped atom 198, because occupancy 0.5 <= existing 0.500001
Skipped atom 200, because occupancy 0.5 <= existing 0.500001
Skipped atom 202, because occupancy 0.5 <= existing 0.500001
Skipped atom 204, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bdmA-orig.a2m
Writing a2m file: tmp/1bdmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-972


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-972/tmp -alignfile tmp/1bdmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bdmA-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-972/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-972/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-972/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-972/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-972/tmp.mod tmp/1bdmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-972 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bdmA-align.mod
tmp/1bdmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-972/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bdmA-orig.a2m tmp/1bdmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bdmA-align.mod
Running w0.5 tmp/1bdmA-orig.a2m tmp/1bdmA-align.mod
Running align2model tmp/1bdmA-align -i tmp/1bdmA-align.mod -db tmp/1bdmA-orig.a2m -db tmp/1bdmA-pdb.a2m
partial PDB gets fragment 87 through 91 extending start extending end
sh: 30074 Floating exception
/projects/kestrel/users/karplus/burial/slicer/slicer: ERROR 'scwrl -v -i tmp/T0124-1bdmA.79.5.pdb -o tmp/T0124-1bdmA.79.5.scwrld-pdb -s tmp/T0124-1bdmA.79.5.scwrl-seq' failed.
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bdmA.79.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bdmA.81.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bdmA.81.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bdmA.81.1.a2m \
	-target T0124 -template 1bdmA \
	-out T0124-1bdmA.81.1 -outdir und
Skipped atom 196, because occupancy 0.5 <= existing 0.500001
Skipped atom 198, because occupancy 0.5 <= existing 0.500001
Skipped atom 200, because occupancy 0.5 <= existing 0.500001
Skipped atom 202, because occupancy 0.5 <= existing 0.500001
Skipped atom 204, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bdmA-orig.a2m
Writing a2m file: tmp/1bdmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7309


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7309/tmp -alignfile tmp/1bdmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bdmA-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7309/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7309/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7309/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7309/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7309/tmp.mod tmp/1bdmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7309 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bdmA-align.mod
tmp/1bdmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7309/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bdmA-orig.a2m tmp/1bdmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bdmA-align.mod
Running w0.5 tmp/1bdmA-orig.a2m tmp/1bdmA-align.mod
Running align2model tmp/1bdmA-align -i tmp/1bdmA-align.mod -db tmp/1bdmA-orig.a2m -db tmp/1bdmA-pdb.a2m
partial PDB gets fragment 87 through 91 extending start extending end
sh: 31995 Floating exception
/projects/kestrel/users/karplus/burial/slicer/slicer: ERROR 'scwrl -v -i tmp/T0124-1bdmA.81.1.pdb -o tmp/T0124-1bdmA.81.1.scwrld-pdb -s tmp/T0124-1bdmA.81.1.scwrl-seq' failed.
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bdmA.81.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bdmA.82.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bdmA.82.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bdmA.82.4.a2m \
	-target T0124 -template 1bdmA \
	-out T0124-1bdmA.82.4 -outdir und
Skipped atom 196, because occupancy 0.5 <= existing 0.500001
Skipped atom 198, because occupancy 0.5 <= existing 0.500001
Skipped atom 200, because occupancy 0.5 <= existing 0.500001
Skipped atom 202, because occupancy 0.5 <= existing 0.500001
Skipped atom 204, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bdmA-orig.a2m
Writing a2m file: tmp/1bdmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27102


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27102/tmp -alignfile tmp/1bdmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bdmA-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27102/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27102/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27102/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27102/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27102/tmp.mod tmp/1bdmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27102 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bdmA-align.mod
tmp/1bdmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27102/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bdmA-orig.a2m tmp/1bdmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bdmA-align.mod
Running w0.5 tmp/1bdmA-orig.a2m tmp/1bdmA-align.mod
Running align2model tmp/1bdmA-align -i tmp/1bdmA-align.mod -db tmp/1bdmA-orig.a2m -db tmp/1bdmA-pdb.a2m
partial PDB gets fragment 86 through 91 extending start extending end
sh: 30045 Floating exception
/projects/kestrel/users/karplus/burial/slicer/slicer: ERROR 'scwrl -v -i tmp/T0124-1bdmA.82.4.pdb -o tmp/T0124-1bdmA.82.4.scwrld-pdb -s tmp/T0124-1bdmA.82.4.scwrl-seq' failed.
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bdmA.82.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1be9A.6.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1be9A.6.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1be9A.6.2.a2m \
	-target T0124 -template 1be9A \
	-out T0124-1be9A.6.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1be9A-orig.a2m
Writing a2m file: tmp/1be9A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29180


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29180/tmp -alignfile tmp/1be9A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1be9A-orig.a2m (1 sequences, 119 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29180/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29180/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29180/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29180/tmp.a2m (1 sequences, 119 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29180/tmp.mod tmp/1be9A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29180 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1be9A-align.mod
tmp/1be9A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29180/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1be9A-orig.a2m tmp/1be9A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1be9A-align.mod
Running w0.5 tmp/1be9A-orig.a2m tmp/1be9A-align.mod
Running align2model tmp/1be9A-align -i tmp/1be9A-align.mod -db tmp/1be9A-orig.a2m -db tmp/1be9A-pdb.a2m
partial PDB gets fragment 104 through 113 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
LEU    2    3
PRO    3    2
GLU    4   15
PRO    5    2
GLN    6   13
THR    7    2
SER    9    3
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1be9A.6.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bi5A.230.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bi5A.230.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bi5A.230.5.a2m \
	-target T0124 -template 1bi5A \
	-out T0124-1bi5A.230.5 -outdir und
Skipped atom 692, because occupancy 0.5 <= existing 0.500001
Skipped atom 694, because occupancy 0.5 <= existing 0.500001
Skipped atom 696, because occupancy 0.5 <= existing 0.500001
Skipped atom 698, because occupancy 0.5 <= existing 0.500001
Skipped atom 700, because occupancy 0.5 <= existing 0.500001
Skipped atom 702, because occupancy 0.5 <= existing 0.500001
Skipped atom 704, because occupancy 0.5 <= existing 0.500001
Skipped atom 706, because occupancy 0.5 <= existing 0.500001
Skipped atom 721, because occupancy 0.37 <= existing 0.630001
Skipped atom 723, because occupancy 0.37 <= existing 0.630001
Skipped atom 725, because occupancy 0.37 <= existing 0.630001
Skipped atom 727, because occupancy 0.37 <= existing 0.630001
Skipped atom 729, because occupancy 0.37 <= existing 0.630001
Skipped atom 731, because occupancy 0.37 <= existing 0.630001
Skipped atom 733, because occupancy 0.37 <= existing 0.630001
Skipped atom 735, because occupancy 0.37 <= existing 0.630001
Skipped atom 737, because occupancy 0.37 <= existing 0.630001
Skipped atom 917, because occupancy 0.43 <= existing 0.570001
Skipped atom 919, because occupancy 0.43 <= existing 0.570001
Skipped atom 921, because occupancy 0.43 <= existing 0.570001
Skipped atom 923, because occupancy 0.43 <= existing 0.570001
Skipped atom 925, because occupancy 0.43 <= existing 0.570001
Skipped atom 927, because occupancy 0.43 <= existing 0.570001
Skipped atom 929, because occupancy 0.43 <= existing 0.570001
Skipped atom 931, because occupancy 0.43 <= existing 0.570001
Skipped atom 933, because occupancy 0.43 <= existing 0.570001
Skipped atom 1010, because occupancy 0.46 <= existing 0.540001
Skipped atom 1012, because occupancy 0.46 <= existing 0.540001
Skipped atom 1014, because occupancy 0.46 <= existing 0.540001
Skipped atom 1016, because occupancy 0.46 <= existing 0.540001
Skipped atom 1018, because occupancy 0.46 <= existing 0.540001
Skipped atom 1020, because occupancy 0.46 <= existing 0.540001
Skipped atom 1022, because occupancy 0.46 <= existing 0.540001
Skipped atom 1024, because occupancy 0.46 <= existing 0.540001
Skipped atom 1026, because occupancy 0.46 <= existing 0.540001
Skipped atom 1268, because occupancy 0.35 <= existing 0.650001
Skipped atom 1270, because occupancy 0.35 <= existing 0.650001
Skipped atom 1272, because occupancy 0.35 <= existing 0.650001
Skipped atom 1274, because occupancy 0.35 <= existing 0.650001
Skipped atom 1276, because occupancy 0.35 <= existing 0.650001
Skipped atom 1278, because occupancy 0.35 <= existing 0.650001
Skipped atom 1280, because occupancy 0.35 <= existing 0.650001
Skipped atom 1838, because occupancy 0.41 <= existing 0.590001
Skipped atom 1840, because occupancy 0.41 <= existing 0.590001
Skipped atom 1842, because occupancy 0.41 <= existing 0.590001
Skipped atom 1844, because occupancy 0.41 <= existing 0.590001
Skipped atom 1846, because occupancy 0.41 <= existing 0.590001
Skipped atom 1848, because occupancy 0.41 <= existing 0.590001
Skipped atom 1850, because occupancy 0.41 <= existing 0.590001
Skipped atom 2390, because occupancy 0.29 <= existing 0.710001
Skipped atom 2392, because occupancy 0.29 <= existing 0.710001
Skipped atom 2394, because occupancy 0.29 <= existing 0.710001
Skipped atom 2396, because occupancy 0.29 <= existing 0.710001
Skipped atom 2398, because occupancy 0.29 <= existing 0.710001
Skipped atom 2400, because occupancy 0.29 <= existing 0.710001
Skipped atom 2635, because occupancy 0.32 <= existing 0.680001
Skipped atom 2637, because occupancy 0.32 <= existing 0.680001
Skipped atom 2639, because occupancy 0.32 <= existing 0.680001
Skipped atom 2641, because occupancy 0.32 <= existing 0.680001
Skipped atom 2643, because occupancy 0.32 <= existing 0.680001
Skipped atom 2645, because occupancy 0.32 <= existing 0.680001
Skipped atom 2647, because occupancy 0.32 <= existing 0.680001
Skipped atom 2649, because occupancy 0.32 <= existing 0.680001
Skipped atom 2651, because occupancy 0.32 <= existing 0.680001
Skipped atom 2653, because occupancy 0.32 <= existing 0.680001
Skipped atom 2655, because occupancy 0.32 <= existing 0.680001
Skipped atom 2687, because occupancy 0.34 <= existing 0.660001
Skipped atom 2689, because occupancy 0.34 <= existing 0.660001
Skipped atom 2691, because occupancy 0.34 <= existing 0.660001
Skipped atom 2693, because occupancy 0.34 <= existing 0.660001
Skipped atom 2695, because occupancy 0.34 <= existing 0.660001
Skipped atom 2697, because occupancy 0.34 <= existing 0.660001
Skipped atom 2699, because occupancy 0.34 <= existing 0.660001
Skipped atom 2701, because occupancy 0.34 <= existing 0.660001
Skipped atom 2703, because occupancy 0.34 <= existing 0.660001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bi5A-orig.a2m
Writing a2m file: tmp/1bi5A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29088


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29088/tmp -alignfile tmp/1bi5A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bi5A-orig.a2m (1 sequences, 389 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29088/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29088/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29088/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29088/tmp.a2m (1 sequences, 389 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29088/tmp.mod tmp/1bi5A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29088 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bi5A-align.mod
tmp/1bi5A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29088/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bi5A-orig.a2m tmp/1bi5A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bi5A-align.mod
Running w0.5 tmp/1bi5A-orig.a2m tmp/1bi5A-align.mod
Running align2model tmp/1bi5A-align -i tmp/1bi5A-align.mod -db tmp/1bi5A-orig.a2m -db tmp/1bi5A-pdb.a2m
partial PDB gets fragment 4 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
MET    2   10
VAL    3    1
LYS    4   26
ASN    5    4
TYR    6    3
MET    7   11
LYS    8   20
GLU    9   13
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bi5A.230.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bi5A.231.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bi5A.231.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bi5A.231.5.a2m \
	-target T0124 -template 1bi5A \
	-out T0124-1bi5A.231.5 -outdir und
Skipped atom 692, because occupancy 0.5 <= existing 0.500001
Skipped atom 694, because occupancy 0.5 <= existing 0.500001
Skipped atom 696, because occupancy 0.5 <= existing 0.500001
Skipped atom 698, because occupancy 0.5 <= existing 0.500001
Skipped atom 700, because occupancy 0.5 <= existing 0.500001
Skipped atom 702, because occupancy 0.5 <= existing 0.500001
Skipped atom 704, because occupancy 0.5 <= existing 0.500001
Skipped atom 706, because occupancy 0.5 <= existing 0.500001
Skipped atom 721, because occupancy 0.37 <= existing 0.630001
Skipped atom 723, because occupancy 0.37 <= existing 0.630001
Skipped atom 725, because occupancy 0.37 <= existing 0.630001
Skipped atom 727, because occupancy 0.37 <= existing 0.630001
Skipped atom 729, because occupancy 0.37 <= existing 0.630001
Skipped atom 731, because occupancy 0.37 <= existing 0.630001
Skipped atom 733, because occupancy 0.37 <= existing 0.630001
Skipped atom 735, because occupancy 0.37 <= existing 0.630001
Skipped atom 737, because occupancy 0.37 <= existing 0.630001
Skipped atom 917, because occupancy 0.43 <= existing 0.570001
Skipped atom 919, because occupancy 0.43 <= existing 0.570001
Skipped atom 921, because occupancy 0.43 <= existing 0.570001
Skipped atom 923, because occupancy 0.43 <= existing 0.570001
Skipped atom 925, because occupancy 0.43 <= existing 0.570001
Skipped atom 927, because occupancy 0.43 <= existing 0.570001
Skipped atom 929, because occupancy 0.43 <= existing 0.570001
Skipped atom 931, because occupancy 0.43 <= existing 0.570001
Skipped atom 933, because occupancy 0.43 <= existing 0.570001
Skipped atom 1010, because occupancy 0.46 <= existing 0.540001
Skipped atom 1012, because occupancy 0.46 <= existing 0.540001
Skipped atom 1014, because occupancy 0.46 <= existing 0.540001
Skipped atom 1016, because occupancy 0.46 <= existing 0.540001
Skipped atom 1018, because occupancy 0.46 <= existing 0.540001
Skipped atom 1020, because occupancy 0.46 <= existing 0.540001
Skipped atom 1022, because occupancy 0.46 <= existing 0.540001
Skipped atom 1024, because occupancy 0.46 <= existing 0.540001
Skipped atom 1026, because occupancy 0.46 <= existing 0.540001
Skipped atom 1268, because occupancy 0.35 <= existing 0.650001
Skipped atom 1270, because occupancy 0.35 <= existing 0.650001
Skipped atom 1272, because occupancy 0.35 <= existing 0.650001
Skipped atom 1274, because occupancy 0.35 <= existing 0.650001
Skipped atom 1276, because occupancy 0.35 <= existing 0.650001
Skipped atom 1278, because occupancy 0.35 <= existing 0.650001
Skipped atom 1280, because occupancy 0.35 <= existing 0.650001
Skipped atom 1838, because occupancy 0.41 <= existing 0.590001
Skipped atom 1840, because occupancy 0.41 <= existing 0.590001
Skipped atom 1842, because occupancy 0.41 <= existing 0.590001
Skipped atom 1844, because occupancy 0.41 <= existing 0.590001
Skipped atom 1846, because occupancy 0.41 <= existing 0.590001
Skipped atom 1848, because occupancy 0.41 <= existing 0.590001
Skipped atom 1850, because occupancy 0.41 <= existing 0.590001
Skipped atom 2390, because occupancy 0.29 <= existing 0.710001
Skipped atom 2392, because occupancy 0.29 <= existing 0.710001
Skipped atom 2394, because occupancy 0.29 <= existing 0.710001
Skipped atom 2396, because occupancy 0.29 <= existing 0.710001
Skipped atom 2398, because occupancy 0.29 <= existing 0.710001
Skipped atom 2400, because occupancy 0.29 <= existing 0.710001
Skipped atom 2635, because occupancy 0.32 <= existing 0.680001
Skipped atom 2637, because occupancy 0.32 <= existing 0.680001
Skipped atom 2639, because occupancy 0.32 <= existing 0.680001
Skipped atom 2641, because occupancy 0.32 <= existing 0.680001
Skipped atom 2643, because occupancy 0.32 <= existing 0.680001
Skipped atom 2645, because occupancy 0.32 <= existing 0.680001
Skipped atom 2647, because occupancy 0.32 <= existing 0.680001
Skipped atom 2649, because occupancy 0.32 <= existing 0.680001
Skipped atom 2651, because occupancy 0.32 <= existing 0.680001
Skipped atom 2653, because occupancy 0.32 <= existing 0.680001
Skipped atom 2655, because occupancy 0.32 <= existing 0.680001
Skipped atom 2687, because occupancy 0.34 <= existing 0.660001
Skipped atom 2689, because occupancy 0.34 <= existing 0.660001
Skipped atom 2691, because occupancy 0.34 <= existing 0.660001
Skipped atom 2693, because occupancy 0.34 <= existing 0.660001
Skipped atom 2695, because occupancy 0.34 <= existing 0.660001
Skipped atom 2697, because occupancy 0.34 <= existing 0.660001
Skipped atom 2699, because occupancy 0.34 <= existing 0.660001
Skipped atom 2701, because occupancy 0.34 <= existing 0.660001
Skipped atom 2703, because occupancy 0.34 <= existing 0.660001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bi5A-orig.a2m
Writing a2m file: tmp/1bi5A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30786


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30786/tmp -alignfile tmp/1bi5A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bi5A-orig.a2m (1 sequences, 389 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30786/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30786/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30786/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30786/tmp.a2m (1 sequences, 389 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30786/tmp.mod tmp/1bi5A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30786 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bi5A-align.mod
tmp/1bi5A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30786/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bi5A-orig.a2m tmp/1bi5A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bi5A-align.mod
Running w0.5 tmp/1bi5A-orig.a2m tmp/1bi5A-align.mod
Running align2model tmp/1bi5A-align -i tmp/1bi5A-align.mod -db tmp/1bi5A-orig.a2m -db tmp/1bi5A-pdb.a2m
partial PDB gets fragment 3 through 12 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
VAL    2    1
LYS    3   26
ASN    4    4
TYR    5    3
MET    6   10
LYS    7   29
GLU    8   15
VAL    9    3
PHE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bi5A.231.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bi5A.232.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bi5A.232.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bi5A.232.5.a2m \
	-target T0124 -template 1bi5A \
	-out T0124-1bi5A.232.5 -outdir und
Skipped atom 692, because occupancy 0.5 <= existing 0.500001
Skipped atom 694, because occupancy 0.5 <= existing 0.500001
Skipped atom 696, because occupancy 0.5 <= existing 0.500001
Skipped atom 698, because occupancy 0.5 <= existing 0.500001
Skipped atom 700, because occupancy 0.5 <= existing 0.500001
Skipped atom 702, because occupancy 0.5 <= existing 0.500001
Skipped atom 704, because occupancy 0.5 <= existing 0.500001
Skipped atom 706, because occupancy 0.5 <= existing 0.500001
Skipped atom 721, because occupancy 0.37 <= existing 0.630001
Skipped atom 723, because occupancy 0.37 <= existing 0.630001
Skipped atom 725, because occupancy 0.37 <= existing 0.630001
Skipped atom 727, because occupancy 0.37 <= existing 0.630001
Skipped atom 729, because occupancy 0.37 <= existing 0.630001
Skipped atom 731, because occupancy 0.37 <= existing 0.630001
Skipped atom 733, because occupancy 0.37 <= existing 0.630001
Skipped atom 735, because occupancy 0.37 <= existing 0.630001
Skipped atom 737, because occupancy 0.37 <= existing 0.630001
Skipped atom 917, because occupancy 0.43 <= existing 0.570001
Skipped atom 919, because occupancy 0.43 <= existing 0.570001
Skipped atom 921, because occupancy 0.43 <= existing 0.570001
Skipped atom 923, because occupancy 0.43 <= existing 0.570001
Skipped atom 925, because occupancy 0.43 <= existing 0.570001
Skipped atom 927, because occupancy 0.43 <= existing 0.570001
Skipped atom 929, because occupancy 0.43 <= existing 0.570001
Skipped atom 931, because occupancy 0.43 <= existing 0.570001
Skipped atom 933, because occupancy 0.43 <= existing 0.570001
Skipped atom 1010, because occupancy 0.46 <= existing 0.540001
Skipped atom 1012, because occupancy 0.46 <= existing 0.540001
Skipped atom 1014, because occupancy 0.46 <= existing 0.540001
Skipped atom 1016, because occupancy 0.46 <= existing 0.540001
Skipped atom 1018, because occupancy 0.46 <= existing 0.540001
Skipped atom 1020, because occupancy 0.46 <= existing 0.540001
Skipped atom 1022, because occupancy 0.46 <= existing 0.540001
Skipped atom 1024, because occupancy 0.46 <= existing 0.540001
Skipped atom 1026, because occupancy 0.46 <= existing 0.540001
Skipped atom 1268, because occupancy 0.35 <= existing 0.650001
Skipped atom 1270, because occupancy 0.35 <= existing 0.650001
Skipped atom 1272, because occupancy 0.35 <= existing 0.650001
Skipped atom 1274, because occupancy 0.35 <= existing 0.650001
Skipped atom 1276, because occupancy 0.35 <= existing 0.650001
Skipped atom 1278, because occupancy 0.35 <= existing 0.650001
Skipped atom 1280, because occupancy 0.35 <= existing 0.650001
Skipped atom 1838, because occupancy 0.41 <= existing 0.590001
Skipped atom 1840, because occupancy 0.41 <= existing 0.590001
Skipped atom 1842, because occupancy 0.41 <= existing 0.590001
Skipped atom 1844, because occupancy 0.41 <= existing 0.590001
Skipped atom 1846, because occupancy 0.41 <= existing 0.590001
Skipped atom 1848, because occupancy 0.41 <= existing 0.590001
Skipped atom 1850, because occupancy 0.41 <= existing 0.590001
Skipped atom 2390, because occupancy 0.29 <= existing 0.710001
Skipped atom 2392, because occupancy 0.29 <= existing 0.710001
Skipped atom 2394, because occupancy 0.29 <= existing 0.710001
Skipped atom 2396, because occupancy 0.29 <= existing 0.710001
Skipped atom 2398, because occupancy 0.29 <= existing 0.710001
Skipped atom 2400, because occupancy 0.29 <= existing 0.710001
Skipped atom 2635, because occupancy 0.32 <= existing 0.680001
Skipped atom 2637, because occupancy 0.32 <= existing 0.680001
Skipped atom 2639, because occupancy 0.32 <= existing 0.680001
Skipped atom 2641, because occupancy 0.32 <= existing 0.680001
Skipped atom 2643, because occupancy 0.32 <= existing 0.680001
Skipped atom 2645, because occupancy 0.32 <= existing 0.680001
Skipped atom 2647, because occupancy 0.32 <= existing 0.680001
Skipped atom 2649, because occupancy 0.32 <= existing 0.680001
Skipped atom 2651, because occupancy 0.32 <= existing 0.680001
Skipped atom 2653, because occupancy 0.32 <= existing 0.680001
Skipped atom 2655, because occupancy 0.32 <= existing 0.680001
Skipped atom 2687, because occupancy 0.34 <= existing 0.660001
Skipped atom 2689, because occupancy 0.34 <= existing 0.660001
Skipped atom 2691, because occupancy 0.34 <= existing 0.660001
Skipped atom 2693, because occupancy 0.34 <= existing 0.660001
Skipped atom 2695, because occupancy 0.34 <= existing 0.660001
Skipped atom 2697, because occupancy 0.34 <= existing 0.660001
Skipped atom 2699, because occupancy 0.34 <= existing 0.660001
Skipped atom 2701, because occupancy 0.34 <= existing 0.660001
Skipped atom 2703, because occupancy 0.34 <= existing 0.660001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bi5A-orig.a2m
Writing a2m file: tmp/1bi5A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23152


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23152/tmp -alignfile tmp/1bi5A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bi5A-orig.a2m (1 sequences, 389 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23152/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23152/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23152/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23152/tmp.a2m (1 sequences, 389 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23152/tmp.mod tmp/1bi5A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23152 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bi5A-align.mod
tmp/1bi5A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23152/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bi5A-orig.a2m tmp/1bi5A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bi5A-align.mod
Running w0.5 tmp/1bi5A-orig.a2m tmp/1bi5A-align.mod
Running align2model tmp/1bi5A-align -i tmp/1bi5A-align.mod -db tmp/1bi5A-orig.a2m -db tmp/1bi5A-pdb.a2m
partial PDB gets fragment 2 through 11 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
LYS    2   30
ASN    3    4
TYR    4    3
MET    5   10
LYS    6   26
GLU    7   12
VAL    8    3
PHE    9    3
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bi5A.232.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bk7A.168.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bk7A.168.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bk7A.168.3.a2m \
	-target T0124 -template 1bk7A \
	-out T0124-1bk7A.168.3 -outdir und
partial PDB gets fragment 33 through 42 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
HIS    2    3
ILE    3    2
GLN    4   12
GLU    5   15
VAL    6    2
VAL    7    2
GLN    8    7
THR    9    2
ILE   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    5     41.9034
Cluster     1 =   3   5
2 clashing residues after turn 
Residue clashes:
3-5
cluster 1 has 2 members and 3.300e+01 combinations:
 3  5 
Energy     41.9034
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 3.300e+01 - Sending to search
35.453537 < 41.903366: keeping 
20.000000 < 35.561993: keeping 
0.000000 < 20.114473: keeping 
Solved cluster 1: residual clashing  0.15
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bk7A.168.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bk7A.169.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bk7A.169.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bk7A.169.1.a2m \
	-target T0124 -template 1bk7A \
	-out T0124-1bk7A.169.1 -outdir und
partial PDB gets fragment 32 through 42 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
ILE    2    2
GLN    3   13
GLU    4   12
VAL    5    1
VAL    6    3
THR    8    2
ILE    9    3
LYS   10   15
LEU   11    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.93370
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bk7A.169.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bk7A.170.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bk7A.170.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bk7A.170.0.a2m \
	-target T0124 -template 1bk7A \
	-out T0124-1bk7A.170.0 -outdir und
partial PDB gets fragment 31 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
GLN    2   12
GLU    3   12
VAL    4    2
VAL    5    1
GLN    6   12
THR    7    3
ILE    8    4
LYS    9   21
LEU   10    2
LEU   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bk7A.170.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bk7A.171.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bk7A.171.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bk7A.171.1.a2m \
	-target T0124 -template 1bk7A \
	-out T0124-1bk7A.171.1 -outdir und
partial PDB gets fragment 30 through 40 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLU    2   14
VAL    3    1
VAL    4    2
GLN    5   13
THR    6    1
ILE    7    2
LYS    8   30
LEU    9    2
LEU   10    3
THR   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    3.57481
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bk7A.171.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bk7A.172.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bk7A.172.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bk7A.172.1.a2m \
	-target T0124 -template 1bk7A \
	-out T0124-1bk7A.172.1 -outdir und
partial PDB gets fragment 29 through 39 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
VAL    2    1
VAL    3    1
GLN    4   12
THR    5    2
ILE    6    3
LYS    7   27
LEU    8    3
LEU    9    3
THR   10    2
GLU   11   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bk7A.172.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bk7A.173.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bk7A.173.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bk7A.173.2.a2m \
	-target T0124 -template 1bk7A \
	-out T0124-1bk7A.173.2 -outdir und
partial PDB gets fragment 28 through 38 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
VAL    2    3
GLN    3   12
LYS    6   25
LEU    7    4
THR    9    1
GLU   10   15
LYS   11   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bk7A.173.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bk7A.174.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bk7A.174.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bk7A.174.5.a2m \
	-target T0124 -template 1bk7A \
	-out T0124-1bk7A.174.5 -outdir und
partial PDB gets fragment 27 through 36 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
GLN    2   11
ILE    4    3
LYS    5   22
LEU    6    3
LEU    7    3
THR    8    2
GLU    9   12
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.99032
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bk7A.174.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bkpA.224.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bkpA.224.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bkpA.224.5.a2m \
	-target T0124 -template 1bkpA \
	-out T0124-1bkpA.224.5 -outdir und
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1796, because occupancy 0.5 <= existing 0.500001
Skipped atom 1798, because occupancy 0.5 <= existing 0.500001
Skipped atom 1800, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 6 through 15 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
THR    2    2
VAL    3    2
GLU    4   12
VAL    5    1
GLN    6   12
GLU    7   15
MET    8   10
VAL    9    1
LYS   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bkpA.224.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bkpA.225.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bkpA.225.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bkpA.225.5.a2m \
	-target T0124 -template 1bkpA \
	-out T0124-1bkpA.225.5 -outdir und
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1796, because occupancy 0.5 <= existing 0.500001
Skipped atom 1798, because occupancy 0.5 <= existing 0.500001
Skipped atom 1800, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 5 through 14 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
VAL    2    1
GLU    3   12
VAL    4    2
GLN    5   12
GLU    6   12
MET    7   10
VAL    8    3
LYS    9   26
ASN   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bkpA.225.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bkpA.226.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bkpA.226.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bkpA.226.3.a2m \
	-target T0124 -template 1bkpA \
	-out T0124-1bkpA.226.3 -outdir und
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1796, because occupancy 0.5 <= existing 0.500001
Skipped atom 1798, because occupancy 0.5 <= existing 0.500001
Skipped atom 1800, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 4 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
GLU    2   12
VAL    3    1
GLN    4   12
GLU    5   12
MET    6   10
VAL    7    1
ASN    9    6
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bkpA.226.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bkpA.226.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bkpA.226.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bkpA.226.5.a2m \
	-target T0124 -template 1bkpA \
	-out T0124-1bkpA.226.5 -outdir und
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1796, because occupancy 0.5 <= existing 0.500001
Skipped atom 1798, because occupancy 0.5 <= existing 0.500001
Skipped atom 1800, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 2 through 12 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
GLU    2   12
VAL    3    1
GLU    5   13
MET    6   10
VAL    7    2
LYS    8   26
ASN    9    4
TYR   10    3
MET   11   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    6     10.4203
Cluster     1 =   2   6
2 clashing residues after turn 
Residue clashes:
2-6
cluster 1 has 2 members and 3.300e+01 combinations:
 2  6 
Energy     11.6299
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 3.300e+01 - Sending to search
5.128350 < 11.629881: keeping 
0.673313 < 7.027973: keeping 
0.000000 < 2.688270: keeping 
Solved cluster 1: residual clashing  0.77
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bkpA.226.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bkpA.227.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bkpA.227.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bkpA.227.4.a2m \
	-target T0124 -template 1bkpA \
	-out T0124-1bkpA.227.4 -outdir und
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1796, because occupancy 0.5 <= existing 0.500001
Skipped atom 1798, because occupancy 0.5 <= existing 0.500001
Skipped atom 1800, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 1 through 11 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
VAL    2    3
GLN    3   12
GLU    4   12
MET    5   10
VAL    6    1
LYS    7   26
ASN    8    4
TYR    9    3
MET   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bkpA.227.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bkpA.229.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bkpA.229.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bkpA.229.0.a2m \
	-target T0124 -template 1bkpA \
	-out T0124-1bkpA.229.0 -outdir und
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1796, because occupancy 0.5 <= existing 0.500001
Skipped atom 1798, because occupancy 0.5 <= existing 0.500001
Skipped atom 1800, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 1 through 10 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   15
MET    3   10
VAL    4    1
LYS    5   26
ASN    6    4
TYR    7    3
MET    8   10
LYS    9   26
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bkpA.229.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bkpA.230.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bkpA.230.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bkpA.230.1.a2m \
	-target T0124 -template 1bkpA \
	-out T0124-1bkpA.230.1 -outdir und
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1796, because occupancy 0.5 <= existing 0.500001
Skipped atom 1798, because occupancy 0.5 <= existing 0.500001
Skipped atom 1800, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 0 through 9 extending end
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
GLU    0   15
MET    1   11
VAL    2    3
LYS    3   26
ASN    4    4
TYR    5    3
MET    6   10
LYS    7   26
GLU    8   12
VAL    9    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.87790
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bkpA.230.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bm8.101.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bm8.101.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bm8.101.5.a2m \
	-target T0124 -template 1bm8 \
	-out T0124-1bm8.101.5 -outdir und
partial PDB gets fragment 50 through 59 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    1
GLN    3   15
THR    4    2
LYS    6   29
ILE    7    3
THR    8    1
GLU    9   13
LEU   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bm8.101.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bm8.103.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bm8.103.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bm8.103.1.a2m \
	-target T0124 -template 1bm8 \
	-out T0124-1bm8.103.1 -outdir und
partial PDB gets fragment 52 through 61 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
THR    2    2
LYS    4   29
ILE    5    3
THR    6    1
GLU    7   13
LEU    8    4
ARG   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bm8.103.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bm8.104.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bm8.104.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bm8.104.0.a2m \
	-target T0124 -template 1bm8 \
	-out T0124-1bm8.104.0 -outdir und
partial PDB gets fragment 51 through 60 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
LYS    3   25
ILE    4    3
THR    5    2
GLU    6   12
LEU    7    2
ARG    9   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bm8.104.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bm8.105.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bm8.105.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bm8.105.2.a2m \
	-target T0124 -template 1bm8 \
	-out T0124-1bm8.105.2 -outdir und
partial PDB gets fragment 50 through 59 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   31
ILE    3    4
THR    4    2
GLU    5   12
ARG    8   28
GLU    9   13
LYS   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bm8.105.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bm8.106.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bm8.106.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bm8.106.5.a2m \
	-target T0124 -template 1bm8 \
	-out T0124-1bm8.106.5 -outdir und
partial PDB gets fragment 49 through 58 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
ILE    2    2
THR    3    2
GLU    4   12
LEU    5    3
ARG    7   32
GLU    8   12
LYS    9   19
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bm8.106.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bs0A.11.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bs0A.11.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bs0A.11.4.a2m \
	-target T0124 -template 1bs0A \
	-out T0124-1bs0A.11.4 -outdir und
Skipped atom 2738, because occupancy 0.46 <= existing 0.540001
Skipped atom 2740, because occupancy 0.46 <= existing 0.540001
Skipped atom 2742, because occupancy 0.46 <= existing 0.540001
Skipped atom 2744, because occupancy 0.46 <= existing 0.540001
Skipped atom 2746, because occupancy 0.46 <= existing 0.540001
Skipped atom 2748, because occupancy 0.46 <= existing 0.540001
Skipped atom 2750, because occupancy 0.46 <= existing 0.540001
Skipped atom 2752, because occupancy 0.46 <= existing 0.540001
Skipped atom 2754, because occupancy 0.46 <= existing 0.540001
Skipped atom 2756, because occupancy 0.46 <= existing 0.540001
Skipped atom 2758, because occupancy 0.46 <= existing 0.540001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bs0A-orig.a2m
Writing a2m file: tmp/1bs0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27323


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27323/tmp -alignfile tmp/1bs0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bs0A-orig.a2m (1 sequences, 384 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27323/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27323/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27323/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27323/tmp.a2m (1 sequences, 384 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27323/tmp.mod tmp/1bs0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27323 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bs0A-align.mod
tmp/1bs0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27323/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bs0A-orig.a2m tmp/1bs0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bs0A-align.mod
Running w0.5 tmp/1bs0A-orig.a2m tmp/1bs0A-align.mod
Running align2model tmp/1bs0A-align -i tmp/1bs0A-align.mod -db tmp/1bs0A-orig.a2m -db tmp/1bs0A-pdb.a2m
partial PDB gets fragment 372 through 382 extending start
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
THR    2    2
SER    4    3
LEU    5    3
GLU    7   15
LEU    8    3
GLN    9   13
GLN   10   14
MET   11    8
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bs0A.11.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bs0A.152.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bs0A.152.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bs0A.152.5.a2m \
	-target T0124 -template 1bs0A \
	-out T0124-1bs0A.152.5 -outdir und
Skipped atom 2738, because occupancy 0.46 <= existing 0.540001
Skipped atom 2740, because occupancy 0.46 <= existing 0.540001
Skipped atom 2742, because occupancy 0.46 <= existing 0.540001
Skipped atom 2744, because occupancy 0.46 <= existing 0.540001
Skipped atom 2746, because occupancy 0.46 <= existing 0.540001
Skipped atom 2748, because occupancy 0.46 <= existing 0.540001
Skipped atom 2750, because occupancy 0.46 <= existing 0.540001
Skipped atom 2752, because occupancy 0.46 <= existing 0.540001
Skipped atom 2754, because occupancy 0.46 <= existing 0.540001
Skipped atom 2756, because occupancy 0.46 <= existing 0.540001
Skipped atom 2758, because occupancy 0.46 <= existing 0.540001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bs0A-orig.a2m
Writing a2m file: tmp/1bs0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21407


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21407/tmp -alignfile tmp/1bs0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bs0A-orig.a2m (1 sequences, 384 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21407/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21407/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21407/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21407/tmp.a2m (1 sequences, 384 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21407/tmp.mod tmp/1bs0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21407 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bs0A-align.mod
tmp/1bs0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21407/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bs0A-orig.a2m tmp/1bs0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bs0A-align.mod
Running w0.5 tmp/1bs0A-orig.a2m tmp/1bs0A-align.mod
Running align2model tmp/1bs0A-align -i tmp/1bs0A-align.mod -db tmp/1bs0A-orig.a2m -db tmp/1bs0A-pdb.a2m
partial PDB gets fragment 43 through 52 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    1
ASP    3    4
LYS    4   21
GLN    7   11
GLU    8   14
ARG    9   32
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   10     42.0856
Cluster     1 =   5  10
2 clashing residues after turn 
Residue clashes:
5-10
cluster 1 has 2 members and 3.600e+02 combinations:
 5  10 
Energy     42.0856
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 3.600e+02 - Sending to search
36.256390 < 42.085552: keeping 
14.069943 < 36.763371: keeping 
6.311995 < 14.597365: keeping 
0.000000 < 7.595527: keeping 
0.000000 < 1.725086: keeping 
Solved cluster 1: residual clashing  1.51
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bs0A.152.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bs0A.153.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bs0A.153.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bs0A.153.3.a2m \
	-target T0124 -template 1bs0A \
	-out T0124-1bs0A.153.3 -outdir und
Skipped atom 2738, because occupancy 0.46 <= existing 0.540001
Skipped atom 2740, because occupancy 0.46 <= existing 0.540001
Skipped atom 2742, because occupancy 0.46 <= existing 0.540001
Skipped atom 2744, because occupancy 0.46 <= existing 0.540001
Skipped atom 2746, because occupancy 0.46 <= existing 0.540001
Skipped atom 2748, because occupancy 0.46 <= existing 0.540001
Skipped atom 2750, because occupancy 0.46 <= existing 0.540001
Skipped atom 2752, because occupancy 0.46 <= existing 0.540001
Skipped atom 2754, because occupancy 0.46 <= existing 0.540001
Skipped atom 2756, because occupancy 0.46 <= existing 0.540001
Skipped atom 2758, because occupancy 0.46 <= existing 0.540001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bs0A-orig.a2m
Writing a2m file: tmp/1bs0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14859


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14859/tmp -alignfile tmp/1bs0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bs0A-orig.a2m (1 sequences, 384 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14859/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14859/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14859/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14859/tmp.a2m (1 sequences, 384 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14859/tmp.mod tmp/1bs0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14859 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bs0A-align.mod
tmp/1bs0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14859/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bs0A-orig.a2m tmp/1bs0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bs0A-align.mod
Running w0.5 tmp/1bs0A-orig.a2m tmp/1bs0A-align.mod
Running align2model tmp/1bs0A-align -i tmp/1bs0A-align.mod -db tmp/1bs0A-orig.a2m -db tmp/1bs0A-pdb.a2m
partial PDB gets fragment 42 through 51 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
ASP    2    4
LYS    3   19
GLN    6   15
GLU    7   12
ARG    8   19
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bs0A.153.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bs0A.154.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bs0A.154.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bs0A.154.1.a2m \
	-target T0124 -template 1bs0A \
	-out T0124-1bs0A.154.1 -outdir und
Skipped atom 2738, because occupancy 0.46 <= existing 0.540001
Skipped atom 2740, because occupancy 0.46 <= existing 0.540001
Skipped atom 2742, because occupancy 0.46 <= existing 0.540001
Skipped atom 2744, because occupancy 0.46 <= existing 0.540001
Skipped atom 2746, because occupancy 0.46 <= existing 0.540001
Skipped atom 2748, because occupancy 0.46 <= existing 0.540001
Skipped atom 2750, because occupancy 0.46 <= existing 0.540001
Skipped atom 2752, because occupancy 0.46 <= existing 0.540001
Skipped atom 2754, because occupancy 0.46 <= existing 0.540001
Skipped atom 2756, because occupancy 0.46 <= existing 0.540001
Skipped atom 2758, because occupancy 0.46 <= existing 0.540001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bs0A-orig.a2m
Writing a2m file: tmp/1bs0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21942


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21942/tmp -alignfile tmp/1bs0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bs0A-orig.a2m (1 sequences, 384 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21942/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21942/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21942/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21942/tmp.a2m (1 sequences, 384 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21942/tmp.mod tmp/1bs0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21942 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bs0A-align.mod
tmp/1bs0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21942/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bs0A-orig.a2m tmp/1bs0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bs0A-align.mod
Running w0.5 tmp/1bs0A-orig.a2m tmp/1bs0A-align.mod
Running align2model tmp/1bs0A-align -i tmp/1bs0A-align.mod -db tmp/1bs0A-orig.a2m -db tmp/1bs0A-pdb.a2m
partial PDB gets fragment 41 through 50 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
LYS    2   25
GLN    5    8
GLU    6   12
ARG    7   32
LYS    9   22
LYS   10   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bs0A.154.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bs0A.155.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bs0A.155.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bs0A.155.1.a2m \
	-target T0124 -template 1bs0A \
	-out T0124-1bs0A.155.1 -outdir und
Skipped atom 2738, because occupancy 0.46 <= existing 0.540001
Skipped atom 2740, because occupancy 0.46 <= existing 0.540001
Skipped atom 2742, because occupancy 0.46 <= existing 0.540001
Skipped atom 2744, because occupancy 0.46 <= existing 0.540001
Skipped atom 2746, because occupancy 0.46 <= existing 0.540001
Skipped atom 2748, because occupancy 0.46 <= existing 0.540001
Skipped atom 2750, because occupancy 0.46 <= existing 0.540001
Skipped atom 2752, because occupancy 0.46 <= existing 0.540001
Skipped atom 2754, because occupancy 0.46 <= existing 0.540001
Skipped atom 2756, because occupancy 0.46 <= existing 0.540001
Skipped atom 2758, because occupancy 0.46 <= existing 0.540001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bs0A-orig.a2m
Writing a2m file: tmp/1bs0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3582


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3582/tmp -alignfile tmp/1bs0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bs0A-orig.a2m (1 sequences, 384 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3582/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3582/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3582/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3582/tmp.a2m (1 sequences, 384 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3582/tmp.mod tmp/1bs0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3582 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bs0A-align.mod
tmp/1bs0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3582/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bs0A-orig.a2m tmp/1bs0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bs0A-align.mod
Running w0.5 tmp/1bs0A-orig.a2m tmp/1bs0A-align.mod
Running align2model tmp/1bs0A-align -i tmp/1bs0A-align.mod -db tmp/1bs0A-orig.a2m -db tmp/1bs0A-pdb.a2m
partial PDB gets fragment 40 through 49 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
GLN    4   14
GLU    5   13
ARG    6   20
LEU    7    3
LYS    8   31
LYS    9   23
GLU   10    8
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bs0A.155.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bs0A.156.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bs0A.156.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bs0A.156.1.a2m \
	-target T0124 -template 1bs0A \
	-out T0124-1bs0A.156.1 -outdir und
Skipped atom 2738, because occupancy 0.46 <= existing 0.540001
Skipped atom 2740, because occupancy 0.46 <= existing 0.540001
Skipped atom 2742, because occupancy 0.46 <= existing 0.540001
Skipped atom 2744, because occupancy 0.46 <= existing 0.540001
Skipped atom 2746, because occupancy 0.46 <= existing 0.540001
Skipped atom 2748, because occupancy 0.46 <= existing 0.540001
Skipped atom 2750, because occupancy 0.46 <= existing 0.540001
Skipped atom 2752, because occupancy 0.46 <= existing 0.540001
Skipped atom 2754, because occupancy 0.46 <= existing 0.540001
Skipped atom 2756, because occupancy 0.46 <= existing 0.540001
Skipped atom 2758, because occupancy 0.46 <= existing 0.540001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bs0A-orig.a2m
Writing a2m file: tmp/1bs0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30148


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30148/tmp -alignfile tmp/1bs0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bs0A-orig.a2m (1 sequences, 384 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30148/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30148/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30148/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30148/tmp.a2m (1 sequences, 384 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30148/tmp.mod tmp/1bs0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30148 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bs0A-align.mod
tmp/1bs0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30148/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bs0A-orig.a2m tmp/1bs0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bs0A-align.mod
Running w0.5 tmp/1bs0A-orig.a2m tmp/1bs0A-align.mod
Running align2model tmp/1bs0A-align -i tmp/1bs0A-align.mod -db tmp/1bs0A-orig.a2m -db tmp/1bs0A-pdb.a2m
partial PDB gets fragment 39 through 48 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    3   12
GLU    4   13
ARG    5   21
LEU    6    2
LYS    7   18
LYS    8   21
GLU    9   15
ILE   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bs0A.156.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bs0A.157.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bs0A.157.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bs0A.157.1.a2m \
	-target T0124 -template 1bs0A \
	-out T0124-1bs0A.157.1 -outdir und
Skipped atom 2738, because occupancy 0.46 <= existing 0.540001
Skipped atom 2740, because occupancy 0.46 <= existing 0.540001
Skipped atom 2742, because occupancy 0.46 <= existing 0.540001
Skipped atom 2744, because occupancy 0.46 <= existing 0.540001
Skipped atom 2746, because occupancy 0.46 <= existing 0.540001
Skipped atom 2748, because occupancy 0.46 <= existing 0.540001
Skipped atom 2750, because occupancy 0.46 <= existing 0.540001
Skipped atom 2752, because occupancy 0.46 <= existing 0.540001
Skipped atom 2754, because occupancy 0.46 <= existing 0.540001
Skipped atom 2756, because occupancy 0.46 <= existing 0.540001
Skipped atom 2758, because occupancy 0.46 <= existing 0.540001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bs0A-orig.a2m
Writing a2m file: tmp/1bs0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22433


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22433/tmp -alignfile tmp/1bs0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bs0A-orig.a2m (1 sequences, 384 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22433/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22433/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22433/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22433/tmp.a2m (1 sequences, 384 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22433/tmp.mod tmp/1bs0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22433 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bs0A-align.mod
tmp/1bs0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22433/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bs0A-orig.a2m tmp/1bs0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bs0A-align.mod
Running w0.5 tmp/1bs0A-orig.a2m tmp/1bs0A-align.mod
Running align2model tmp/1bs0A-align -i tmp/1bs0A-align.mod -db tmp/1bs0A-orig.a2m -db tmp/1bs0A-pdb.a2m
partial PDB gets fragment 38 through 47 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    2   14
GLU    3   13
ARG    4   26
LEU    5    2
LYS    6   24
LYS    7   19
GLU    8   12
ILE    9    3
ASN   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bs0A.157.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bs0A.158.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bs0A.158.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bs0A.158.5.a2m \
	-target T0124 -template 1bs0A \
	-out T0124-1bs0A.158.5 -outdir und
Skipped atom 2738, because occupancy 0.46 <= existing 0.540001
Skipped atom 2740, because occupancy 0.46 <= existing 0.540001
Skipped atom 2742, because occupancy 0.46 <= existing 0.540001
Skipped atom 2744, because occupancy 0.46 <= existing 0.540001
Skipped atom 2746, because occupancy 0.46 <= existing 0.540001
Skipped atom 2748, because occupancy 0.46 <= existing 0.540001
Skipped atom 2750, because occupancy 0.46 <= existing 0.540001
Skipped atom 2752, because occupancy 0.46 <= existing 0.540001
Skipped atom 2754, because occupancy 0.46 <= existing 0.540001
Skipped atom 2756, because occupancy 0.46 <= existing 0.540001
Skipped atom 2758, because occupancy 0.46 <= existing 0.540001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1bs0A-orig.a2m
Writing a2m file: tmp/1bs0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29191


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29191/tmp -alignfile tmp/1bs0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1bs0A-orig.a2m (1 sequences, 384 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29191/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29191/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29191/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29191/tmp.a2m (1 sequences, 384 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29191/tmp.mod tmp/1bs0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29191 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1bs0A-align.mod
tmp/1bs0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29191/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1bs0A-orig.a2m tmp/1bs0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1bs0A-align.mod
Running w0.5 tmp/1bs0A-orig.a2m tmp/1bs0A-align.mod
Running align2model tmp/1bs0A-align -i tmp/1bs0A-align.mod -db tmp/1bs0A-orig.a2m -db tmp/1bs0A-pdb.a2m
partial PDB gets fragment 37 through 46 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
GLU    2   12
ARG    3   31
LYS    5   26
LYS    6   25
GLU    7   12
ILE    8    3
ASN   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    9     31.5417
Cluster     1 =   6   9
2 clashing residues after turn 
Residue clashes:
6-9
cluster 1 has 2 members and 4.400e+01 combinations:
 9  6 
Energy     31.5417
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 4.400e+01 - Sending to search
23.189873 < 31.541737: keeping 
1.497269 < 24.381279: keeping 
0.000000 < 2.812417: keeping 
Solved cluster 1: residual clashing  1.51
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bs0A.158.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bu7A.188.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bu7A.188.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bu7A.188.2.a2m \
	-target T0124 -template 1bu7A \
	-out T0124-1bu7A.188.2 -outdir und
partial PDB gets fragment 30 through 39 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLN    2   11
LYS    3   26
LEU    4    3
GLU    6   16
LYS    7   24
GLN    8   15
GLU   10   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7   11     77.5891
Cluster     1 =   7  11
2 clashing residues after turn 
Residue clashes:
7-11
cluster 1 has 2 members and 7.700e+01 combinations:
 7  11 
Energy     78.1853
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 7.700e+01 - Sending to search
1.377039 < 78.185326: keeping 
0.000000 < 2.117445: keeping 
Solved cluster 1: residual clashing  0.87
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bu7A.188.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bu7A.189.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bu7A.189.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bu7A.189.3.a2m \
	-target T0124 -template 1bu7A \
	-out T0124-1bu7A.189.3 -outdir und
partial PDB gets fragment 29 through 38 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
LEU    3    3
GLU    4   12
GLU    5   12
LYS    6   28
GLN    7   11
ASN   10    6
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bu7A.189.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bu7A.190.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bu7A.190.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bu7A.190.3.a2m \
	-target T0124 -template 1bu7A \
	-out T0124-1bu7A.190.3 -outdir und
partial PDB gets fragment 28 through 39 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
LEU    2    3
GLU    3   12
GLU    4   12
LYS    5   26
GLN    6   12
GLU    8   13
ASN    9    6
LEU   10    3
ARG   11   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bu7A.190.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1bu7A.193.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1bu7A.193.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1bu7A.193.4.a2m \
	-target T0124 -template 1bu7A \
	-out T0124-1bu7A.193.4 -outdir und
partial PDB gets fragment 29 through 38 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
GLN    3   12
GLU    5   13
ASN    6    4
ARG    8   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    6.06228
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1bu7A.193.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1byrA.1.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1byrA.1.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1byrA.1.2.a2m \
	-target T0124 -template 1byrA \
	-out T0124-1byrA.1.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1byrA-orig.a2m
Writing a2m file: tmp/1byrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30485


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30485/tmp -alignfile tmp/1byrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1byrA-orig.a2m (1 sequences, 155 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30485/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30485/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30485/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30485/tmp.a2m (1 sequences, 155 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30485/tmp.mod tmp/1byrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30485 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1byrA-align.mod
tmp/1byrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30485/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1byrA-orig.a2m tmp/1byrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1byrA-align.mod
Running w0.5 tmp/1byrA-orig.a2m tmp/1byrA-align.mod
Running align2model tmp/1byrA-align -i tmp/1byrA-align.mod -db tmp/1byrA-orig.a2m -db tmp/1byrA-pdb.a2m
partial PDB gets fragment 144 through 151 extending start
Debugging on !
Reading sequence file
Reading input structure 
9 residues read 
Measuring phi and psi 
Getting chi values
MET    1   12
LYS    2   20
GLU    3   13
VAL    4    1
THR    5    3
GLN    6   12
LEU    7    2
PRO    8    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.60848
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1byrA.1.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1byrA.2.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1byrA.2.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1byrA.2.0.a2m \
	-target T0124 -template 1byrA \
	-out T0124-1byrA.2.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1byrA-orig.a2m
Writing a2m file: tmp/1byrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30439


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30439/tmp -alignfile tmp/1byrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1byrA-orig.a2m (1 sequences, 155 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30439/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30439/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30439/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30439/tmp.a2m (1 sequences, 155 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30439/tmp.mod tmp/1byrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30439 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1byrA-align.mod
tmp/1byrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30439/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1byrA-orig.a2m tmp/1byrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1byrA-align.mod
Running w0.5 tmp/1byrA-orig.a2m tmp/1byrA-align.mod
Running align2model tmp/1byrA-align -i tmp/1byrA-align.mod -db tmp/1byrA-orig.a2m -db tmp/1byrA-pdb.a2m
partial PDB gets fragment 143 through 151 extending start
Debugging on !
Reading sequence file
Reading input structure 
10 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
GLU    2   15
VAL    3    1
THR    4    1
GLN    5   13
LEU    6    3
PRO    7    2
GLU    8   13
PRO    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1byrA.2.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1byrA.3.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1byrA.3.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1byrA.3.0.a2m \
	-target T0124 -template 1byrA \
	-out T0124-1byrA.3.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1byrA-orig.a2m
Writing a2m file: tmp/1byrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22242


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22242/tmp -alignfile tmp/1byrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1byrA-orig.a2m (1 sequences, 155 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22242/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22242/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22242/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22242/tmp.a2m (1 sequences, 155 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22242/tmp.mod tmp/1byrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22242 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1byrA-align.mod
tmp/1byrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22242/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1byrA-orig.a2m tmp/1byrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1byrA-align.mod
Running w0.5 tmp/1byrA-orig.a2m tmp/1byrA-align.mod
Running align2model tmp/1byrA-align -i tmp/1byrA-align.mod -db tmp/1byrA-orig.a2m -db tmp/1byrA-pdb.a2m
partial PDB gets fragment 142 through 151 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
VAL    2    1
THR    3    2
LEU    5    2
PRO    6    2
GLU    7   15
PRO    8    2
GLN    9   10
THR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   10     53.9379
Cluster     1 =   8  10
2 clashing residues after turn 
Residue clashes:
8-10
cluster 1 has 2 members and 1.350e+02 combinations:
 10  8 
Energy     53.9379
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 1.350e+02 - Sending to search
0.000000 < 53.937901: keeping 
Solved cluster 1: residual clashing  0.06
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1byrA.3.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1byrA.4.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1byrA.4.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1byrA.4.3.a2m \
	-target T0124 -template 1byrA \
	-out T0124-1byrA.4.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1byrA-orig.a2m
Writing a2m file: tmp/1byrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18944


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18944/tmp -alignfile tmp/1byrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1byrA-orig.a2m (1 sequences, 155 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18944/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18944/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18944/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18944/tmp.a2m (1 sequences, 155 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18944/tmp.mod tmp/1byrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18944 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1byrA-align.mod
tmp/1byrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18944/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1byrA-orig.a2m tmp/1byrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1byrA-align.mod
Running w0.5 tmp/1byrA-orig.a2m tmp/1byrA-align.mod
Running align2model tmp/1byrA-align -i tmp/1byrA-align.mod -db tmp/1byrA-orig.a2m -db tmp/1byrA-pdb.a2m
partial PDB gets fragment 141 through 151 extending start
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
THR    2    2
GLN    3   11
LEU    4    3
PRO    5    2
GLU    6   13
PRO    7    2
GLN    8   14
THR    9    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1byrA.4.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1c3cA.132.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1c3cA.132.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1c3cA.132.2.a2m \
	-target T0124 -template 1c3cA \
	-out T0124-1c3cA.132.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1c3cA-orig.a2m
Writing a2m file: tmp/1c3cA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18859


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18859/tmp -alignfile tmp/1c3cA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1c3cA-orig.a2m (1 sequences, 429 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18859/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18859/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18859/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18859/tmp.a2m (1 sequences, 429 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18859/tmp.mod tmp/1c3cA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18859 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1c3cA-align.mod
tmp/1c3cA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18859/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1c3cA-orig.a2m tmp/1c3cA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1c3cA-align.mod
Running w0.5 tmp/1c3cA-orig.a2m tmp/1c3cA-align.mod
Running align2model tmp/1c3cA-align -i tmp/1c3cA-align.mod -db tmp/1c3cA-orig.a2m -db tmp/1c3cA-pdb.a2m
partial PDB gets fragment 111 through 120 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
ILE    2    3
LYS    3   26
LYS    4   26
LYS    5   26
LEU    6    3
LYS    9   26
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1c3cA.132.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1c3cA.133.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1c3cA.133.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1c3cA.133.1.a2m \
	-target T0124 -template 1c3cA \
	-out T0124-1c3cA.133.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1c3cA-orig.a2m
Writing a2m file: tmp/1c3cA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-977


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-977/tmp -alignfile tmp/1c3cA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1c3cA-orig.a2m (1 sequences, 429 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-977/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-977/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-977/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-977/tmp.a2m (1 sequences, 429 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-977/tmp.mod tmp/1c3cA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-977 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1c3cA-align.mod
tmp/1c3cA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-977/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1c3cA-orig.a2m tmp/1c3cA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1c3cA-align.mod
Running w0.5 tmp/1c3cA-orig.a2m tmp/1c3cA-align.mod
Running align2model tmp/1c3cA-align -i tmp/1c3cA-align.mod -db tmp/1c3cA-orig.a2m -db tmp/1c3cA-pdb.a2m
partial PDB gets fragment 110 through 119 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   23
LYS    3   26
LYS    4   26
LEU    5    3
GLU    6   12
LYS    8   26
ARG    9   26
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1c3cA.133.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1c3cA.28.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1c3cA.28.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1c3cA.28.3.a2m \
	-target T0124 -template 1c3cA \
	-out T0124-1c3cA.28.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1c3cA-orig.a2m
Writing a2m file: tmp/1c3cA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7413


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7413/tmp -alignfile tmp/1c3cA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1c3cA-orig.a2m (1 sequences, 429 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7413/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7413/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7413/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7413/tmp.a2m (1 sequences, 429 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7413/tmp.mod tmp/1c3cA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7413 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1c3cA-align.mod
tmp/1c3cA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7413/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1c3cA-orig.a2m tmp/1c3cA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1c3cA-align.mod
Running w0.5 tmp/1c3cA-orig.a2m tmp/1c3cA-align.mod
Running align2model tmp/1c3cA-align -i tmp/1c3cA-align.mod -db tmp/1c3cA-orig.a2m -db tmp/1c3cA-pdb.a2m
partial PDB gets fragment 402 through 412 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   28
LYS    3   29
GLN    4    8
GLU    5   12
LYS    6   29
GLU    7   15
LEU    8    3
LYS    9   24
GLU   10   12
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1c3cA.28.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1c3cA.29.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1c3cA.29.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1c3cA.29.1.a2m \
	-target T0124 -template 1c3cA \
	-out T0124-1c3cA.29.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1c3cA-orig.a2m
Writing a2m file: tmp/1c3cA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20045


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20045/tmp -alignfile tmp/1c3cA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1c3cA-orig.a2m (1 sequences, 429 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20045/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20045/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20045/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20045/tmp.a2m (1 sequences, 429 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20045/tmp.mod tmp/1c3cA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20045 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1c3cA-align.mod
tmp/1c3cA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20045/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1c3cA-orig.a2m tmp/1c3cA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1c3cA-align.mod
Running w0.5 tmp/1c3cA-orig.a2m tmp/1c3cA-align.mod
Running align2model tmp/1c3cA-align -i tmp/1c3cA-align.mod -db tmp/1c3cA-orig.a2m -db tmp/1c3cA-pdb.a2m
partial PDB gets fragment 401 through 411 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
LYS    2   30
GLN    3   15
GLU    4   15
LYS    5   18
GLU    6   12
LEU    7    3
LYS    8   30
GLU    9   13
LEU   10    2
GLU   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1c3cA.29.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1c3cA.30.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1c3cA.30.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1c3cA.30.3.a2m \
	-target T0124 -template 1c3cA \
	-out T0124-1c3cA.30.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1c3cA-orig.a2m
Writing a2m file: tmp/1c3cA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20694


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20694/tmp -alignfile tmp/1c3cA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1c3cA-orig.a2m (1 sequences, 429 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20694/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20694/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20694/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20694/tmp.a2m (1 sequences, 429 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20694/tmp.mod tmp/1c3cA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20694 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1c3cA-align.mod
tmp/1c3cA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20694/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1c3cA-orig.a2m tmp/1c3cA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1c3cA-align.mod
Running w0.5 tmp/1c3cA-orig.a2m tmp/1c3cA-align.mod
Running align2model tmp/1c3cA-align -i tmp/1c3cA-align.mod -db tmp/1c3cA-orig.a2m -db tmp/1c3cA-pdb.a2m
partial PDB gets fragment 400 through 410 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
GLN    2   11
LYS    4   25
GLU    5   15
LEU    6    2
LYS    7   24
GLU    8   15
LEU    9    3
GLU   10   13
ARG   11   28
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.58583
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1c3cA.30.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.186.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.186.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.186.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.186.2 -outdir und
partial PDB gets fragment 28 through 37 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
TYR    2    3
GLN    3   12
GLN    4   12
LYS    5   24
LEU    6    3
GLU    7   12
GLU    8   12
LYS    9   26
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    7     23.0177
Cluster     1 =   4   7
2 clashing residues after turn 
Residue clashes:
4-7
cluster 1 has 2 members and 3.300e+01 combinations:
 7  4 
Energy     23.0177
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 3.300e+01 - Sending to search
0.000000 < 23.017738: keeping 
Solved cluster 1: residual clashing  0.07
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.186.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.187.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.187.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.187.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.187.2 -outdir und
partial PDB gets fragment 23 through 32 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    2
GLN    2   15
GLN    3   15
LYS    4   30
LEU    5    3
GLU    7   13
LYS    8   26
GLN    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.187.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.187.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.187.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.187.3.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.187.3 -outdir und
partial PDB gets fragment 27 through 36 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
GLN    2   14
GLN    3   12
LYS    4   26
GLU    6   12
LYS    8   23
GLN    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.187.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.188.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.188.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.188.0.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.188.0 -outdir und
partial PDB gets fragment 26 through 35 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
GLN    2   15
LYS    3   25
LEU    4    3
GLU    5   14
GLU    6   12
LYS    7   24
GLN    8   12
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    9     25.2024
Cluster     1 =   6   9
2 clashing residues after turn 
Residue clashes:
6-9
cluster 1 has 2 members and 1.440e+02 combinations:
 9  6 
Energy     25.2024
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 1.440e+02 - Sending to search
10.230777 < 25.202425: keeping 
2.979828 < 10.355251: keeping 
0.120603 < 3.701369: keeping 
0.000000 < 0.892674: keeping 
0.000000 < 0.883365: keeping 
Solved cluster 1: residual clashing  0.24
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.188.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.188.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.188.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.188.5.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.188.5 -outdir und
partial PDB gets fragment 22 through 31 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    2    6
LYS    3   31
LEU    4    3
GLU    5   15
GLU    6   15
LYS    7   25
GLN    8   12
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.188.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.189.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.189.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.189.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.189.2 -outdir und
partial PDB gets fragment 25 through 34 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   15
LYS    2   30
LEU    3    3
GLU    5   13
LYS    6   26
GLN    7   12
ASN   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.189.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.190.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.190.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.190.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.190.2 -outdir und
partial PDB gets fragment 24 through 33 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   31
LEU    2    3
GLU    3   15
GLU    4   15
LYS    5   25
GLN    6   12
GLU    8   12
ASN    9    4
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.190.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.191.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.191.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.191.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.191.2 -outdir und
partial PDB gets fragment 23 through 32 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    5
GLU    2   15
GLU    3   15
LYS    4   30
GLN    5   15
GLU    7   12
ASN    8    4
ARG   10   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.191.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.192.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.192.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.192.0.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.192.0 -outdir und
partial PDB gets fragment 22 through 31 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
GLU    2   15
LYS    3   31
GLN    4   15
GLU    6   15
ASN    7    5
LEU    8    3
ARG    9   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.192.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.193.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.193.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.193.0.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.193.0 -outdir und
partial PDB gets fragment 21 through 30 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
LYS    2   25
GLN    3   16
GLU    5   15
ASN    6    4
LEU    7    3
ARG    8   27
ILE   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 4 rotamers of residue N 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.193.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.194.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.194.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.194.1.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.194.1 -outdir und
partial PDB gets fragment 20 through 29 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   29
GLU    4   15
ASN    5    5
LEU    6    3
ARG    7   32
ILE    9    4
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 32 rotamers of residue R 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.194.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.195.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.195.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.195.1.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.195.1 -outdir und
partial PDB gets fragment 23 through 32 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   16
GLU    3   15
ASN    4    4
LEU    5    3
ARG    6   27
ILE    8    2
GLN    9   12
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.195.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.195.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.195.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.195.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.195.2 -outdir und
partial PDB gets fragment 19 through 28 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLU    3   13
ASN    4    5
LEU    5    5
ARG    6   32
ILE    8    5
GLN    9   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 5 rotamers of residue I 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.195.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.196.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.196.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.196.0.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.196.0 -outdir und
partial PDB gets fragment 22 through 31 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   15
ASN    3    5
LEU    4    3
ARG    5   32
ILE    7    4
GLN    8   12
GLU    9   14
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.196.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.196.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.196.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.196.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.196.2 -outdir und
partial PDB gets fragment 18 through 27 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   12
ASN    3    5
LEU    4    2
ARG    5   27
ILE    7    4
GLN    8   15
GLU    9   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 15 rotamers of residue E 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.196.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.197.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.197.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.197.0.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.197.0 -outdir und
partial PDB gets fragment 21 through 30 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
ASN    2    5
LEU    3    5
ARG    4   32
ILE    6    5
GLN    7   15
LYS    9   26
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 5 rotamers of residue I 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.197.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.197.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.197.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.197.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.197.2 -outdir und
partial PDB gets fragment 17 through 26 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    2    6
LEU    3    3
ARG    4   32
ILE    6    4
GLN    7   16
GLU    8   15
LYS    9   28
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 15 rotamers of residue E 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.76301
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.197.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.198.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.198.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.198.0.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.198.0 -outdir und
partial PDB gets fragment 20 through 29 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    5
LEU    2    2
ARG    3   27
ILE    5    4
GLN    6   15
GLU    7   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 15 rotamers of residue E 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.198.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.198.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.198.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.198.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.198.2 -outdir und
partial PDB gets fragment 16 through 25 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
LEU    2    3
ARG    3   26
ILE    5    4
GLU    7   12
LYS    8   31
GLU    9   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.198.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.199.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.199.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.199.0.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.199.0 -outdir und
partial PDB gets fragment 19 through 31 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ARG    2   32
ILE    4    4
GLN    5   16
GLU    6   15
LYS    7   28
GLU    8   15
GLN   10   14
LEU   11    3
GLN   12   12
GLN   13   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 15 rotamers of residue E 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.76301
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.199.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.200.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.200.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.200.0.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.200.0 -outdir und
partial PDB gets fragment 18 through 30 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
ILE    3    4
GLU    5   12
LYS    6   31
GLU    7   15
GLN    9   14
LEU   10    3
GLN   11   14
GLN   12   12
GLU   13   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 14 rotamers of residue Q 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.200.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.201.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.201.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.201.0.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.201.0 -outdir und
partial PDB gets fragment 17 through 26 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    2    2
GLN    3   12
GLU    4   15
LYS    5   22
GLU    6   14
GLN    8   15
LEU    9    3
GLN   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 14 rotamers of residue Q 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.201.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.201.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.201.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.201.4.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.201.4 -outdir und
partial PDB gets fragment 23 through 32 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    2    4
GLN    3   15
GLU    4   15
GLN    8   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.201.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.202.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.202.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.202.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.202.2 -outdir und
partial PDB gets fragment 16 through 25 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    4
GLN    2   14
LYS    4   29
GLU    5   15
LEU    8    4
GLN    9   15
GLN   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.202.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.38.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.38.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.38.2.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.38.2 -outdir und
partial PDB gets fragment 456 through 465 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
GLU    2    7
LYS    4   30
LYS    7   29
ARG    8   27
ARG    9   27
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.38.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.39.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.39.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.39.0.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.39.0 -outdir und
partial PDB gets fragment 455 through 464 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
ARG    2   28
LYS    3   19
SER    5    3
LYS    6   29
ARG    7   25
ARG    8   32
GLU    9   12
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.39.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.40.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.40.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.40.1.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.40.1 -outdir und
partial PDB gets fragment 454 through 463 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
LYS    2   26
SER    4    2
LYS    5   32
ARG    6   32
ARG    7   30
GLU    8    9
GLU    9   15
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.40.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.41.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.41.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.41.3.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.41.3 -outdir und
partial PDB gets fragment 453 through 462 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
SER    3    3
LYS    4   24
ARG    5   19
GLU    7   16
GLU    8   14
LEU    9    4
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.11434
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.41.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ccwB.42.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ccwB.42.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ccwB.42.3.a2m \
	-target T0124 -template 1ccwB \
	-out T0124-1ccwB.42.3 -outdir und
partial PDB gets fragment 452 through 461 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    2    3
ARG    4   28
ARG    5   28
GLU    6    7
GLU    7   16
LEU    8    3
LEU    9    3
GLN   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ccwB.42.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ceqA.205.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ceqA.205.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ceqA.205.5.a2m \
	-target T0124 -template 1ceqA \
	-out T0124-1ceqA.205.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ceqA-orig.a2m
Writing a2m file: tmp/1ceqA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5126


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5126/tmp -alignfile tmp/1ceqA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ceqA-orig.a2m (1 sequences, 316 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5126/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5126/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5126/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5126/tmp.a2m (1 sequences, 316 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5126/tmp.mod tmp/1ceqA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5126 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ceqA-align.mod
tmp/1ceqA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5126/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ceqA-orig.a2m tmp/1ceqA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ceqA-align.mod
Running w0.5 tmp/1ceqA-orig.a2m tmp/1ceqA-align.mod
Running align2model tmp/1ceqA-align -i tmp/1ceqA-align.mod -db tmp/1ceqA-orig.a2m -db tmp/1ceqA-pdb.a2m
partial PDB gets fragment 3 through 12 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   11
GLN    4   11
LEU    5    3
GLN    6   12
GLN    7   13
GLU    8   14
VAL   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ceqA.205.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cghA.111.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cghA.111.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cghA.111.2.a2m \
	-target T0124 -template 1cghA \
	-out T0124-1cghA.111.2 -outdir und
partial PDB gets fragment 123 through 133 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   26
GLU    3   10
LYS    4   20
GLN    5   11
ILE    6    5
GLU    8    8
LEU    9    3
LYS   10   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    6     22.6638
Cluster     1 =   4   6
2 clashing residues after turn 
Residue clashes:
4-6
cluster 1 has 2 members and 8.100e+01 combinations:
 4  6 
Energy     22.6638
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 8.100e+01 - Sending to search
5.878429 < 22.663792: keeping 
0.000000 < 5.992898: keeping 
Solved cluster 1: residual clashing  0.64
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cghA.111.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cghA.112.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cghA.112.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cghA.112.0.a2m \
	-target T0124 -template 1cghA \
	-out T0124-1cghA.112.0 -outdir und
partial PDB gets fragment 122 through 132 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   30
GLU    2   14
LYS    3   25
GLN    4   10
ILE    5    2
GLU    7   15
LEU    8    2
LYS    9   29
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cghA.112.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cghA.113.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cghA.113.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cghA.113.0.a2m \
	-target T0124 -template 1cghA \
	-out T0124-1cghA.113.0 -outdir und
partial PDB gets fragment 121 through 131 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
LYS    2   28
GLN    3   14
ILE    4    4
GLU    6   11
LEU    7    3
LYS    8   29
LEU   10    4
LYS   11   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cghA.113.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cghA.114.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cghA.114.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cghA.114.0.a2m \
	-target T0124 -template 1cghA \
	-out T0124-1cghA.114.0 -outdir und
partial PDB gets fragment 120 through 130 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
GLN    2   12
ILE    3    4
GLU    5   14
LEU    6    4
LYS    7   20
LEU    9    3
LYS   10   22
GLU   11    8
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cghA.114.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cghA.115.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cghA.115.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cghA.115.0.a2m \
	-target T0124 -template 1cghA \
	-out T0124-1cghA.115.0 -outdir und
partial PDB gets fragment 119 through 129 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
ILE    2    2
GLU    4   14
LEU    5    3
LYS    6   25
LEU    8    2
LYS    9   22
GLU   10   15
SER   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cghA.115.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cghA.116.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cghA.116.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cghA.116.0.a2m \
	-target T0124 -template 1cghA \
	-out T0124-1cghA.116.0 -outdir und
partial PDB gets fragment 118 through 128 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    5
GLU    3   12
LEU    4    3
LYS    5   28
LEU    7    3
LYS    8   22
GLU    9   11
SER   10    2
SER   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     9   11     10.9973
Cluster     1 =   9  11
2 clashing residues after turn 
Residue clashes:
9-11
cluster 1 has 2 members and 2.600e+01 combinations:
 11  9 
Energy     12.4831
Searching cluster 9
Combinations for 2 members in cluster 1 OK: 2.600e+01 - Sending to search
5.770693 < 12.483071: keeping 
0.000000 < 10.111759: keeping 
Solved cluster 1: residual clashing  1.73
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cghA.116.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cghA.117.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cghA.117.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cghA.117.1.a2m \
	-target T0124 -template 1cghA \
	-out T0124-1cghA.117.1 -outdir und
partial PDB gets fragment 117 through 126 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   15
LEU    3    3
LYS    4   25
LEU    6    3
LYS    7   28
GLU    8   14
SER    9    2
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cghA.117.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cghA.118.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cghA.118.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cghA.118.4.a2m \
	-target T0124 -template 1cghA \
	-out T0124-1cghA.118.4 -outdir und
partial PDB gets fragment 116 through 125 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
LEU    2    3
LYS    3   29
LYS    6   21
GLU    7   14
SER    8    3
SER    9    3
GLU   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cghA.118.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chd.123.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chd.123.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chd.123.0.a2m \
	-target T0124 -template 1chd \
	-out T0124-1chd.123.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1chd-orig.a2m
Writing a2m file: tmp/1chd-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31072


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31072/tmp -alignfile tmp/1chd-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1chd-orig.a2m (1 sequences, 203 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31072/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31072/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31072/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31072/tmp.a2m (1 sequences, 203 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31072/tmp.mod tmp/1chd-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31072 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1chd-align.mod
tmp/1chd-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31072/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1chd-orig.a2m tmp/1chd-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1chd-align.mod
Running w0.5 tmp/1chd-orig.a2m tmp/1chd-align.mod
Running align2model tmp/1chd-align -i tmp/1chd-align.mod -db tmp/1chd-orig.a2m -db tmp/1chd-pdb.a2m
partial PDB gets fragment 87 through 98 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
GLU    2    8
SER    3    2
SER    4    3
GLU    5   14
SER    6    3
ASN    7    5
ILE    8    3
LYS    9   27
ASP   10    6
ILE   11    2
LYS   12   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chd.123.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chd.124.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chd.124.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chd.124.1.a2m \
	-target T0124 -template 1chd \
	-out T0124-1chd.124.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1chd-orig.a2m
Writing a2m file: tmp/1chd-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12321


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12321/tmp -alignfile tmp/1chd-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1chd-orig.a2m (1 sequences, 203 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12321/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12321/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12321/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12321/tmp.a2m (1 sequences, 203 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12321/tmp.mod tmp/1chd-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12321 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1chd-align.mod
tmp/1chd-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12321/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1chd-orig.a2m tmp/1chd-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1chd-align.mod
Running w0.5 tmp/1chd-orig.a2m tmp/1chd-align.mod
Running align2model tmp/1chd-align -i tmp/1chd-align.mod -db tmp/1chd-orig.a2m -db tmp/1chd-pdb.a2m
partial PDB gets fragment 86 through 97 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
SER    3    3
GLU    4   14
SER    5    3
ASN    6    5
ILE    7    4
LYS    8   26
ASP    9    4
LYS   11   20
LYS   12   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chd.124.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chd.125.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chd.125.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chd.125.2.a2m \
	-target T0124 -template 1chd \
	-out T0124-1chd.125.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1chd-orig.a2m
Writing a2m file: tmp/1chd-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15533


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15533/tmp -alignfile tmp/1chd-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1chd-orig.a2m (1 sequences, 203 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15533/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15533/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15533/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15533/tmp.a2m (1 sequences, 203 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15533/tmp.mod tmp/1chd-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15533 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1chd-align.mod
tmp/1chd-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15533/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1chd-orig.a2m tmp/1chd-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1chd-align.mod
Running w0.5 tmp/1chd-orig.a2m tmp/1chd-align.mod
Running align2model tmp/1chd-align -i tmp/1chd-align.mod -db tmp/1chd-orig.a2m -db tmp/1chd-pdb.a2m
partial PDB gets fragment 85 through 96 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
SER    2    2
GLU    3   12
SER    4    2
ASN    5    5
ILE    6    4
LYS    7   27
ASP    8    7
LYS   11   27
LYS   12   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chd.125.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chd.126.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chd.126.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chd.126.2.a2m \
	-target T0124 -template 1chd \
	-out T0124-1chd.126.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1chd-orig.a2m
Writing a2m file: tmp/1chd-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30431


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30431/tmp -alignfile tmp/1chd-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1chd-orig.a2m (1 sequences, 203 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30431/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30431/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30431/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30431/tmp.a2m (1 sequences, 203 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30431/tmp.mod tmp/1chd-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30431 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1chd-align.mod
tmp/1chd-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30431/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1chd-orig.a2m tmp/1chd-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1chd-align.mod
Running w0.5 tmp/1chd-orig.a2m tmp/1chd-align.mod
Running align2model tmp/1chd-align -i tmp/1chd-align.mod -db tmp/1chd-orig.a2m -db tmp/1chd-pdb.a2m
partial PDB gets fragment 84 through 95 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
GLU    2   13
SER    3    2
ASN    4    4
ILE    5    3
LYS    6   25
ASP    7    7
ILE    8    4
LYS    9   29
LYS   10   26
LEU   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chd.126.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chd.127.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chd.127.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chd.127.4.a2m \
	-target T0124 -template 1chd \
	-out T0124-1chd.127.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1chd-orig.a2m
Writing a2m file: tmp/1chd-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26228


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26228/tmp -alignfile tmp/1chd-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1chd-orig.a2m (1 sequences, 203 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26228/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26228/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26228/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26228/tmp.a2m (1 sequences, 203 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26228/tmp.mod tmp/1chd-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26228 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1chd-align.mod
tmp/1chd-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26228/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1chd-orig.a2m tmp/1chd-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1chd-align.mod
Running w0.5 tmp/1chd-orig.a2m tmp/1chd-align.mod
Running align2model tmp/1chd-align -i tmp/1chd-align.mod -db tmp/1chd-orig.a2m -db tmp/1chd-pdb.a2m
partial PDB gets fragment 83 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
SER    2    3
ASN    3    4
ILE    4    3
LYS    5   27
ASP    6    4
ILE    7    4
LYS    8   28
LYS    9   27
LYS   10   29
LEU   11    3
GLU   12   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.81485
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chd.127.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chd.129.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chd.129.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chd.129.4.a2m \
	-target T0124 -template 1chd \
	-out T0124-1chd.129.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1chd-orig.a2m
Writing a2m file: tmp/1chd-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31504


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31504/tmp -alignfile tmp/1chd-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1chd-orig.a2m (1 sequences, 203 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31504/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31504/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31504/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31504/tmp.a2m (1 sequences, 203 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31504/tmp.mod tmp/1chd-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31504 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1chd-align.mod
tmp/1chd-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31504/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1chd-orig.a2m tmp/1chd-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1chd-align.mod
Running w0.5 tmp/1chd-orig.a2m tmp/1chd-align.mod
Running align2model tmp/1chd-align -i tmp/1chd-align.mod -db tmp/1chd-orig.a2m -db tmp/1chd-pdb.a2m
partial PDB gets fragment 83 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    6
ILE    2    4
LYS    3   28
ASP    4    3
ILE    5    2
LYS    6   19
LYS    7   25
LYS    8   28
LEU    9    3
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   11     21.9622
Cluster     1 =   6  11
2 clashing residues after turn 
Residue clashes:
6-11
cluster 1 has 2 members and 2.200e+01 combinations:
 6  11 
Energy     21.9622
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 2.200e+01 - Sending to search
0.000000 < 21.962204: keeping 
Solved cluster 1: residual clashing  0.76
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chd.129.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chd.131.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chd.131.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chd.131.2.a2m \
	-target T0124 -template 1chd \
	-out T0124-1chd.131.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1chd-orig.a2m
Writing a2m file: tmp/1chd-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30396


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30396/tmp -alignfile tmp/1chd-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1chd-orig.a2m (1 sequences, 203 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30396/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30396/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30396/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30396/tmp.a2m (1 sequences, 203 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30396/tmp.mod tmp/1chd-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30396 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1chd-align.mod
tmp/1chd-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30396/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1chd-orig.a2m tmp/1chd-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1chd-align.mod
Running w0.5 tmp/1chd-orig.a2m tmp/1chd-align.mod
Running align2model tmp/1chd-align -i tmp/1chd-align.mod -db tmp/1chd-orig.a2m -db tmp/1chd-pdb.a2m
partial PDB gets fragment 83 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
ASP    2    5
ILE    3    2
LYS    4   27
LYS    5   27
LYS    6   19
LEU    7    2
GLU    8   14
LYS   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.81485
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chd.131.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chd.132.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chd.132.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chd.132.3.a2m \
	-target T0124 -template 1chd \
	-out T0124-1chd.132.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1chd-orig.a2m
Writing a2m file: tmp/1chd-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15312


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15312/tmp -alignfile tmp/1chd-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1chd-orig.a2m (1 sequences, 203 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15312/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15312/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15312/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15312/tmp.a2m (1 sequences, 203 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15312/tmp.mod tmp/1chd-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15312 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1chd-align.mod
tmp/1chd-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15312/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1chd-orig.a2m tmp/1chd-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1chd-align.mod
Running w0.5 tmp/1chd-orig.a2m tmp/1chd-align.mod
Running align2model tmp/1chd-align -i tmp/1chd-align.mod -db tmp/1chd-orig.a2m -db tmp/1chd-pdb.a2m
partial PDB gets fragment 82 through 91 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    5
ILE    2    4
LYS    3   26
LYS    4   28
LYS    5   27
LEU    6    3
GLU    7    8
LYS    9   28
ARG   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chd.132.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chmA.62.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chmA.62.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chmA.62.1.a2m \
	-target T0124 -template 1chmA \
	-out T0124-1chmA.62.1 -outdir und
partial PDB gets fragment 160 through 169 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
PRO    2    2
ARG    3   26
LEU    5    3
ASP    6    4
SER    7    3
GLN    8   12
VAL    9    3
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chmA.62.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chmA.63.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chmA.63.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chmA.63.1.a2m \
	-target T0124 -template 1chmA \
	-out T0124-1chmA.63.1 -outdir und
partial PDB gets fragment 159 through 168 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
ARG    2   32
LEU    4    3
ASP    5    4
SER    6    3
GLN    7   14
VAL    8    2
VAL    9    1
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chmA.63.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chmA.64.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chmA.64.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chmA.64.2.a2m \
	-target T0124 -template 1chmA \
	-out T0124-1chmA.64.2 -outdir und
partial PDB gets fragment 158 through 167 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   29
LEU    3    3
ASP    4    4
SER    5    3
GLN    6   14
VAL    7    1
VAL    8    3
GLU    9   12
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chmA.64.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chmA.65.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chmA.65.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chmA.65.1.a2m \
	-target T0124 -template 1chmA \
	-out T0124-1chmA.65.1 -outdir und
partial PDB gets fragment 157 through 166 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    2
ASP    3    4
SER    4    2
GLN    5   14
VAL    6    1
GLU    8   12
LEU    9    3
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chmA.65.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chmA.66.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chmA.66.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chmA.66.4.a2m \
	-target T0124 -template 1chmA \
	-out T0124-1chmA.66.4 -outdir und
partial PDB gets fragment 156 through 165 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ASP    2    6
GLN    4   13
VAL    5    3
VAL    6    3
GLU    7   12
LEU    8    3
LYS    9   26
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chmA.66.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1chmA.68.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1chmA.68.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1chmA.68.5.a2m \
	-target T0124 -template 1chmA \
	-out T0124-1chmA.68.5 -outdir und
partial PDB gets fragment 154 through 163 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
GLN    2   15
VAL    3    1
VAL    4    2
GLU    5   13
LEU    6    3
LYS    7   30
ARG    9   25
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1chmA.68.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1clxA.111.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1clxA.111.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1clxA.111.5.a2m \
	-target T0124 -template 1clxA \
	-out T0124-1clxA.111.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1clxA-orig.a2m
Writing a2m file: tmp/1clxA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2279


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2279/tmp -alignfile tmp/1clxA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1clxA-orig.a2m (1 sequences, 347 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2279/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2279/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2279/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2279/tmp.a2m (1 sequences, 347 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2279/tmp.mod tmp/1clxA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2279 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1clxA-align.mod
tmp/1clxA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2279/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1clxA-orig.a2m tmp/1clxA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1clxA-align.mod
Running w0.5 tmp/1clxA-orig.a2m tmp/1clxA-align.mod
Running align2model tmp/1clxA-align -i tmp/1clxA-align.mod -db tmp/1clxA-orig.a2m -db tmp/1clxA-pdb.a2m
partial PDB gets fragment 104 through 113 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    3   12
LYS    4   24
GLN    5   11
ILE    6    2
GLU    8   12
LEU    9    3
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1clxA.111.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1clxA.112.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1clxA.112.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1clxA.112.4.a2m \
	-target T0124 -template 1clxA \
	-out T0124-1clxA.112.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1clxA-orig.a2m
Writing a2m file: tmp/1clxA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22508


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22508/tmp -alignfile tmp/1clxA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1clxA-orig.a2m (1 sequences, 347 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22508/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22508/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22508/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22508/tmp.a2m (1 sequences, 347 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22508/tmp.mod tmp/1clxA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22508 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1clxA-align.mod
tmp/1clxA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22508/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1clxA-orig.a2m tmp/1clxA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1clxA-align.mod
Running w0.5 tmp/1clxA-orig.a2m tmp/1clxA-align.mod
Running align2model tmp/1clxA-align -i tmp/1clxA-align.mod -db tmp/1clxA-orig.a2m -db tmp/1clxA-pdb.a2m
partial PDB gets fragment 103 through 113 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
GLU    2   12
LYS    3   26
GLN    4   11
GLU    7   12
LEU    8    3
LYS    9   26
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1clxA.112.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1clxA.113.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1clxA.113.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1clxA.113.4.a2m \
	-target T0124 -template 1clxA \
	-out T0124-1clxA.113.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1clxA-orig.a2m
Writing a2m file: tmp/1clxA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30755


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30755/tmp -alignfile tmp/1clxA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1clxA-orig.a2m (1 sequences, 347 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30755/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30755/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30755/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30755/tmp.a2m (1 sequences, 347 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30755/tmp.mod tmp/1clxA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30755 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1clxA-align.mod
tmp/1clxA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30755/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1clxA-orig.a2m tmp/1clxA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1clxA-align.mod
Running w0.5 tmp/1clxA-orig.a2m tmp/1clxA-align.mod
Running align2model tmp/1clxA-align -i tmp/1clxA-align.mod -db tmp/1clxA-orig.a2m -db tmp/1clxA-pdb.a2m
partial PDB gets fragment 102 through 112 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
LYS    2   24
GLN    3   12
ILE    4    3
GLU    6   12
LEU    7    3
LYS    8   25
LEU   10    3
LYS   11   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.26596
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1clxA.113.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1clxA.82.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1clxA.82.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1clxA.82.1.a2m \
	-target T0124 -template 1clxA \
	-out T0124-1clxA.82.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1clxA-orig.a2m
Writing a2m file: tmp/1clxA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28438


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28438/tmp -alignfile tmp/1clxA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1clxA-orig.a2m (1 sequences, 347 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28438/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28438/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28438/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28438/tmp.a2m (1 sequences, 347 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28438/tmp.mod tmp/1clxA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28438 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1clxA-align.mod
tmp/1clxA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28438/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1clxA-orig.a2m tmp/1clxA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1clxA-align.mod
Running w0.5 tmp/1clxA-orig.a2m tmp/1clxA-align.mod
Running align2model tmp/1clxA-align -i tmp/1clxA-align.mod -db tmp/1clxA-orig.a2m -db tmp/1clxA-pdb.a2m
partial PDB gets fragment 130 through 139 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
HIS    2    4
LEU    3    2
GLU    5   14
GLU    6   15
TYR    7    3
HIS    8    3
ASP    9    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1clxA.82.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1clxA.83.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1clxA.83.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1clxA.83.0.a2m \
	-target T0124 -template 1clxA \
	-out T0124-1clxA.83.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1clxA-orig.a2m
Writing a2m file: tmp/1clxA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30664


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30664/tmp -alignfile tmp/1clxA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1clxA-orig.a2m (1 sequences, 347 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30664/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30664/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30664/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30664/tmp.a2m (1 sequences, 347 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30664/tmp.mod tmp/1clxA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30664 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1clxA-align.mod
tmp/1clxA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30664/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1clxA-orig.a2m tmp/1clxA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1clxA-align.mod
Running w0.5 tmp/1clxA-orig.a2m tmp/1clxA-align.mod
Running align2model tmp/1clxA-align -i tmp/1clxA-align.mod -db tmp/1clxA-orig.a2m -db tmp/1clxA-pdb.a2m
partial PDB gets fragment 129 through 139 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
LEU    2    3
GLU    4   12
GLU    5   13
TYR    6    3
HIS    7    4
ILE   10    4
ARG   11   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue Y 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    7    111.0067
Cluster     1 =   2   7
2 clashing residues after turn 
Residue clashes:
2-7
cluster 1 has 2 members and 3.000e+00 combinations:
 2  7 
Energy    255.8733
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 3.000e+00 - Sending to search
111.006714 < 255.873260: keeping 
0.000000 < 255.873245: keeping 
Solved cluster 1: residual clashing 133.50
Still clashes at these sidechain pairs:
ires=    7 irot=    2 jres=   11 jrot=    1      29.3186
Residual clashes =   29.31862
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1clxA.83.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1clxA.84.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1clxA.84.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1clxA.84.1.a2m \
	-target T0124 -template 1clxA \
	-out T0124-1clxA.84.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1clxA-orig.a2m
Writing a2m file: tmp/1clxA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1514


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1514/tmp -alignfile tmp/1clxA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1clxA-orig.a2m (1 sequences, 347 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1514/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1514/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1514/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1514/tmp.a2m (1 sequences, 347 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1514/tmp.mod tmp/1clxA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1514 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1clxA-align.mod
tmp/1clxA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1514/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1clxA-orig.a2m tmp/1clxA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1clxA-align.mod
Running w0.5 tmp/1clxA-orig.a2m tmp/1clxA-align.mod
Running align2model tmp/1clxA-align -i tmp/1clxA-align.mod -db tmp/1clxA-orig.a2m -db tmp/1clxA-pdb.a2m
partial PDB gets fragment 128 through 138 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    3   13
GLU    4   15
TYR    5    3
HIS    6    4
ILE    9    4
ARG   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.91127
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1clxA.84.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1clxA.85.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1clxA.85.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1clxA.85.1.a2m \
	-target T0124 -template 1clxA \
	-out T0124-1clxA.85.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1clxA-orig.a2m
Writing a2m file: tmp/1clxA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22310


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22310/tmp -alignfile tmp/1clxA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1clxA-orig.a2m (1 sequences, 347 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22310/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22310/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22310/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22310/tmp.a2m (1 sequences, 347 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22310/tmp.mod tmp/1clxA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22310 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1clxA-align.mod
tmp/1clxA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22310/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1clxA-orig.a2m tmp/1clxA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1clxA-align.mod
Running w0.5 tmp/1clxA-orig.a2m tmp/1clxA-align.mod
Running align2model tmp/1clxA-align -i tmp/1clxA-align.mod -db tmp/1clxA-orig.a2m -db tmp/1clxA-pdb.a2m
partial PDB gets fragment 127 through 137 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   14
GLU    3   13
TYR    4    3
HIS    5    4
ASP    6    5
ILE    8    3
ARG    9   32
ARG   10   32
ARG   11   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1clxA.85.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1clxA.86.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1clxA.86.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1clxA.86.4.a2m \
	-target T0124 -template 1clxA \
	-out T0124-1clxA.86.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1clxA-orig.a2m
Writing a2m file: tmp/1clxA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30518


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30518/tmp -alignfile tmp/1clxA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1clxA-orig.a2m (1 sequences, 347 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30518/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30518/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30518/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30518/tmp.a2m (1 sequences, 347 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30518/tmp.mod tmp/1clxA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30518 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1clxA-align.mod
tmp/1clxA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30518/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1clxA-orig.a2m tmp/1clxA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1clxA-align.mod
Running w0.5 tmp/1clxA-orig.a2m tmp/1clxA-align.mod
Running align2model tmp/1clxA-align -i tmp/1clxA-align.mod -db tmp/1clxA-orig.a2m -db tmp/1clxA-pdb.a2m
partial PDB gets fragment 126 through 136 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   14
TYR    3    3
HIS    4    3
ILE    7    3
ARG    8   31
ARG    9   22
ARG   10   32
LYS   11   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   10    101.6864
Cluster     1 =   5  10
2 clashing residues after turn 
Residue clashes:
5-10
cluster 1 has 2 members and 4.500e+01 combinations:
 5  10 
Energy    101.6864
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 4.500e+01 - Sending to search
18.942463 < 101.686424: keeping 
11.685853 < 19.376877: keeping 
0.000000 < 13.319242: keeping 
0.000000 < 2.941193: keeping 
Solved cluster 1: residual clashing  1.21
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1clxA.86.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1clxA.87.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1clxA.87.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1clxA.87.4.a2m \
	-target T0124 -template 1clxA \
	-out T0124-1clxA.87.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1clxA-orig.a2m
Writing a2m file: tmp/1clxA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21713


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21713/tmp -alignfile tmp/1clxA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1clxA-orig.a2m (1 sequences, 347 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21713/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21713/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21713/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21713/tmp.a2m (1 sequences, 347 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21713/tmp.mod tmp/1clxA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21713 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1clxA-align.mod
tmp/1clxA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21713/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1clxA-orig.a2m tmp/1clxA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1clxA-align.mod
Running w0.5 tmp/1clxA-orig.a2m tmp/1clxA-align.mod
Running align2model tmp/1clxA-align -i tmp/1clxA-align.mod -db tmp/1clxA-orig.a2m -db tmp/1clxA-pdb.a2m
partial PDB gets fragment 125 through 135 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
TYR    2    2
HIS    3    3
ASP    4    5
ILE    6    3
ARG    7   32
ARG    8   24
ARG    9   31
LYS   10   23
GLU   11   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    3     41.2636
Cluster     1 =   2   3
2 clashing residues after turn 
Residue clashes:
2-3
cluster 1 has 2 members and 2.400e+01 combinations:
 3  2 
Energy     41.2636
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 2.400e+01 - Sending to search
0.000000 < 41.263565: keeping 
Solved cluster 1: residual clashing  0.10
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1clxA.87.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.101.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.101.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.101.3.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.101.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3623


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3623/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3623/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3623/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3623/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3623/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3623/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3623 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3623/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 105 through 114 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
GLU    2   12
GLN    3   14
THR    4    1
LYS    6   26
ILE    7    3
THR    8    2
GLU    9   12
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.101.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.102.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.102.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.102.1.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.102.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23293


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23293/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23293/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23293/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23293/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23293/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23293/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23293 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23293/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 104 through 113 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
GLN    2   12
THR    3    2
LYS    5   21
ILE    6    3
THR    7    2
GLU    8   12
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.102.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.103.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.103.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.103.2.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.103.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12939


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12939/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12939/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12939/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12939/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12939/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12939/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12939 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12939/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 103 through 112 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   11
THR    2    2
ILE    5    5
THR    6    1
GLU    7   12
LEU    8    3
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.103.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.108.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.108.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.108.4.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.108.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15118


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15118/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15118/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15118/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15118/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15118/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15118/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15118 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15118/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 98 through 107 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    1
GLU    2   15
LEU    3    2
ARG    5   29
LYS    7   29
GLN    8   12
ILE    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.108.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.115.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.115.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.115.4.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.115.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25964


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25964/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25964/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25964/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25964/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25964/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25964/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25964 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25964/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 99 through 108 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   15
ILE    2    2
GLU    4   13
LEU    5    3
LYS    6   26
LEU    8    3
LYS    9   27
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.115.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.116.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.116.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.116.2.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.116.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28123


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28123/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28123/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28123/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28123/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28123/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28123/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28123 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28123/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 98 through 107 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    4
GLU    3   12
LEU    4    3
LYS    5   27
LEU    7    3
LYS    8   26
GLU    9   12
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue L 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.34521
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.116.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.117.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.117.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.117.0.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.117.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7008


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7008/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7008/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7008/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7008/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7008/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7008/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7008 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7008/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 97 through 106 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   13
LEU    3    3
LYS    4   21
LEU    6    3
LYS    7   24
GLU    8   12
SER    9    3
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.117.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.118.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.118.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.118.2.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.118.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29237


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29237/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29237/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29237/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29237/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29237/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29237/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29237 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29237/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 96 through 105 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
LEU    2    3
LYS    3   27
LEU    5    2
LYS    6   31
GLU    7   13
SER    8    3
SER    9    3
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.118.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.119.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.119.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.119.3.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.119.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31968


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31968/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31968/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31968/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31968/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31968/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31968/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31968 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31968/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 95 through 104 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   25
LEU    4    3
LYS    5   29
GLU    6   12
SER    7    3
SER    8    3
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.119.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.120.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.120.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.120.2.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.120.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30992


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30992/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30992/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30992/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30992/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30992/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30992/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30992 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30992/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 94 through 103 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
LEU    3    2
LYS    4   30
GLU    5   13
SER    6    2
SER    7    2
GLU    8   15
SER    9    3
ASN   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.120.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.122.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.122.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.122.3.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.122.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30366


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30366/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30366/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30366/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30366/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30366/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30366/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30366 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30366/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 96 through 105 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
LYS    2   30
GLU    3   13
SER    4    2
SER    5    2
GLU    6   15
SER    7    3
ASN    8    4
ILE    9    3
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue I 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.122.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.128.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.128.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.128.4.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.128.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-19255


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-19255/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-19255/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-19255/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-19255/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19255/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-19255/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-19255 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19255/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 90 through 99 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
ASN    2    4
ILE    3    3
LYS    4   26
ASP    5    5
ILE    6    5
LYS    7   25
LYS    8   30
LYS    9   27
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.128.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.135.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.135.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.135.3.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.135.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-16238


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-16238/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-16238/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16238/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16238/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16238/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16238/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16238 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16238/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 82 through 91 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
LYS    2   20
LEU    3    2
GLU    4   14
LYS    6   21
ARG    7   27
LEU    8    3
ASP    9    5
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.135.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.218.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.218.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.218.4.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.218.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32405


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32405/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32405/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32405/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32405/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32405/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32405/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32405 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32405/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 12 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   16
LYS    3   30
LEU    4    3
LYS    5   26
THR    6    1
LEU    7    3
THR    8    2
VAL    9    2
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.31756
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.218.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.223.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.223.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.223.4.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.223.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23724


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23724/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23724/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23724/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23724/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23724/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23724/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23724 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23724/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 7 through 16 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    3
LEU    2    3
THR    3    2
VAL    4    1
GLU    5   13
VAL    6    3
GLN    7   13
GLU    8   15
MET    9   11
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3   10     55.3122
Cluster     1 =   3  10
2 clashing residues after turn 
Residue clashes:
3-10
cluster 1 has 2 members and 9.000e+00 combinations:
 3  10 
Energy     61.5412
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 9.000e+00 - Sending to search
55.312241 < 61.541168: keeping 
51.545414 < 61.541164: keeping 
10.000000 < 57.803753: keeping 
0.000000 < 15.046160: keeping 
Solved cluster 1: residual clashing  5.22
Still clashes at these sidechain pairs:
Residual clashes =    4.55136
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.223.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.224.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.224.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.224.2.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.224.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32429


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32429/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32429/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32429/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32429/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32429/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32429/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32429 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32429/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 6 through 15 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
THR    2    3
VAL    3    3
GLU    4    9
VAL    5    1
GLN    6    9
MET    8   13
VAL    9    3
LYS   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue V 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4   11     10.1587
keepclash     5    8     19.7134
Cluster     1 =   4  11
Cluster     2 =   5   8
4 clashing residues after turn 
Residue clashes:
4-11
5-8
cluster 1 has 2 members and 5.700e+01 combinations:
 4  11 
Energy     34.4941
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 5.700e+01 - Sending to search
0.000000 < 34.494076: keeping 
0.000000 < 22.248341: keeping 
Solved cluster 1: residual clashing  8.40
cluster 2 has 2 members and 0.000e+00 combinations:
 8  5 
Energy     24.5810
Searching cluster 5
Combinations for 2 members in cluster 2 OK: 0.000e+00 - Sending to search
19.713371 < 24.580994: keeping 
0.000000 < 24.433756: keeping 
Solved cluster 2: residual clashing  2.23
Still clashes at these sidechain pairs:
Residual clashes =    2.22352
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.224.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.225.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.225.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.225.1.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.225.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12161


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12161/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12161/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12161/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12161/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12161/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12161/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12161 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12161/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 5 through 14 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    1
VAL    2    3
GLU    3   15
VAL    4    3
GLN    5   11
GLU    6   15
MET    7    8
VAL    8    3
LYS    9   24
ASN   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue V 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 5 rotamers of residue N 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2   11     20.0000
Cluster     1 =   2  11
2 clashing residues after turn 
Residue clashes:
2-11
cluster 1 has 2 members and 5.000e+00 combinations:
 2  11 
Energy     68.1189
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 5.000e+00 - Sending to search
9.753729 < 68.118912: keeping 
Solved cluster 1: residual clashing 40.80
Still clashes at these sidechain pairs:
Residual clashes =   28.66304
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.225.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.226.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.226.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.226.1.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.226.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-143


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-143/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-143/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-143/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-143/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-143/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-143/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-143 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-143/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 4 through 14 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
GLU    2   14
VAL    3    3
GLN    4   15
GLU    5   15
MET    6    5
VAL    7    1
LYS    8   17
ASN    9    6
TYR   10    3
MET   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 12 rotamers of residue M 12 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7   10     31.2781
Cluster     1 =   7  10
2 clashing residues after turn 
Residue clashes:
7-10
cluster 1 has 2 members and 9.000e+00 combinations:
 10  7 
Energy     31.6611
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 9.000e+00 - Sending to search
25.894598 < 31.661139: keeping 
6.847869 < 26.445930: keeping 
5.853419 < 8.696593: keeping 
Solved cluster 1: residual clashing  7.87
Still clashes at these sidechain pairs:
Residual clashes =    5.85342
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.226.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.227.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.227.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.227.1.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.227.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31352


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31352/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31352/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31352/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31352/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31352/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31352/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31352 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31352/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 3 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   16
VAL    2    2
GLN    3   10
GLU    4   15
MET    5   12
VAL    6    3
LYS    7   24
ASN    8    5
TYR    9    3
MET   10   10
LYS   11   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   11     12.0468
Cluster     1 =   8  11
2 clashing residues after turn 
Residue clashes:
8-11
cluster 1 has 2 members and 1.440e+02 combinations:
 11  8 
Energy     12.0468
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 1.440e+02 - Sending to search
10.929399 < 12.046836: keeping 
9.273569 < 12.008638: keeping 
0.000000 < 10.546728: keeping 
0.000000 < 2.070289: keeping 
Solved cluster 1: residual clashing  1.93
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.227.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.228.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.228.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.228.2.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.228.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31401


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31401/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31401/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31401/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31401/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31401/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31401/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31401 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31401/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 2 through 12 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
GLN    2   15
GLU    3   16
MET    4    8
VAL    5    3
LYS    6   31
ASN    7    5
TYR    8    1
MET    9   10
LYS   10   17
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue Y 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     9   12     44.3617
Cluster     1 =   9  12
2 clashing residues after turn 
Residue clashes:
9-12
cluster 1 has 2 members and 0.000e+00 combinations:
 9  12 
Energy    153.8713
Searching cluster 9
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
Solved cluster 1: residual clashing 153.87
Still clashes at these sidechain pairs:
ires=    9 irot=    1 jres=   12 jrot=    1      44.3617
Residual clashes =   44.36167
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.228.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.229.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.229.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.229.1.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.229.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30717


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30717/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30717/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30717/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30717/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30717/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30717/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30717 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30717/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 1 through 11 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   15
GLU    2   14
MET    3   13
VAL    4    2
LYS    5   21
ASN    6    6
TYR    7    3
MET    8   12
LYS    9   24
GLU   10   15
VAL   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.13888
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.229.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.230.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.230.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.230.0.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.230.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31514


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31514/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31514/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31514/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31514/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31514/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31514/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31514 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31514/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 0 through 11
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    0   12
MET    1    9
VAL    2    3
LYS    3   31
ASN    4    5
TYR    5    3
MET    6   10
LYS    7   31
GLU    8   15
VAL    9    2
PHE   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.230.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.231.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.231.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.231.0.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.231.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32401


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32401/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32401/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32401/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32401/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32401/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32401/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32401 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32401/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 0 through 9
Debugging on !
Reading sequence file
Reading input structure 
10 residues read 
Measuring phi and psi 
Getting chi values
VAL    0    1
LYS    1   28
ASN    2    5
TYR    3    3
MET    4   10
LYS    5   21
GLU    6   15
VAL    7    3
PHE    8    4
PRO    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.231.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cmnA.232.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cmnA.232.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cmnA.232.1.a2m \
	-target T0124 -template 1cmnA \
	-out T0124-1cmnA.232.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cmnA-orig.a2m
Writing a2m file: tmp/1cmnA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22308


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22308/tmp -alignfile tmp/1cmnA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cmnA-orig.a2m (1 sequences, 402 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22308/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22308/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22308/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22308/tmp.a2m (1 sequences, 402 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22308/tmp.mod tmp/1cmnA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22308 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cmnA-align.mod
tmp/1cmnA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22308/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cmnA-orig.a2m tmp/1cmnA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cmnA-align.mod
Running w0.5 tmp/1cmnA-orig.a2m tmp/1cmnA-align.mod
Running align2model tmp/1cmnA-align -i tmp/1cmnA-align.mod -db tmp/1cmnA-orig.a2m -db tmp/1cmnA-pdb.a2m
partial PDB gets fragment 0 through 7
Debugging on !
Reading sequence file
Reading input structure 
8 residues read 
Measuring phi and psi 
Getting chi values
ASN    0    5
TYR    1    3
MET    2   11
LYS    3   31
GLU    4   16
VAL    5    2
PHE    6    3
PRO    7    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cmnA.232.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cqxA.128.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cqxA.128.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cqxA.128.5.a2m \
	-target T0124 -template 1cqxA \
	-out T0124-1cqxA.128.5 -outdir und
partial PDB gets fragment 57 through 66 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
ASN    2    4
ILE    3    2
LYS    4   24
ASP    5    4
ILE    6    3
LYS    7   25
LYS    8   26
LYS    9   30
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cqxA.128.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cqxA.129.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cqxA.129.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cqxA.129.1.a2m \
	-target T0124 -template 1cqxA \
	-out T0124-1cqxA.129.1 -outdir und
partial PDB gets fragment 56 through 65 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
ILE    2    3
LYS    3   26
ASP    4    4
ILE    5    2
LYS    6   30
LYS    7   26
LYS    8   25
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cqxA.129.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cqxA.130.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cqxA.130.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cqxA.130.1.a2m \
	-target T0124 -template 1cqxA \
	-out T0124-1cqxA.130.1 -outdir und
partial PDB gets fragment 55 through 64 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
LYS    2   26
ASP    3    4
ILE    4    3
LYS    5   24
LYS    6   24
LYS    7   30
LEU    8    3
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cqxA.130.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cqxA.131.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cqxA.131.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cqxA.131.5.a2m \
	-target T0124 -template 1cqxA \
	-out T0124-1cqxA.131.5 -outdir und
partial PDB gets fragment 54 through 63 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
ASP    2    4
ILE    3    3
LYS    4   26
LYS    5   26
LYS    6   24
LEU    7    3
GLU    8   15
LYS   10   28
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cqxA.131.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cqxA.132.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cqxA.132.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cqxA.132.5.a2m \
	-target T0124 -template 1cqxA \
	-out T0124-1cqxA.132.5 -outdir und
partial PDB gets fragment 53 through 62 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
ILE    2    2
LYS    3   24
LYS    4   26
LYS    5   26
LEU    6    3
GLU    7   12
LYS    9   30
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cqxA.132.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ctqA.179.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ctqA.179.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ctqA.179.3.a2m \
	-target T0124 -template 1ctqA \
	-out T0124-1ctqA.179.3 -outdir und
Skipped atom 21, because occupancy 0.4 <= existing 0.600001
Skipped atom 23, because occupancy 0.4 <= existing 0.600001
Skipped atom 25, because occupancy 0.4 <= existing 0.600001
Skipped atom 27, because occupancy 0.4 <= existing 0.600001
Skipped atom 29, because occupancy 0.4 <= existing 0.600001
Skipped atom 219, because occupancy 0.39 <= existing 0.610001
Skipped atom 221, because occupancy 0.39 <= existing 0.610001
Skipped atom 223, because occupancy 0.39 <= existing 0.610001
Skipped atom 305, because occupancy 0.47 <= existing 0.530001
Skipped atom 307, because occupancy 0.47 <= existing 0.530001
Skipped atom 350, because occupancy 0.5 <= existing 0.740001
Skipped atom 352, because occupancy 0.5 <= existing 0.740001
Skipped atom 354, because occupancy 0.5 <= existing 0.740001
Skipped atom 356, because occupancy 0.5 <= existing 0.740001
Skipped atom 358, because occupancy 0.5 <= existing 0.740001
Skipped atom 704, because occupancy 0.41 <= existing 0.590001
Skipped atom 706, because occupancy 0.41 <= existing 0.590001
Skipped atom 708, because occupancy 0.41 <= existing 0.590001
Skipped atom 877, because occupancy 0.13 <= existing 0.870001
Skipped atom 879, because occupancy 0.13 <= existing 0.870001
Skipped atom 966, because occupancy 0.33 <= existing 0.670001
Skipped atom 968, because occupancy 0.33 <= existing 0.670001
Skipped atom 1040, because occupancy 0.4 <= existing 0.600001
Skipped atom 1042, because occupancy 0.4 <= existing 0.600001
Skipped atom 1044, because occupancy 0.4 <= existing 0.600001
Skipped atom 1046, because occupancy 0.4 <= existing 0.600001
Skipped atom 1048, because occupancy 0.4 <= existing 0.600001
Skipped atom 1050, because occupancy 0.4 <= existing 0.600001
Skipped atom 1052, because occupancy 0.4 <= existing 0.600001
Skipped atom 1357, because occupancy 0.5 <= existing 0.500001
Skipped atom 1359, because occupancy 0.5 <= existing 0.500001
Skipped atom 1361, because occupancy 0.5 <= existing 0.500001
Skipped atom 1363, because occupancy 0.5 <= existing 0.500001
Skipped atom 1365, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 32 through 42 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LEU    2    3
GLU    4   13
LYS    5   24
THR    6    3
ARG    8   29
TYR    9    3
GLN   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ctqA.179.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ctqA.180.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ctqA.180.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ctqA.180.3.a2m \
	-target T0124 -template 1ctqA \
	-out T0124-1ctqA.180.3 -outdir und
Skipped atom 21, because occupancy 0.4 <= existing 0.600001
Skipped atom 23, because occupancy 0.4 <= existing 0.600001
Skipped atom 25, because occupancy 0.4 <= existing 0.600001
Skipped atom 27, because occupancy 0.4 <= existing 0.600001
Skipped atom 29, because occupancy 0.4 <= existing 0.600001
Skipped atom 219, because occupancy 0.39 <= existing 0.610001
Skipped atom 221, because occupancy 0.39 <= existing 0.610001
Skipped atom 223, because occupancy 0.39 <= existing 0.610001
Skipped atom 305, because occupancy 0.47 <= existing 0.530001
Skipped atom 307, because occupancy 0.47 <= existing 0.530001
Skipped atom 350, because occupancy 0.5 <= existing 0.740001
Skipped atom 352, because occupancy 0.5 <= existing 0.740001
Skipped atom 354, because occupancy 0.5 <= existing 0.740001
Skipped atom 356, because occupancy 0.5 <= existing 0.740001
Skipped atom 358, because occupancy 0.5 <= existing 0.740001
Skipped atom 704, because occupancy 0.41 <= existing 0.590001
Skipped atom 706, because occupancy 0.41 <= existing 0.590001
Skipped atom 708, because occupancy 0.41 <= existing 0.590001
Skipped atom 877, because occupancy 0.13 <= existing 0.870001
Skipped atom 879, because occupancy 0.13 <= existing 0.870001
Skipped atom 966, because occupancy 0.33 <= existing 0.670001
Skipped atom 968, because occupancy 0.33 <= existing 0.670001
Skipped atom 1040, because occupancy 0.4 <= existing 0.600001
Skipped atom 1042, because occupancy 0.4 <= existing 0.600001
Skipped atom 1044, because occupancy 0.4 <= existing 0.600001
Skipped atom 1046, because occupancy 0.4 <= existing 0.600001
Skipped atom 1048, because occupancy 0.4 <= existing 0.600001
Skipped atom 1050, because occupancy 0.4 <= existing 0.600001
Skipped atom 1052, because occupancy 0.4 <= existing 0.600001
Skipped atom 1357, because occupancy 0.5 <= existing 0.500001
Skipped atom 1359, because occupancy 0.5 <= existing 0.500001
Skipped atom 1361, because occupancy 0.5 <= existing 0.500001
Skipped atom 1363, because occupancy 0.5 <= existing 0.500001
Skipped atom 1365, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 31 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
THR    2    3
GLU    3   15
LYS    4   25
THR    5    2
ARG    7   29
TYR    8    3
GLN    9   13
GLN   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ctqA.180.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ctqA.181.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ctqA.181.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ctqA.181.2.a2m \
	-target T0124 -template 1ctqA \
	-out T0124-1ctqA.181.2 -outdir und
Skipped atom 21, because occupancy 0.4 <= existing 0.600001
Skipped atom 23, because occupancy 0.4 <= existing 0.600001
Skipped atom 25, because occupancy 0.4 <= existing 0.600001
Skipped atom 27, because occupancy 0.4 <= existing 0.600001
Skipped atom 29, because occupancy 0.4 <= existing 0.600001
Skipped atom 219, because occupancy 0.39 <= existing 0.610001
Skipped atom 221, because occupancy 0.39 <= existing 0.610001
Skipped atom 223, because occupancy 0.39 <= existing 0.610001
Skipped atom 305, because occupancy 0.47 <= existing 0.530001
Skipped atom 307, because occupancy 0.47 <= existing 0.530001
Skipped atom 350, because occupancy 0.5 <= existing 0.740001
Skipped atom 352, because occupancy 0.5 <= existing 0.740001
Skipped atom 354, because occupancy 0.5 <= existing 0.740001
Skipped atom 356, because occupancy 0.5 <= existing 0.740001
Skipped atom 358, because occupancy 0.5 <= existing 0.740001
Skipped atom 704, because occupancy 0.41 <= existing 0.590001
Skipped atom 706, because occupancy 0.41 <= existing 0.590001
Skipped atom 708, because occupancy 0.41 <= existing 0.590001
Skipped atom 877, because occupancy 0.13 <= existing 0.870001
Skipped atom 879, because occupancy 0.13 <= existing 0.870001
Skipped atom 966, because occupancy 0.33 <= existing 0.670001
Skipped atom 968, because occupancy 0.33 <= existing 0.670001
Skipped atom 1040, because occupancy 0.4 <= existing 0.600001
Skipped atom 1042, because occupancy 0.4 <= existing 0.600001
Skipped atom 1044, because occupancy 0.4 <= existing 0.600001
Skipped atom 1046, because occupancy 0.4 <= existing 0.600001
Skipped atom 1048, because occupancy 0.4 <= existing 0.600001
Skipped atom 1050, because occupancy 0.4 <= existing 0.600001
Skipped atom 1052, because occupancy 0.4 <= existing 0.600001
Skipped atom 1357, because occupancy 0.5 <= existing 0.500001
Skipped atom 1359, because occupancy 0.5 <= existing 0.500001
Skipped atom 1361, because occupancy 0.5 <= existing 0.500001
Skipped atom 1363, because occupancy 0.5 <= existing 0.500001
Skipped atom 1365, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 30 through 40 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
GLU    2   12
LYS    3   28
THR    4    3
ARG    6   26
TYR    7    2
GLN    8   14
GLN    9   14
LYS   10   29
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.56689
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ctqA.181.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ctqA.183.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ctqA.183.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ctqA.183.0.a2m \
	-target T0124 -template 1ctqA \
	-out T0124-1ctqA.183.0 -outdir und
Skipped atom 21, because occupancy 0.4 <= existing 0.600001
Skipped atom 23, because occupancy 0.4 <= existing 0.600001
Skipped atom 25, because occupancy 0.4 <= existing 0.600001
Skipped atom 27, because occupancy 0.4 <= existing 0.600001
Skipped atom 29, because occupancy 0.4 <= existing 0.600001
Skipped atom 219, because occupancy 0.39 <= existing 0.610001
Skipped atom 221, because occupancy 0.39 <= existing 0.610001
Skipped atom 223, because occupancy 0.39 <= existing 0.610001
Skipped atom 305, because occupancy 0.47 <= existing 0.530001
Skipped atom 307, because occupancy 0.47 <= existing 0.530001
Skipped atom 350, because occupancy 0.5 <= existing 0.740001
Skipped atom 352, because occupancy 0.5 <= existing 0.740001
Skipped atom 354, because occupancy 0.5 <= existing 0.740001
Skipped atom 356, because occupancy 0.5 <= existing 0.740001
Skipped atom 358, because occupancy 0.5 <= existing 0.740001
Skipped atom 704, because occupancy 0.41 <= existing 0.590001
Skipped atom 706, because occupancy 0.41 <= existing 0.590001
Skipped atom 708, because occupancy 0.41 <= existing 0.590001
Skipped atom 877, because occupancy 0.13 <= existing 0.870001
Skipped atom 879, because occupancy 0.13 <= existing 0.870001
Skipped atom 966, because occupancy 0.33 <= existing 0.670001
Skipped atom 968, because occupancy 0.33 <= existing 0.670001
Skipped atom 1040, because occupancy 0.4 <= existing 0.600001
Skipped atom 1042, because occupancy 0.4 <= existing 0.600001
Skipped atom 1044, because occupancy 0.4 <= existing 0.600001
Skipped atom 1046, because occupancy 0.4 <= existing 0.600001
Skipped atom 1048, because occupancy 0.4 <= existing 0.600001
Skipped atom 1050, because occupancy 0.4 <= existing 0.600001
Skipped atom 1052, because occupancy 0.4 <= existing 0.600001
Skipped atom 1357, because occupancy 0.5 <= existing 0.500001
Skipped atom 1359, because occupancy 0.5 <= existing 0.500001
Skipped atom 1361, because occupancy 0.5 <= existing 0.500001
Skipped atom 1363, because occupancy 0.5 <= existing 0.500001
Skipped atom 1365, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 30 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
THR    2    1
ARG    4   32
TYR    5    3
GLN    6   14
GLN    7   14
LYS    8   26
LEU    9    3
GLU   10   13
GLU   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    9     10.1334
Cluster     1 =   6   9
2 clashing residues after turn 
Residue clashes:
6-9
cluster 1 has 2 members and 5.000e+01 combinations:
 6  9 
Energy     10.1334
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 5.000e+01 - Sending to search
0.000000 < 10.133358: keeping 
Solved cluster 1: residual clashing  0.98
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ctqA.183.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ctqA.184.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ctqA.184.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ctqA.184.0.a2m \
	-target T0124 -template 1ctqA \
	-out T0124-1ctqA.184.0 -outdir und
Skipped atom 21, because occupancy 0.4 <= existing 0.600001
Skipped atom 23, because occupancy 0.4 <= existing 0.600001
Skipped atom 25, because occupancy 0.4 <= existing 0.600001
Skipped atom 27, because occupancy 0.4 <= existing 0.600001
Skipped atom 29, because occupancy 0.4 <= existing 0.600001
Skipped atom 219, because occupancy 0.39 <= existing 0.610001
Skipped atom 221, because occupancy 0.39 <= existing 0.610001
Skipped atom 223, because occupancy 0.39 <= existing 0.610001
Skipped atom 305, because occupancy 0.47 <= existing 0.530001
Skipped atom 307, because occupancy 0.47 <= existing 0.530001
Skipped atom 350, because occupancy 0.5 <= existing 0.740001
Skipped atom 352, because occupancy 0.5 <= existing 0.740001
Skipped atom 354, because occupancy 0.5 <= existing 0.740001
Skipped atom 356, because occupancy 0.5 <= existing 0.740001
Skipped atom 358, because occupancy 0.5 <= existing 0.740001
Skipped atom 704, because occupancy 0.41 <= existing 0.590001
Skipped atom 706, because occupancy 0.41 <= existing 0.590001
Skipped atom 708, because occupancy 0.41 <= existing 0.590001
Skipped atom 877, because occupancy 0.13 <= existing 0.870001
Skipped atom 879, because occupancy 0.13 <= existing 0.870001
Skipped atom 966, because occupancy 0.33 <= existing 0.670001
Skipped atom 968, because occupancy 0.33 <= existing 0.670001
Skipped atom 1040, because occupancy 0.4 <= existing 0.600001
Skipped atom 1042, because occupancy 0.4 <= existing 0.600001
Skipped atom 1044, because occupancy 0.4 <= existing 0.600001
Skipped atom 1046, because occupancy 0.4 <= existing 0.600001
Skipped atom 1048, because occupancy 0.4 <= existing 0.600001
Skipped atom 1050, because occupancy 0.4 <= existing 0.600001
Skipped atom 1052, because occupancy 0.4 <= existing 0.600001
Skipped atom 1357, because occupancy 0.5 <= existing 0.500001
Skipped atom 1359, because occupancy 0.5 <= existing 0.500001
Skipped atom 1361, because occupancy 0.5 <= existing 0.500001
Skipped atom 1363, because occupancy 0.5 <= existing 0.500001
Skipped atom 1365, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 29 through 40 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
ARG    3   26
TYR    4    2
GLN    5   14
GLN    6   14
LYS    7   26
LEU    8    3
GLU    9   14
GLU   10   14
LYS   11   29
GLN   12   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ctqA.184.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ctqA.185.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ctqA.185.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ctqA.185.2.a2m \
	-target T0124 -template 1ctqA \
	-out T0124-1ctqA.185.2 -outdir und
Skipped atom 21, because occupancy 0.4 <= existing 0.600001
Skipped atom 23, because occupancy 0.4 <= existing 0.600001
Skipped atom 25, because occupancy 0.4 <= existing 0.600001
Skipped atom 27, because occupancy 0.4 <= existing 0.600001
Skipped atom 29, because occupancy 0.4 <= existing 0.600001
Skipped atom 219, because occupancy 0.39 <= existing 0.610001
Skipped atom 221, because occupancy 0.39 <= existing 0.610001
Skipped atom 223, because occupancy 0.39 <= existing 0.610001
Skipped atom 305, because occupancy 0.47 <= existing 0.530001
Skipped atom 307, because occupancy 0.47 <= existing 0.530001
Skipped atom 350, because occupancy 0.5 <= existing 0.740001
Skipped atom 352, because occupancy 0.5 <= existing 0.740001
Skipped atom 354, because occupancy 0.5 <= existing 0.740001
Skipped atom 356, because occupancy 0.5 <= existing 0.740001
Skipped atom 358, because occupancy 0.5 <= existing 0.740001
Skipped atom 704, because occupancy 0.41 <= existing 0.590001
Skipped atom 706, because occupancy 0.41 <= existing 0.590001
Skipped atom 708, because occupancy 0.41 <= existing 0.590001
Skipped atom 877, because occupancy 0.13 <= existing 0.870001
Skipped atom 879, because occupancy 0.13 <= existing 0.870001
Skipped atom 966, because occupancy 0.33 <= existing 0.670001
Skipped atom 968, because occupancy 0.33 <= existing 0.670001
Skipped atom 1040, because occupancy 0.4 <= existing 0.600001
Skipped atom 1042, because occupancy 0.4 <= existing 0.600001
Skipped atom 1044, because occupancy 0.4 <= existing 0.600001
Skipped atom 1046, because occupancy 0.4 <= existing 0.600001
Skipped atom 1048, because occupancy 0.4 <= existing 0.600001
Skipped atom 1050, because occupancy 0.4 <= existing 0.600001
Skipped atom 1052, because occupancy 0.4 <= existing 0.600001
Skipped atom 1357, because occupancy 0.5 <= existing 0.500001
Skipped atom 1359, because occupancy 0.5 <= existing 0.500001
Skipped atom 1361, because occupancy 0.5 <= existing 0.500001
Skipped atom 1363, because occupancy 0.5 <= existing 0.500001
Skipped atom 1365, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 28 through 37 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   28
TYR    3    3
GLN    4   12
GLN    5   13
LYS    6   30
LEU    7    3
GLU    8   12
LYS   10   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.29552
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ctqA.185.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cv8.174.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cv8.174.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cv8.174.3.a2m \
	-target T0124 -template 1cv8 \
	-out T0124-1cv8.174.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cv8-orig.a2m
Writing a2m file: tmp/1cv8-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9572


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9572/tmp -alignfile tmp/1cv8-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cv8-orig.a2m (1 sequences, 174 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9572/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9572/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9572/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9572/tmp.a2m (1 sequences, 174 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9572/tmp.mod tmp/1cv8-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9572 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cv8-align.mod
tmp/1cv8-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9572/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cv8-orig.a2m tmp/1cv8-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cv8-align.mod
Running w0.5 tmp/1cv8-orig.a2m tmp/1cv8-align.mod
Running align2model tmp/1cv8-align -i tmp/1cv8-align.mod -db tmp/1cv8-orig.a2m -db tmp/1cv8-pdb.a2m
partial PDB gets fragment 47 through 57 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
GLN    2   11
THR    3    2
ILE    4    3
LYS    5   29
LEU    6    2
THR    8    1
GLU    9   11
LYS   10   30
THR   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue I 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cv8.174.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cv8.175.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cv8.175.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cv8.175.1.a2m \
	-target T0124 -template 1cv8 \
	-out T0124-1cv8.175.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cv8-orig.a2m
Writing a2m file: tmp/1cv8-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12059


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12059/tmp -alignfile tmp/1cv8-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cv8-orig.a2m (1 sequences, 174 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12059/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12059/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12059/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12059/tmp.a2m (1 sequences, 174 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12059/tmp.mod tmp/1cv8-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12059 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cv8-align.mod
tmp/1cv8-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12059/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cv8-orig.a2m tmp/1cv8-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cv8-align.mod
Running w0.5 tmp/1cv8-orig.a2m tmp/1cv8-align.mod
Running align2model tmp/1cv8-align -i tmp/1cv8-align.mod -db tmp/1cv8-orig.a2m -db tmp/1cv8-pdb.a2m
partial PDB gets fragment 46 through 56 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
THR    2    2
ILE    3    2
LYS    4   29
LEU    5    3
LEU    6    3
THR    7    1
GLU    8   14
LYS    9   28
THR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cv8.175.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cv8.176.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cv8.176.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cv8.176.1.a2m \
	-target T0124 -template 1cv8 \
	-out T0124-1cv8.176.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cv8-orig.a2m
Writing a2m file: tmp/1cv8-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32600


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32600/tmp -alignfile tmp/1cv8-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cv8-orig.a2m (1 sequences, 174 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32600/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32600/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32600/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32600/tmp.a2m (1 sequences, 174 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32600/tmp.mod tmp/1cv8-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32600 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cv8-align.mod
tmp/1cv8-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32600/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cv8-orig.a2m tmp/1cv8-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cv8-align.mod
Running w0.5 tmp/1cv8-orig.a2m tmp/1cv8-align.mod
Running align2model tmp/1cv8-align -i tmp/1cv8-align.mod -db tmp/1cv8-orig.a2m -db tmp/1cv8-pdb.a2m
partial PDB gets fragment 45 through 56 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
THR    1    1
ILE    2    3
LYS    3   30
LEU    4    3
THR    6    3
GLU    7   15
LYS    8   22
THR    9    2
ARG   11   25
TYR   12    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.68812
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cv8.176.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cv8.177.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cv8.177.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cv8.177.2.a2m \
	-target T0124 -template 1cv8 \
	-out T0124-1cv8.177.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cv8-orig.a2m
Writing a2m file: tmp/1cv8-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30937


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30937/tmp -alignfile tmp/1cv8-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cv8-orig.a2m (1 sequences, 174 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30937/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30937/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30937/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30937/tmp.a2m (1 sequences, 174 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30937/tmp.mod tmp/1cv8-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30937 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cv8-align.mod
tmp/1cv8-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30937/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cv8-orig.a2m tmp/1cv8-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cv8-align.mod
Running w0.5 tmp/1cv8-orig.a2m tmp/1cv8-align.mod
Running align2model tmp/1cv8-align -i tmp/1cv8-align.mod -db tmp/1cv8-orig.a2m -db tmp/1cv8-pdb.a2m
partial PDB gets fragment 44 through 55 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    5
LYS    2   24
LEU    3    3
LEU    4    3
THR    5    1
GLU    6   15
LYS    7   23
THR    8    2
ARG   10   29
TYR   11    2
GLN   12    8
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash    12   13     24.6736
Cluster     1 =  12  13
2 clashing residues after turn 
Residue clashes:
12-13
cluster 1 has 2 members and 1.600e+01 combinations:
 12  13 
Energy     24.6736
Searching cluster 12
Combinations for 2 members in cluster 1 OK: 1.600e+01 - Sending to search
11.191309 < 24.673555: keeping 
0.000000 < 11.305781: keeping 
Solved cluster 1: residual clashing  0.78
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cv8.177.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cv8.178.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cv8.178.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cv8.178.3.a2m \
	-target T0124 -template 1cv8 \
	-out T0124-1cv8.178.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cv8-orig.a2m
Writing a2m file: tmp/1cv8-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9398


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9398/tmp -alignfile tmp/1cv8-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cv8-orig.a2m (1 sequences, 174 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9398/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9398/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9398/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9398/tmp.a2m (1 sequences, 174 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9398/tmp.mod tmp/1cv8-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9398 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cv8-align.mod
tmp/1cv8-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9398/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cv8-orig.a2m tmp/1cv8-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cv8-align.mod
Running w0.5 tmp/1cv8-orig.a2m tmp/1cv8-align.mod
Running align2model tmp/1cv8-align -i tmp/1cv8-align.mod -db tmp/1cv8-orig.a2m -db tmp/1cv8-pdb.a2m
partial PDB gets fragment 43 through 53 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LEU    2    3
LEU    3    3
THR    4    2
GLU    5   15
LYS    6   24
THR    7    2
ARG    9   32
TYR   10    3
GLN   11   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cv8.178.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cv8.180.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cv8.180.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cv8.180.1.a2m \
	-target T0124 -template 1cv8 \
	-out T0124-1cv8.180.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cv8-orig.a2m
Writing a2m file: tmp/1cv8-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-418


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-418/tmp -alignfile tmp/1cv8-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cv8-orig.a2m (1 sequences, 174 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-418/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-418/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-418/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-418/tmp.a2m (1 sequences, 174 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-418/tmp.mod tmp/1cv8-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-418 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cv8-align.mod
tmp/1cv8-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-418/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cv8-orig.a2m tmp/1cv8-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cv8-align.mod
Running w0.5 tmp/1cv8-orig.a2m tmp/1cv8-align.mod
Running align2model tmp/1cv8-align -i tmp/1cv8-align.mod -db tmp/1cv8-orig.a2m -db tmp/1cv8-pdb.a2m
partial PDB gets fragment 43 through 52 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
THR    2    2
GLU    3   12
LYS    4   26
THR    5    2
ARG    7   32
TYR    8    3
GLN    9   15
GLN   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cv8.180.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cv8.181.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cv8.181.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cv8.181.3.a2m \
	-target T0124 -template 1cv8 \
	-out T0124-1cv8.181.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cv8-orig.a2m
Writing a2m file: tmp/1cv8-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28735


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28735/tmp -alignfile tmp/1cv8-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cv8-orig.a2m (1 sequences, 174 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28735/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28735/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28735/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28735/tmp.a2m (1 sequences, 174 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28735/tmp.mod tmp/1cv8-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28735 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cv8-align.mod
tmp/1cv8-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28735/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cv8-orig.a2m tmp/1cv8-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cv8-align.mod
Running w0.5 tmp/1cv8-orig.a2m tmp/1cv8-align.mod
Running align2model tmp/1cv8-align -i tmp/1cv8-align.mod -db tmp/1cv8-orig.a2m -db tmp/1cv8-pdb.a2m
partial PDB gets fragment 42 through 51 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
LYS    3   28
THR    4    1
TYR    7    3
GLN    8   13
GLN    9   13
LYS   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cv8.181.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cvrA.162.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cvrA.162.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cvrA.162.4.a2m \
	-target T0124 -template 1cvrA \
	-out T0124-1cvrA.162.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cvrA-orig.a2m
Writing a2m file: tmp/1cvrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6547


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6547/tmp -alignfile tmp/1cvrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cvrA-orig.a2m (1 sequences, 435 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6547/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6547/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6547/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6547/tmp.a2m (1 sequences, 435 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6547/tmp.mod tmp/1cvrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6547 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cvrA-align.mod
tmp/1cvrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6547/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cvrA-orig.a2m tmp/1cvrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cvrA-align.mod
Running w0.5 tmp/1cvrA-orig.a2m tmp/1cvrA-align.mod
Running align2model tmp/1cvrA-align -i tmp/1cvrA-align.mod -db tmp/1cvrA-orig.a2m -db tmp/1cvrA-pdb.a2m
partial PDB gets fragment 75 through 84 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LYS    2   31
GLU    3   14
ILE    4    5
ASN    5    4
ASN    6    4
SER    7    2
HIS    8    4
ILE    9    5
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 31 rotamers of residue K 3 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    7     53.1279
Cluster     1 =   3   7
2 clashing residues after turn 
Residue clashes:
3-7
cluster 1 has 2 members and 9.300e+01 combinations:
 7  3 
Energy    132.8881
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 9.300e+01 - Sending to search
0.000000 < 132.888123: keeping 
2.064560 < 12.377607: keeping 
Solved cluster 1: residual clashing  7.11
Still clashes at these sidechain pairs:
Residual clashes =    2.06456
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cvrA.162.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cvrA.163.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cvrA.163.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cvrA.163.2.a2m \
	-target T0124 -template 1cvrA \
	-out T0124-1cvrA.163.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cvrA-orig.a2m
Writing a2m file: tmp/1cvrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17498


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17498/tmp -alignfile tmp/1cvrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cvrA-orig.a2m (1 sequences, 435 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17498/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17498/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17498/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17498/tmp.a2m (1 sequences, 435 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17498/tmp.mod tmp/1cvrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17498 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cvrA-align.mod
tmp/1cvrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17498/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cvrA-orig.a2m tmp/1cvrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cvrA-align.mod
Running w0.5 tmp/1cvrA-orig.a2m tmp/1cvrA-align.mod
Running align2model tmp/1cvrA-align -i tmp/1cvrA-align.mod -db tmp/1cvrA-orig.a2m -db tmp/1cvrA-pdb.a2m
partial PDB gets fragment 74 through 83 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
GLU    2   11
ILE    3    4
ASN    4    5
ASN    5    4
SER    6    2
HIS    7    3
GLN    9   15
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 4 rotamers of residue I 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.86920
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cvrA.163.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cvrA.164.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cvrA.164.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cvrA.164.2.a2m \
	-target T0124 -template 1cvrA \
	-out T0124-1cvrA.164.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cvrA-orig.a2m
Writing a2m file: tmp/1cvrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32632


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32632/tmp -alignfile tmp/1cvrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cvrA-orig.a2m (1 sequences, 435 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32632/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32632/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32632/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32632/tmp.a2m (1 sequences, 435 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32632/tmp.mod tmp/1cvrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32632 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cvrA-align.mod
tmp/1cvrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32632/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cvrA-orig.a2m tmp/1cvrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cvrA-align.mod
Running w0.5 tmp/1cvrA-orig.a2m tmp/1cvrA-align.mod
Running align2model tmp/1cvrA-align -i tmp/1cvrA-align.mod -db tmp/1cvrA-orig.a2m -db tmp/1cvrA-pdb.a2m
partial PDB gets fragment 73 through 82 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
ILE    2    3
ASN    3    4
ASN    4    6
SER    5    2
ILE    7    4
GLN    8   12
GLU    9   15
VAL   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3   10     20.0000
keepclash     5    9     28.8717
Cluster     1 =   3  10
Cluster     2 =   5   9
4 clashing residues after turn 
Residue clashes:
3-10
5-9
cluster 1 has 2 members and 2.200e+01 combinations:
 3  10 
Energy     20.0000
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 2.200e+01 - Sending to search
11.131014 < 20.000000: keeping 
1.236950 < 11.655133: keeping 
0.000000 < 2.358135: keeping 
Solved cluster 1: residual clashing  1.15
cluster 2 has 2 members and 6.000e+00 combinations:
 5  9 
Energy     36.4405
Searching cluster 5
Combinations for 2 members in cluster 2 OK: 6.000e+00 - Sending to search
28.871712 < 36.440506: keeping 
14.706596 < 36.440502: keeping 
0.000000 < 22.144981: keeping 
Solved cluster 2: residual clashing  3.77
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cvrA.164.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cvrA.165.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cvrA.165.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cvrA.165.5.a2m \
	-target T0124 -template 1cvrA \
	-out T0124-1cvrA.165.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cvrA-orig.a2m
Writing a2m file: tmp/1cvrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-24973


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-24973/tmp -alignfile tmp/1cvrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cvrA-orig.a2m (1 sequences, 435 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-24973/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-24973/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-24973/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24973/tmp.a2m (1 sequences, 435 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-24973/tmp.mod tmp/1cvrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-24973 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cvrA-align.mod
tmp/1cvrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24973/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cvrA-orig.a2m tmp/1cvrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cvrA-align.mod
Running w0.5 tmp/1cvrA-orig.a2m tmp/1cvrA-align.mod
Running align2model tmp/1cvrA-align -i tmp/1cvrA-align.mod -db tmp/1cvrA-orig.a2m -db tmp/1cvrA-pdb.a2m
partial PDB gets fragment 72 through 81 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
ASN    2    5
ASN    3    5
SER    4    2
HIS    5    4
ILE    6    3
GLN    7   14
GLU    8   15
VAL    9    1
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue V 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   10     20.1309
Cluster     1 =   6  10
2 clashing residues after turn 
Residue clashes:
6-10
cluster 1 has 2 members and 1.000e+00 combinations:
 10  6 
Energy     34.2842
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 1.000e+00 - Sending to search
20.130871 < 34.284168: keeping 
Solved cluster 1: residual clashing 34.28
Still clashes at these sidechain pairs:
ires=    6 irot=    3 jres=   10 jrot=    1      20.1309
Residual clashes =   20.13087
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cvrA.165.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cxqA.52.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cxqA.52.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cxqA.52.2.a2m \
	-target T0124 -template 1cxqA \
	-out T0124-1cxqA.52.2 -outdir und
Skipped atom 150, because occupancy 0.44 <= existing 0.560001
Skipped atom 152, because occupancy 0.44 <= existing 0.560001
Skipped atom 154, because occupancy 0.44 <= existing 0.560001
Skipped atom 156, because occupancy 0.44 <= existing 0.560001
Skipped atom 158, because occupancy 0.44 <= existing 0.560001
Skipped atom 160, because occupancy 0.44 <= existing 0.560001
Skipped atom 244, because occupancy 0.23 <= existing 0.770001
Skipped atom 246, because occupancy 0.23 <= existing 0.770001
Skipped atom 248, because occupancy 0.23 <= existing 0.770001
Skipped atom 291, because occupancy 0.34 <= existing 0.660001
Skipped atom 293, because occupancy 0.34 <= existing 0.660001
Skipped atom 295, because occupancy 0.34 <= existing 0.660001
Skipped atom 297, because occupancy 0.34 <= existing 0.660001
Skipped atom 321, because occupancy 0.35 <= existing 0.650001
Skipped atom 325, because occupancy 0.35 <= existing 0.650001
Skipped atom 327, because occupancy 0.35 <= existing 0.650001
Skipped atom 329, because occupancy 0.35 <= existing 0.650001
Skipped atom 331, because occupancy 0.35 <= existing 0.650001
Skipped atom 333, because occupancy 0.35 <= existing 0.650001
Skipped atom 384, because occupancy 0.17 <= existing 0.830001
Skipped atom 386, because occupancy 0.17 <= existing 0.830001
Skipped atom 388, because occupancy 0.17 <= existing 0.830001
Skipped atom 572, because occupancy 0.46 <= existing 0.540001
Skipped atom 574, because occupancy 0.46 <= existing 0.540001
Skipped atom 580, because occupancy 0.31 <= existing 0.690001
Skipped atom 582, because occupancy 0.31 <= existing 0.690001
Skipped atom 784, because occupancy 0.37 <= existing 0.630001
Skipped atom 786, because occupancy 0.37 <= existing 0.630001
Skipped atom 788, because occupancy 0.37 <= existing 0.630001
Skipped atom 790, because occupancy 0.37 <= existing 0.630001
Skipped atom 803, because occupancy 0.33 <= existing 0.670001
Skipped atom 805, because occupancy 0.33 <= existing 0.670001
Skipped atom 807, because occupancy 0.33 <= existing 0.670001
Skipped atom 809, because occupancy 0.33 <= existing 0.670001
Skipped atom 811, because occupancy 0.33 <= existing 0.670001
Skipped atom 860, because occupancy 0.45 <= existing 0.550001
Skipped atom 862, because occupancy 0.45 <= existing 0.550001
Skipped atom 864, because occupancy 0.45 <= existing 0.550001
Skipped atom 866, because occupancy 0.45 <= existing 0.550001
Skipped atom 881, because occupancy 0.43 <= existing 0.570001
Skipped atom 883, because occupancy 0.43 <= existing 0.570001
Skipped atom 885, because occupancy 0.43 <= existing 0.570001
Skipped atom 887, because occupancy 0.43 <= existing 0.570001
Skipped atom 911, because occupancy 0.48 <= existing 0.520001
Skipped atom 913, because occupancy 0.48 <= existing 0.520001
Skipped atom 915, because occupancy 0.48 <= existing 0.520001
Skipped atom 917, because occupancy 0.48 <= existing 0.520001
Skipped atom 919, because occupancy 0.48 <= existing 0.520001
Skipped atom 921, because occupancy 0.48 <= existing 0.520001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cxqA-orig.a2m
Writing a2m file: tmp/1cxqA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-421


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-421/tmp -alignfile tmp/1cxqA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cxqA-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-421/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-421/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-421/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-421/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-421/tmp.mod tmp/1cxqA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-421 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cxqA-align.mod
tmp/1cxqA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-421/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cxqA-orig.a2m tmp/1cxqA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cxqA-align.mod
Running w0.5 tmp/1cxqA-orig.a2m tmp/1cxqA-align.mod
Running align2model tmp/1cxqA-align -i tmp/1cxqA-align.mod -db tmp/1cxqA-orig.a2m -db tmp/1cxqA-pdb.a2m
partial PDB gets fragment 132 through 141 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
TYR    2    3
SER    3    3
VAL    4    1
LEU    5    3
PHE    6    2
LEU    7    3
GLU    8   12
PRO    9    2
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cxqA.52.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cxqA.53.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cxqA.53.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cxqA.53.2.a2m \
	-target T0124 -template 1cxqA \
	-out T0124-1cxqA.53.2 -outdir und
Skipped atom 150, because occupancy 0.44 <= existing 0.560001
Skipped atom 152, because occupancy 0.44 <= existing 0.560001
Skipped atom 154, because occupancy 0.44 <= existing 0.560001
Skipped atom 156, because occupancy 0.44 <= existing 0.560001
Skipped atom 158, because occupancy 0.44 <= existing 0.560001
Skipped atom 160, because occupancy 0.44 <= existing 0.560001
Skipped atom 244, because occupancy 0.23 <= existing 0.770001
Skipped atom 246, because occupancy 0.23 <= existing 0.770001
Skipped atom 248, because occupancy 0.23 <= existing 0.770001
Skipped atom 291, because occupancy 0.34 <= existing 0.660001
Skipped atom 293, because occupancy 0.34 <= existing 0.660001
Skipped atom 295, because occupancy 0.34 <= existing 0.660001
Skipped atom 297, because occupancy 0.34 <= existing 0.660001
Skipped atom 321, because occupancy 0.35 <= existing 0.650001
Skipped atom 325, because occupancy 0.35 <= existing 0.650001
Skipped atom 327, because occupancy 0.35 <= existing 0.650001
Skipped atom 329, because occupancy 0.35 <= existing 0.650001
Skipped atom 331, because occupancy 0.35 <= existing 0.650001
Skipped atom 333, because occupancy 0.35 <= existing 0.650001
Skipped atom 384, because occupancy 0.17 <= existing 0.830001
Skipped atom 386, because occupancy 0.17 <= existing 0.830001
Skipped atom 388, because occupancy 0.17 <= existing 0.830001
Skipped atom 572, because occupancy 0.46 <= existing 0.540001
Skipped atom 574, because occupancy 0.46 <= existing 0.540001
Skipped atom 580, because occupancy 0.31 <= existing 0.690001
Skipped atom 582, because occupancy 0.31 <= existing 0.690001
Skipped atom 784, because occupancy 0.37 <= existing 0.630001
Skipped atom 786, because occupancy 0.37 <= existing 0.630001
Skipped atom 788, because occupancy 0.37 <= existing 0.630001
Skipped atom 790, because occupancy 0.37 <= existing 0.630001
Skipped atom 803, because occupancy 0.33 <= existing 0.670001
Skipped atom 805, because occupancy 0.33 <= existing 0.670001
Skipped atom 807, because occupancy 0.33 <= existing 0.670001
Skipped atom 809, because occupancy 0.33 <= existing 0.670001
Skipped atom 811, because occupancy 0.33 <= existing 0.670001
Skipped atom 860, because occupancy 0.45 <= existing 0.550001
Skipped atom 862, because occupancy 0.45 <= existing 0.550001
Skipped atom 864, because occupancy 0.45 <= existing 0.550001
Skipped atom 866, because occupancy 0.45 <= existing 0.550001
Skipped atom 881, because occupancy 0.43 <= existing 0.570001
Skipped atom 883, because occupancy 0.43 <= existing 0.570001
Skipped atom 885, because occupancy 0.43 <= existing 0.570001
Skipped atom 887, because occupancy 0.43 <= existing 0.570001
Skipped atom 911, because occupancy 0.48 <= existing 0.520001
Skipped atom 913, because occupancy 0.48 <= existing 0.520001
Skipped atom 915, because occupancy 0.48 <= existing 0.520001
Skipped atom 917, because occupancy 0.48 <= existing 0.520001
Skipped atom 919, because occupancy 0.48 <= existing 0.520001
Skipped atom 921, because occupancy 0.48 <= existing 0.520001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cxqA-orig.a2m
Writing a2m file: tmp/1cxqA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31249


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31249/tmp -alignfile tmp/1cxqA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cxqA-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31249/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31249/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31249/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31249/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31249/tmp.mod tmp/1cxqA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31249 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cxqA-align.mod
tmp/1cxqA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31249/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cxqA-orig.a2m tmp/1cxqA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cxqA-align.mod
Running w0.5 tmp/1cxqA-orig.a2m tmp/1cxqA-align.mod
Running align2model tmp/1cxqA-align -i tmp/1cxqA-align.mod -db tmp/1cxqA-orig.a2m -db tmp/1cxqA-pdb.a2m
partial PDB gets fragment 127 through 138 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
SER    2    2
VAL    3    2
LEU    4    3
PHE    5    3
GLU    7   13
PRO    8    2
VAL    9    1
TYR   10    3
PRO   11    2
ARG   12   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 12 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cxqA.53.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cxqA.53.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cxqA.53.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cxqA.53.4.a2m \
	-target T0124 -template 1cxqA \
	-out T0124-1cxqA.53.4 -outdir und
Skipped atom 150, because occupancy 0.44 <= existing 0.560001
Skipped atom 152, because occupancy 0.44 <= existing 0.560001
Skipped atom 154, because occupancy 0.44 <= existing 0.560001
Skipped atom 156, because occupancy 0.44 <= existing 0.560001
Skipped atom 158, because occupancy 0.44 <= existing 0.560001
Skipped atom 160, because occupancy 0.44 <= existing 0.560001
Skipped atom 244, because occupancy 0.23 <= existing 0.770001
Skipped atom 246, because occupancy 0.23 <= existing 0.770001
Skipped atom 248, because occupancy 0.23 <= existing 0.770001
Skipped atom 291, because occupancy 0.34 <= existing 0.660001
Skipped atom 293, because occupancy 0.34 <= existing 0.660001
Skipped atom 295, because occupancy 0.34 <= existing 0.660001
Skipped atom 297, because occupancy 0.34 <= existing 0.660001
Skipped atom 321, because occupancy 0.35 <= existing 0.650001
Skipped atom 325, because occupancy 0.35 <= existing 0.650001
Skipped atom 327, because occupancy 0.35 <= existing 0.650001
Skipped atom 329, because occupancy 0.35 <= existing 0.650001
Skipped atom 331, because occupancy 0.35 <= existing 0.650001
Skipped atom 333, because occupancy 0.35 <= existing 0.650001
Skipped atom 384, because occupancy 0.17 <= existing 0.830001
Skipped atom 386, because occupancy 0.17 <= existing 0.830001
Skipped atom 388, because occupancy 0.17 <= existing 0.830001
Skipped atom 572, because occupancy 0.46 <= existing 0.540001
Skipped atom 574, because occupancy 0.46 <= existing 0.540001
Skipped atom 580, because occupancy 0.31 <= existing 0.690001
Skipped atom 582, because occupancy 0.31 <= existing 0.690001
Skipped atom 784, because occupancy 0.37 <= existing 0.630001
Skipped atom 786, because occupancy 0.37 <= existing 0.630001
Skipped atom 788, because occupancy 0.37 <= existing 0.630001
Skipped atom 790, because occupancy 0.37 <= existing 0.630001
Skipped atom 803, because occupancy 0.33 <= existing 0.670001
Skipped atom 805, because occupancy 0.33 <= existing 0.670001
Skipped atom 807, because occupancy 0.33 <= existing 0.670001
Skipped atom 809, because occupancy 0.33 <= existing 0.670001
Skipped atom 811, because occupancy 0.33 <= existing 0.670001
Skipped atom 860, because occupancy 0.45 <= existing 0.550001
Skipped atom 862, because occupancy 0.45 <= existing 0.550001
Skipped atom 864, because occupancy 0.45 <= existing 0.550001
Skipped atom 866, because occupancy 0.45 <= existing 0.550001
Skipped atom 881, because occupancy 0.43 <= existing 0.570001
Skipped atom 883, because occupancy 0.43 <= existing 0.570001
Skipped atom 885, because occupancy 0.43 <= existing 0.570001
Skipped atom 887, because occupancy 0.43 <= existing 0.570001
Skipped atom 911, because occupancy 0.48 <= existing 0.520001
Skipped atom 913, because occupancy 0.48 <= existing 0.520001
Skipped atom 915, because occupancy 0.48 <= existing 0.520001
Skipped atom 917, because occupancy 0.48 <= existing 0.520001
Skipped atom 919, because occupancy 0.48 <= existing 0.520001
Skipped atom 921, because occupancy 0.48 <= existing 0.520001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cxqA-orig.a2m
Writing a2m file: tmp/1cxqA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-560


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-560/tmp -alignfile tmp/1cxqA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cxqA-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-560/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-560/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-560/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-560/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-560/tmp.mod tmp/1cxqA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-560 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cxqA-align.mod
tmp/1cxqA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-560/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cxqA-orig.a2m tmp/1cxqA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cxqA-align.mod
Running w0.5 tmp/1cxqA-orig.a2m tmp/1cxqA-align.mod
Running align2model tmp/1cxqA-align -i tmp/1cxqA-align.mod -db tmp/1cxqA-orig.a2m -db tmp/1cxqA-pdb.a2m
partial PDB gets fragment 129 through 139 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
SER    2    3
VAL    3    3
PHE    5    3
LEU    6    3
GLU    7   12
PRO    8    2
VAL    9    1
PRO   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 12 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    9     25.3781
Cluster     1 =   5   9
2 clashing residues after turn 
Residue clashes:
5-9
cluster 1 has 2 members and 0.000e+00 combinations:
 5  9 
Energy     39.8407
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
Solved cluster 1: residual clashing 39.84
Still clashes at these sidechain pairs:
ires=    5 irot=    1 jres=    9 jrot=    1      25.3781
Residual clashes =   29.70029
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cxqA.53.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cxqA.53.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cxqA.53.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cxqA.53.5.a2m \
	-target T0124 -template 1cxqA \
	-out T0124-1cxqA.53.5 -outdir und
Skipped atom 150, because occupancy 0.44 <= existing 0.560001
Skipped atom 152, because occupancy 0.44 <= existing 0.560001
Skipped atom 154, because occupancy 0.44 <= existing 0.560001
Skipped atom 156, because occupancy 0.44 <= existing 0.560001
Skipped atom 158, because occupancy 0.44 <= existing 0.560001
Skipped atom 160, because occupancy 0.44 <= existing 0.560001
Skipped atom 244, because occupancy 0.23 <= existing 0.770001
Skipped atom 246, because occupancy 0.23 <= existing 0.770001
Skipped atom 248, because occupancy 0.23 <= existing 0.770001
Skipped atom 291, because occupancy 0.34 <= existing 0.660001
Skipped atom 293, because occupancy 0.34 <= existing 0.660001
Skipped atom 295, because occupancy 0.34 <= existing 0.660001
Skipped atom 297, because occupancy 0.34 <= existing 0.660001
Skipped atom 321, because occupancy 0.35 <= existing 0.650001
Skipped atom 325, because occupancy 0.35 <= existing 0.650001
Skipped atom 327, because occupancy 0.35 <= existing 0.650001
Skipped atom 329, because occupancy 0.35 <= existing 0.650001
Skipped atom 331, because occupancy 0.35 <= existing 0.650001
Skipped atom 333, because occupancy 0.35 <= existing 0.650001
Skipped atom 384, because occupancy 0.17 <= existing 0.830001
Skipped atom 386, because occupancy 0.17 <= existing 0.830001
Skipped atom 388, because occupancy 0.17 <= existing 0.830001
Skipped atom 572, because occupancy 0.46 <= existing 0.540001
Skipped atom 574, because occupancy 0.46 <= existing 0.540001
Skipped atom 580, because occupancy 0.31 <= existing 0.690001
Skipped atom 582, because occupancy 0.31 <= existing 0.690001
Skipped atom 784, because occupancy 0.37 <= existing 0.630001
Skipped atom 786, because occupancy 0.37 <= existing 0.630001
Skipped atom 788, because occupancy 0.37 <= existing 0.630001
Skipped atom 790, because occupancy 0.37 <= existing 0.630001
Skipped atom 803, because occupancy 0.33 <= existing 0.670001
Skipped atom 805, because occupancy 0.33 <= existing 0.670001
Skipped atom 807, because occupancy 0.33 <= existing 0.670001
Skipped atom 809, because occupancy 0.33 <= existing 0.670001
Skipped atom 811, because occupancy 0.33 <= existing 0.670001
Skipped atom 860, because occupancy 0.45 <= existing 0.550001
Skipped atom 862, because occupancy 0.45 <= existing 0.550001
Skipped atom 864, because occupancy 0.45 <= existing 0.550001
Skipped atom 866, because occupancy 0.45 <= existing 0.550001
Skipped atom 881, because occupancy 0.43 <= existing 0.570001
Skipped atom 883, because occupancy 0.43 <= existing 0.570001
Skipped atom 885, because occupancy 0.43 <= existing 0.570001
Skipped atom 887, because occupancy 0.43 <= existing 0.570001
Skipped atom 911, because occupancy 0.48 <= existing 0.520001
Skipped atom 913, because occupancy 0.48 <= existing 0.520001
Skipped atom 915, because occupancy 0.48 <= existing 0.520001
Skipped atom 917, because occupancy 0.48 <= existing 0.520001
Skipped atom 919, because occupancy 0.48 <= existing 0.520001
Skipped atom 921, because occupancy 0.48 <= existing 0.520001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cxqA-orig.a2m
Writing a2m file: tmp/1cxqA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21266


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21266/tmp -alignfile tmp/1cxqA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cxqA-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21266/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21266/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21266/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21266/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21266/tmp.mod tmp/1cxqA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21266 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cxqA-align.mod
tmp/1cxqA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21266/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cxqA-orig.a2m tmp/1cxqA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cxqA-align.mod
Running w0.5 tmp/1cxqA-orig.a2m tmp/1cxqA-align.mod
Running align2model tmp/1cxqA-align -i tmp/1cxqA-align.mod -db tmp/1cxqA-orig.a2m -db tmp/1cxqA-pdb.a2m
partial PDB gets fragment 131 through 140 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    4
SER    2    3
VAL    3    1
LEU    4    3
PHE    5    3
LEU    6    3
GLU    7   12
PRO    8    2
VAL    9    1
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cxqA.53.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cxqA.55.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cxqA.55.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cxqA.55.3.a2m \
	-target T0124 -template 1cxqA \
	-out T0124-1cxqA.55.3 -outdir und
Skipped atom 150, because occupancy 0.44 <= existing 0.560001
Skipped atom 152, because occupancy 0.44 <= existing 0.560001
Skipped atom 154, because occupancy 0.44 <= existing 0.560001
Skipped atom 156, because occupancy 0.44 <= existing 0.560001
Skipped atom 158, because occupancy 0.44 <= existing 0.560001
Skipped atom 160, because occupancy 0.44 <= existing 0.560001
Skipped atom 244, because occupancy 0.23 <= existing 0.770001
Skipped atom 246, because occupancy 0.23 <= existing 0.770001
Skipped atom 248, because occupancy 0.23 <= existing 0.770001
Skipped atom 291, because occupancy 0.34 <= existing 0.660001
Skipped atom 293, because occupancy 0.34 <= existing 0.660001
Skipped atom 295, because occupancy 0.34 <= existing 0.660001
Skipped atom 297, because occupancy 0.34 <= existing 0.660001
Skipped atom 321, because occupancy 0.35 <= existing 0.650001
Skipped atom 325, because occupancy 0.35 <= existing 0.650001
Skipped atom 327, because occupancy 0.35 <= existing 0.650001
Skipped atom 329, because occupancy 0.35 <= existing 0.650001
Skipped atom 331, because occupancy 0.35 <= existing 0.650001
Skipped atom 333, because occupancy 0.35 <= existing 0.650001
Skipped atom 384, because occupancy 0.17 <= existing 0.830001
Skipped atom 386, because occupancy 0.17 <= existing 0.830001
Skipped atom 388, because occupancy 0.17 <= existing 0.830001
Skipped atom 572, because occupancy 0.46 <= existing 0.540001
Skipped atom 574, because occupancy 0.46 <= existing 0.540001
Skipped atom 580, because occupancy 0.31 <= existing 0.690001
Skipped atom 582, because occupancy 0.31 <= existing 0.690001
Skipped atom 784, because occupancy 0.37 <= existing 0.630001
Skipped atom 786, because occupancy 0.37 <= existing 0.630001
Skipped atom 788, because occupancy 0.37 <= existing 0.630001
Skipped atom 790, because occupancy 0.37 <= existing 0.630001
Skipped atom 803, because occupancy 0.33 <= existing 0.670001
Skipped atom 805, because occupancy 0.33 <= existing 0.670001
Skipped atom 807, because occupancy 0.33 <= existing 0.670001
Skipped atom 809, because occupancy 0.33 <= existing 0.670001
Skipped atom 811, because occupancy 0.33 <= existing 0.670001
Skipped atom 860, because occupancy 0.45 <= existing 0.550001
Skipped atom 862, because occupancy 0.45 <= existing 0.550001
Skipped atom 864, because occupancy 0.45 <= existing 0.550001
Skipped atom 866, because occupancy 0.45 <= existing 0.550001
Skipped atom 881, because occupancy 0.43 <= existing 0.570001
Skipped atom 883, because occupancy 0.43 <= existing 0.570001
Skipped atom 885, because occupancy 0.43 <= existing 0.570001
Skipped atom 887, because occupancy 0.43 <= existing 0.570001
Skipped atom 911, because occupancy 0.48 <= existing 0.520001
Skipped atom 913, because occupancy 0.48 <= existing 0.520001
Skipped atom 915, because occupancy 0.48 <= existing 0.520001
Skipped atom 917, because occupancy 0.48 <= existing 0.520001
Skipped atom 919, because occupancy 0.48 <= existing 0.520001
Skipped atom 921, because occupancy 0.48 <= existing 0.520001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cxqA-orig.a2m
Writing a2m file: tmp/1cxqA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26224


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26224/tmp -alignfile tmp/1cxqA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cxqA-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26224/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26224/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26224/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26224/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26224/tmp.mod tmp/1cxqA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26224 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cxqA-align.mod
tmp/1cxqA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26224/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cxqA-orig.a2m tmp/1cxqA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cxqA-align.mod
Running w0.5 tmp/1cxqA-orig.a2m tmp/1cxqA-align.mod
Running align2model tmp/1cxqA-align -i tmp/1cxqA-align.mod -db tmp/1cxqA-orig.a2m -db tmp/1cxqA-pdb.a2m
partial PDB gets fragment 127 through 137 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
LEU    2    2
PHE    3    3
LEU    4    3
PRO    6    2
VAL    7    1
TYR    8    3
PRO    9    2
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   10     28.4939
Cluster     1 =   6  10
2 clashing residues after turn 
Residue clashes:
6-10
cluster 1 has 2 members and 0.000e+00 combinations:
 6  10 
Energy     46.2612
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
Solved cluster 1: residual clashing 46.26
Still clashes at these sidechain pairs:
ires=    6 irot=    1 jres=   10 jrot=    1      28.4939
Residual clashes =   40.38991
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cxqA.55.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1cxqA.56.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1cxqA.56.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1cxqA.56.5.a2m \
	-target T0124 -template 1cxqA \
	-out T0124-1cxqA.56.5 -outdir und
Skipped atom 150, because occupancy 0.44 <= existing 0.560001
Skipped atom 152, because occupancy 0.44 <= existing 0.560001
Skipped atom 154, because occupancy 0.44 <= existing 0.560001
Skipped atom 156, because occupancy 0.44 <= existing 0.560001
Skipped atom 158, because occupancy 0.44 <= existing 0.560001
Skipped atom 160, because occupancy 0.44 <= existing 0.560001
Skipped atom 244, because occupancy 0.23 <= existing 0.770001
Skipped atom 246, because occupancy 0.23 <= existing 0.770001
Skipped atom 248, because occupancy 0.23 <= existing 0.770001
Skipped atom 291, because occupancy 0.34 <= existing 0.660001
Skipped atom 293, because occupancy 0.34 <= existing 0.660001
Skipped atom 295, because occupancy 0.34 <= existing 0.660001
Skipped atom 297, because occupancy 0.34 <= existing 0.660001
Skipped atom 321, because occupancy 0.35 <= existing 0.650001
Skipped atom 325, because occupancy 0.35 <= existing 0.650001
Skipped atom 327, because occupancy 0.35 <= existing 0.650001
Skipped atom 329, because occupancy 0.35 <= existing 0.650001
Skipped atom 331, because occupancy 0.35 <= existing 0.650001
Skipped atom 333, because occupancy 0.35 <= existing 0.650001
Skipped atom 384, because occupancy 0.17 <= existing 0.830001
Skipped atom 386, because occupancy 0.17 <= existing 0.830001
Skipped atom 388, because occupancy 0.17 <= existing 0.830001
Skipped atom 572, because occupancy 0.46 <= existing 0.540001
Skipped atom 574, because occupancy 0.46 <= existing 0.540001
Skipped atom 580, because occupancy 0.31 <= existing 0.690001
Skipped atom 582, because occupancy 0.31 <= existing 0.690001
Skipped atom 784, because occupancy 0.37 <= existing 0.630001
Skipped atom 786, because occupancy 0.37 <= existing 0.630001
Skipped atom 788, because occupancy 0.37 <= existing 0.630001
Skipped atom 790, because occupancy 0.37 <= existing 0.630001
Skipped atom 803, because occupancy 0.33 <= existing 0.670001
Skipped atom 805, because occupancy 0.33 <= existing 0.670001
Skipped atom 807, because occupancy 0.33 <= existing 0.670001
Skipped atom 809, because occupancy 0.33 <= existing 0.670001
Skipped atom 811, because occupancy 0.33 <= existing 0.670001
Skipped atom 860, because occupancy 0.45 <= existing 0.550001
Skipped atom 862, because occupancy 0.45 <= existing 0.550001
Skipped atom 864, because occupancy 0.45 <= existing 0.550001
Skipped atom 866, because occupancy 0.45 <= existing 0.550001
Skipped atom 881, because occupancy 0.43 <= existing 0.570001
Skipped atom 883, because occupancy 0.43 <= existing 0.570001
Skipped atom 885, because occupancy 0.43 <= existing 0.570001
Skipped atom 887, because occupancy 0.43 <= existing 0.570001
Skipped atom 911, because occupancy 0.48 <= existing 0.520001
Skipped atom 913, because occupancy 0.48 <= existing 0.520001
Skipped atom 915, because occupancy 0.48 <= existing 0.520001
Skipped atom 917, because occupancy 0.48 <= existing 0.520001
Skipped atom 919, because occupancy 0.48 <= existing 0.520001
Skipped atom 921, because occupancy 0.48 <= existing 0.520001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cxqA-orig.a2m
Writing a2m file: tmp/1cxqA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-286


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-286/tmp -alignfile tmp/1cxqA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cxqA-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-286/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-286/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-286/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-286/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-286/tmp.mod tmp/1cxqA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-286 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cxqA-align.mod
tmp/1cxqA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-286/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cxqA-orig.a2m tmp/1cxqA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cxqA-align.mod
Running w0.5 tmp/1cxqA-orig.a2m tmp/1cxqA-align.mod
Running align2model tmp/1cxqA-align -i tmp/1cxqA-align.mod -db tmp/1cxqA-orig.a2m -db tmp/1cxqA-pdb.a2m
partial PDB gets fragment 126 through 135 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
PHE    2    3
LEU    3    2
GLU    4   12
PRO    5    2
VAL    6    3
TYR    7    3
PRO    8    2
ARG    9   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1cxqA.56.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1d2nA.193.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1d2nA.193.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1d2nA.193.5.a2m \
	-target T0124 -template 1d2nA \
	-out T0124-1d2nA.193.5 -outdir und
Skipped atom 665, because occupancy 0.5 <= existing 0.500001
Skipped atom 667, because occupancy 0.5 <= existing 0.500001
Skipped atom 669, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 793, because occupancy 0.5 <= existing 0.500001
Skipped atom 860, because occupancy 0.5 <= existing 0.500001
Skipped atom 862, because occupancy 0.5 <= existing 0.500001
Skipped atom 864, because occupancy 0.5 <= existing 0.500001
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 920, because occupancy 0.5 <= existing 0.500001
Skipped atom 950, because occupancy 0.5 <= existing 0.500001
Skipped atom 952, because occupancy 0.5 <= existing 0.500001
Skipped atom 954, because occupancy 0.5 <= existing 0.500001
Skipped atom 1390, because occupancy 0.5 <= existing 0.500001
Skipped atom 1392, because occupancy 0.5 <= existing 0.500001
Skipped atom 1394, because occupancy 0.5 <= existing 0.500001
Skipped atom 1396, because occupancy 0.5 <= existing 0.500001
Skipped atom 1450, because occupancy 0.5 <= existing 0.500001
Skipped atom 1452, because occupancy 0.5 <= existing 0.500001
Skipped atom 1454, because occupancy 0.5 <= existing 0.500001
Skipped atom 1456, because occupancy 0.5 <= existing 0.500001
Skipped atom 1747, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1d2nA-orig.a2m
Writing a2m file: tmp/1d2nA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-16147


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-16147/tmp -alignfile tmp/1d2nA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1d2nA-orig.a2m (1 sequences, 272 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-16147/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16147/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16147/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16147/tmp.a2m (1 sequences, 272 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16147/tmp.mod tmp/1d2nA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16147 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1d2nA-align.mod
tmp/1d2nA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16147/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1d2nA-orig.a2m tmp/1d2nA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1d2nA-align.mod
Running w0.5 tmp/1d2nA-orig.a2m tmp/1d2nA-align.mod
Running align2model tmp/1d2nA-align -i tmp/1d2nA-align.mod -db tmp/1d2nA-orig.a2m -db tmp/1d2nA-pdb.a2m
partial PDB gets fragment 0 through 6 extending end
Debugging on !
Reading sequence file
Reading input structure 
8 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
ASN    2    4
LEU    3    3
ARG    4   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    5     24.0767
Cluster     1 =   2   5
2 clashing residues after turn 
Residue clashes:
2-5
cluster 1 has 2 members and 3.000e+02 combinations:
 2  5 
Energy     24.0767
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 3.000e+02 - Sending to search
0.000000 < 24.076666: keeping 
Solved cluster 1: residual clashing  0.33
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1d2nA.193.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1d2nA.194.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1d2nA.194.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1d2nA.194.3.a2m \
	-target T0124 -template 1d2nA \
	-out T0124-1d2nA.194.3 -outdir und
Skipped atom 665, because occupancy 0.5 <= existing 0.500001
Skipped atom 667, because occupancy 0.5 <= existing 0.500001
Skipped atom 669, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 793, because occupancy 0.5 <= existing 0.500001
Skipped atom 860, because occupancy 0.5 <= existing 0.500001
Skipped atom 862, because occupancy 0.5 <= existing 0.500001
Skipped atom 864, because occupancy 0.5 <= existing 0.500001
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 920, because occupancy 0.5 <= existing 0.500001
Skipped atom 950, because occupancy 0.5 <= existing 0.500001
Skipped atom 952, because occupancy 0.5 <= existing 0.500001
Skipped atom 954, because occupancy 0.5 <= existing 0.500001
Skipped atom 1390, because occupancy 0.5 <= existing 0.500001
Skipped atom 1392, because occupancy 0.5 <= existing 0.500001
Skipped atom 1394, because occupancy 0.5 <= existing 0.500001
Skipped atom 1396, because occupancy 0.5 <= existing 0.500001
Skipped atom 1450, because occupancy 0.5 <= existing 0.500001
Skipped atom 1452, because occupancy 0.5 <= existing 0.500001
Skipped atom 1454, because occupancy 0.5 <= existing 0.500001
Skipped atom 1456, because occupancy 0.5 <= existing 0.500001
Skipped atom 1747, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1d2nA-orig.a2m
Writing a2m file: tmp/1d2nA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31356


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31356/tmp -alignfile tmp/1d2nA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1d2nA-orig.a2m (1 sequences, 272 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31356/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31356/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31356/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31356/tmp.a2m (1 sequences, 272 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31356/tmp.mod tmp/1d2nA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31356 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1d2nA-align.mod
tmp/1d2nA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31356/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1d2nA-orig.a2m tmp/1d2nA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1d2nA-align.mod
Running w0.5 tmp/1d2nA-orig.a2m tmp/1d2nA-align.mod
Running align2model tmp/1d2nA-align -i tmp/1d2nA-align.mod -db tmp/1d2nA-orig.a2m -db tmp/1d2nA-pdb.a2m
partial PDB gets fragment 0 through 5 extending end
Debugging on !
Reading sequence file
Reading input structure 
7 residues read 
Measuring phi and psi 
Getting chi values
ASN    0    5
LEU    1    3
ARG    2   32
ILE    4    4
GLN    5   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    5     29.0514
Cluster     1 =   2   5
2 clashing residues after turn 
Residue clashes:
2-5
cluster 1 has 2 members and 4.000e+00 combinations:
 5  2 
Energy     29.0514
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
29.051373 < 29.051374: keeping 
1.289044 < 29.051373: keeping 
Solved cluster 1: residual clashing  1.41
Still clashes at these sidechain pairs:
Residual clashes =    1.28904
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1d2nA.194.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1d2nA.195.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1d2nA.195.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1d2nA.195.5.a2m \
	-target T0124 -template 1d2nA \
	-out T0124-1d2nA.195.5 -outdir und
Skipped atom 665, because occupancy 0.5 <= existing 0.500001
Skipped atom 667, because occupancy 0.5 <= existing 0.500001
Skipped atom 669, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 793, because occupancy 0.5 <= existing 0.500001
Skipped atom 860, because occupancy 0.5 <= existing 0.500001
Skipped atom 862, because occupancy 0.5 <= existing 0.500001
Skipped atom 864, because occupancy 0.5 <= existing 0.500001
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 920, because occupancy 0.5 <= existing 0.500001
Skipped atom 950, because occupancy 0.5 <= existing 0.500001
Skipped atom 952, because occupancy 0.5 <= existing 0.500001
Skipped atom 954, because occupancy 0.5 <= existing 0.500001
Skipped atom 1390, because occupancy 0.5 <= existing 0.500001
Skipped atom 1392, because occupancy 0.5 <= existing 0.500001
Skipped atom 1394, because occupancy 0.5 <= existing 0.500001
Skipped atom 1396, because occupancy 0.5 <= existing 0.500001
Skipped atom 1450, because occupancy 0.5 <= existing 0.500001
Skipped atom 1452, because occupancy 0.5 <= existing 0.500001
Skipped atom 1454, because occupancy 0.5 <= existing 0.500001
Skipped atom 1456, because occupancy 0.5 <= existing 0.500001
Skipped atom 1747, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1d2nA-orig.a2m
Writing a2m file: tmp/1d2nA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31393


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31393/tmp -alignfile tmp/1d2nA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1d2nA-orig.a2m (1 sequences, 272 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31393/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31393/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31393/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31393/tmp.a2m (1 sequences, 272 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31393/tmp.mod tmp/1d2nA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31393 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1d2nA-align.mod
tmp/1d2nA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31393/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1d2nA-orig.a2m tmp/1d2nA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1d2nA-align.mod
Running w0.5 tmp/1d2nA-orig.a2m tmp/1d2nA-align.mod
Running align2model tmp/1d2nA-align -i tmp/1d2nA-align.mod -db tmp/1d2nA-orig.a2m -db tmp/1d2nA-pdb.a2m
partial PDB gets fragment 0 through 4 extending end
Debugging on !
Reading sequence file
Reading input structure 
6 residues read 
Measuring phi and psi 
Getting chi values
ARG    0   32
ILE    2    5
GLN    3   15
GLU    4   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1d2nA.195.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1d3vA.213.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1d3vA.213.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1d3vA.213.5.a2m \
	-target T0124 -template 1d3vA \
	-out T0124-1d3vA.213.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1d3vA-orig.a2m
Writing a2m file: tmp/1d3vA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-411


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-411/tmp -alignfile tmp/1d3vA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1d3vA-orig.a2m (1 sequences, 323 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-411/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-411/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-411/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-411/tmp.a2m (1 sequences, 323 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-411/tmp.mod tmp/1d3vA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-411 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1d3vA-align.mod
tmp/1d3vA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-411/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1d3vA-orig.a2m tmp/1d3vA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1d3vA-align.mod
Running w0.5 tmp/1d3vA-orig.a2m tmp/1d3vA-align.mod
Running align2model tmp/1d3vA-align -i tmp/1d3vA-align.mod -db tmp/1d3vA-orig.a2m -db tmp/1d3vA-pdb.a2m
partial PDB gets fragment 0 through 9 extending end
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
TYR    4    2
GLU    5   13
GLU    6   14
LYS    7   23
LEU    8    3
LYS    9   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.91903
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1d3vA.213.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1d3vA.214.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1d3vA.214.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1d3vA.214.4.a2m \
	-target T0124 -template 1d3vA \
	-out T0124-1d3vA.214.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1d3vA-orig.a2m
Writing a2m file: tmp/1d3vA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9790


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9790/tmp -alignfile tmp/1d3vA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1d3vA-orig.a2m (1 sequences, 323 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9790/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9790/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9790/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9790/tmp.a2m (1 sequences, 323 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9790/tmp.mod tmp/1d3vA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9790 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1d3vA-align.mod
tmp/1d3vA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9790/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1d3vA-orig.a2m tmp/1d3vA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1d3vA-align.mod
Running w0.5 tmp/1d3vA-orig.a2m tmp/1d3vA-align.mod
Running align2model tmp/1d3vA-align -i tmp/1d3vA-align.mod -db tmp/1d3vA-orig.a2m -db tmp/1d3vA-pdb.a2m
partial PDB gets fragment 0 through 8 extending end
Debugging on !
Reading sequence file
Reading input structure 
10 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
TYR    2    3
GLU    4   12
LYS    5   26
LEU    6    3
LYS    7   23
THR    8    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1d3vA.214.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1d3vA.215.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1d3vA.215.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1d3vA.215.5.a2m \
	-target T0124 -template 1d3vA \
	-out T0124-1d3vA.215.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1d3vA-orig.a2m
Writing a2m file: tmp/1d3vA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30158


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30158/tmp -alignfile tmp/1d3vA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1d3vA-orig.a2m (1 sequences, 323 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30158/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30158/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30158/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30158/tmp.a2m (1 sequences, 323 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30158/tmp.mod tmp/1d3vA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30158 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1d3vA-align.mod
tmp/1d3vA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30158/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1d3vA-orig.a2m tmp/1d3vA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1d3vA-align.mod
Running w0.5 tmp/1d3vA-orig.a2m tmp/1d3vA-align.mod
Running align2model tmp/1d3vA-align -i tmp/1d3vA-align.mod -db tmp/1d3vA-orig.a2m -db tmp/1d3vA-pdb.a2m
partial PDB gets fragment 0 through 7 extending end
Debugging on !
Reading sequence file
Reading input structure 
9 residues read 
Measuring phi and psi 
Getting chi values
TYR    0    2
GLU    1   15
GLU    2   15
LYS    3   26
LEU    4    3
LYS    5   26
THR    6    2
LEU    7    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1d3vA.215.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.100.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.100.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.100.3.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.100.3 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 78 through 87 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    2    1
GLU    3   14
GLN    4   12
THR    5    2
LYS    7   24
ILE    8    3
THR    9    1
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.100.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.100.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.100.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.100.5.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.100.5 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 74 through 83 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    2    2
GLU    3   14
GLN    4   15
THR    5    1
LYS    7   28
ILE    8    3
THR    9    2
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.100.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.92.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.92.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.92.3.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.92.3 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 82 through 91 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
ARG    3   26
ARG    4   27
LYS    5   25
GLU    6   12
GLN    7   14
HIS    8    4
THR   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.92.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.93.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.93.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.93.1.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.93.1 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 81 through 90 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
ARG    2   27
LYS    4   23
GLU    5   12
GLN    6   12
HIS    7    4
THR    9    2
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.93.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.94.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.94.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.94.0.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.94.0 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 80 through 89 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   30
ARG    2   27
LYS    3   26
GLU    4   15
GLN    5   11
HIS    6    4
THR    8    2
GLU    9   15
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.66110
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.94.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.94.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.94.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.94.2.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.94.2 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 84 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
ARG    2   27
LYS    3   25
GLU    4   12
GLN    5   14
HIS    6    4
THR    8    1
GLU    9   12
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7   11     14.3366
Cluster     1 =   7  11
2 clashing residues after turn 
Residue clashes:
7-11
cluster 1 has 2 members and 3.300e+01 combinations:
 7  11 
Energy     14.3366
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 3.300e+01 - Sending to search
13.271631 < 14.336607: keeping 
2.298379 < 13.326361: keeping 
0.000000 < 2.406835: keeping 
Solved cluster 1: residual clashing  0.11
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.94.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.95.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.95.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.95.0.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.95.0 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 83 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   23
GLU    3   12
GLN    4   12
HIS    5    4
THR    7    2
GLU    8   12
GLN    9   11
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.95.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.95.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.95.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.95.1.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.95.1 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 79 through 88 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   20
LYS    2   28
GLU    3   12
GLN    4   12
HIS    5    4
THR    7    2
GLU    8   12
GLN    9   12
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    6     21.9936
Cluster     1 =   3   6
2 clashing residues after turn 
Residue clashes:
3-6
cluster 1 has 2 members and 4.600e+01 combinations:
 6  3 
Energy     21.9936
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 4.600e+01 - Sending to search
19.188622 < 21.993557: keeping 
10.705868 < 20.267864: keeping 
0.000000 < 11.979035: keeping 
0.000000 < 1.615772: keeping 
Solved cluster 1: residual clashing  1.37
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.95.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.96.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.96.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.96.0.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.96.0 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 78 through 87 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
GLU    2   13
GLN    3   15
HIS    4    4
THR    6    3
GLU    7   12
GLN    8   12
THR    9    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 26 rotamers of residue K 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   15.11165
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.96.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.96.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.96.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.96.1.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.96.1 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 82 through 91 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
GLU    2   15
GLN    3   11
HIS    4    4
THR    6    2
GLU    7   15
GLN    8   12
THR    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.66110
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.96.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.97.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.97.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.97.0.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.97.0 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 81 through 90 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
GLN    2   12
HIS    3    4
THR    5    2
GLU    6   12
GLN    7   12
THR    8    2
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.97.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.97.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.97.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.97.1.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.97.1 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 77 through 86 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
GLN    2   12
HIS    3    3
THR    5    2
GLU    6   12
GLN    7   14
THR    8    1
LYS   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 12 rotamers of residue Q 3 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    9     13.4974
Cluster     1 =   3   9
2 clashing residues after turn 
Residue clashes:
3-9
cluster 1 has 2 members and 1.200e+01 combinations:
 9  3 
Energy    195.6982
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 1.200e+01 - Sending to search
3.427618 < 195.698242: keeping 
2.580529 < 178.972549: keeping 
0.000000 < 166.251740: keeping 
0.000000 < 160.489105: keeping 
Solved cluster 1: residual clashing 107.92
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.97.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.98.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.98.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.98.0.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.98.0 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 80 through 89 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   15
HIS    2    4
THR    4    3
GLU    5   12
GLN    6   12
THR    7    1
LYS    9   30
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.11165
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.98.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.98.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.98.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.98.2.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.98.2 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 76 through 85 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
HIS    2    4
THR    4    1
GLU    5   14
GLN    6   12
THR    7    2
LYS    9   24
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.98.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.99.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.99.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.99.1.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.99.1 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 79 through 88 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
THR    3    2
GLU    4   12
GLN    5   14
THR    6    1
LYS    8   24
ILE    9    3
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.99.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dciA.99.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dciA.99.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dciA.99.3.a2m \
	-target T0124 -template 1dciA \
	-out T0124-1dciA.99.3 -outdir und
Skipped atom 24, because occupancy 0.3 <= existing 0.700001
Skipped atom 26, because occupancy 0.3 <= existing 0.700001
Skipped atom 28, because occupancy 0.3 <= existing 0.700001
Skipped atom 30, because occupancy 0.3 <= existing 0.700001
Skipped atom 37, because occupancy 0.4 <= existing 0.600001
Skipped atom 75, because occupancy 0.4 <= existing 0.600001
Skipped atom 208, because occupancy 0.4 <= existing 0.600001
Skipped atom 210, because occupancy 0.4 <= existing 0.600001
Skipped atom 212, because occupancy 0.4 <= existing 0.600001
Skipped atom 214, because occupancy 0.4 <= existing 0.600001
Skipped atom 216, because occupancy 0.4 <= existing 0.600001
Skipped atom 218, because occupancy 0.4 <= existing 0.600001
Skipped atom 365, because occupancy 0.4 <= existing 0.600001
Skipped atom 367, because occupancy 0.4 <= existing 0.600001
Skipped atom 369, because occupancy 0.4 <= existing 0.600001
Skipped atom 371, because occupancy 0.4 <= existing 0.600001
Skipped atom 583, because occupancy 0.45 <= existing 0.650001
Skipped atom 1551, because occupancy 0.4 <= existing 0.600001
Skipped atom 1553, because occupancy 0.4 <= existing 0.600001
Skipped atom 1555, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1930, because occupancy 0.5 <= existing 0.500001
Skipped atom 1937, because occupancy 0.4 <= existing 0.600001
Skipped atom 1939, because occupancy 0.4 <= existing 0.600001
Skipped atom 1941, because occupancy 0.4 <= existing 0.600001
Skipped atom 2063, because occupancy 0.35 <= existing 0.650001
Skipped atom 2065, because occupancy 0.35 <= existing 0.650001
Skipped atom 2067, because occupancy 0.35 <= existing 0.650001
Skipped atom 2069, because occupancy 0.35 <= existing 0.650001
partial PDB gets fragment 75 through 84 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
THR    3    1
GLU    4   12
GLN    5    9
THR    6    2
LYS    8   26
ILE    9    5
THR   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 12 rotamers of residue E 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   11     13.4276
Cluster     1 =   5  11
2 clashing residues after turn 
Residue clashes:
5-11
cluster 1 has 2 members and 1.200e+01 combinations:
 11  5 
Energy    198.3141
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 1.200e+01 - Sending to search
2.829971 < 198.314056: keeping 
0.000000 < 171.264511: keeping 
0.000000 < 170.999496: keeping 
0.000000 < 112.413551: keeping 
Solved cluster 1: residual clashing 40.33
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dciA.99.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.165.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.165.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.165.0.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.165.0 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32696


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32696/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32696/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32696/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32696/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32696/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32696/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32696 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32696/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 39 through 50 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    5
ASN    2    4
ASN    3    4
SER    4    3
HIS    5    4
ILE    6    5
GLN    7   12
GLU    8   12
VAL    9    1
VAL   10    1
GLN   11   14
THR   12    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    8.76198
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.165.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.165.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.165.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.165.2.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.165.2 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-16538


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-16538/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-16538/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16538/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16538/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16538/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16538/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16538 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16538/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 43 through 52 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    4
ASN    2    5
ASN    3    4
SER    4    3
HIS    5    3
ILE    6    2
GLN    7   14
GLU    8   15
VAL    9    2
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.165.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.166.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.166.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.166.0.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.166.0 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10614


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10614/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10614/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10614/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10614/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10614/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10614/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10614 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10614/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 42 through 51 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
ASN    2    4
SER    3    2
HIS    4    4
ILE    5    2
GLN    6   11
GLU    7   12
VAL    8    3
GLN   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.166.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.166.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.166.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.166.1.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.166.1 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31654


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31654/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31654/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31654/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31654/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31654/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31654/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31654 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31654/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 38 through 49 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
ASN    2    6
SER    3    3
HIS    4    3
ILE    5    2
GLN    6   13
GLU    7   15
VAL    8    2
VAL    9    1
GLN   10   11
THR   11    1
ILE   12    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.166.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.167.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.167.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.167.1.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.167.1 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23965


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23965/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23965/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23965/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23965/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23965/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23965/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23965 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23965/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 37 through 48 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    5
SER    2    3
HIS    3    4
ILE    4    3
GLN    5   11
VAL    7    2
VAL    8    3
GLN    9   12
THR   10    1
ILE   11    2
LYS   12   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.96455
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.167.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.168.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.168.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.168.1.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.168.1 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30365


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30365/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30365/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30365/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30365/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30365/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30365/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30365 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30365/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 36 through 48 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
HIS    2    2
ILE    3    2
GLN    4   14
GLU    5   12
VAL    6    1
VAL    7    1
GLN    8   13
THR    9    2
ILE   10    3
LYS   11   24
LEU   12    3
LEU   13    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.168.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.169.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.169.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.169.2.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.169.2 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30586


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30586/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30586/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30586/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30586/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30586/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30586/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30586 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30586/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 35 through 47 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    2
ILE    2    2
GLN    3    9
GLU    4   11
VAL    5    2
VAL    6    2
GLN    7   11
THR    8    1
ILE    9    4
LEU   11    3
LEU   12    3
THR   13    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.66415
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.169.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.170.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.170.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.170.4.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.170.4 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26580


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26580/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26580/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26580/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26580/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26580/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26580/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26580 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26580/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 34 through 46 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
GLN    2    7
GLU    3   12
VAL    4    2
VAL    5    1
GLN    6   14
THR    7    2
ILE    8    2
LYS    9   24
LEU   11    3
THR   12    2
GLU   13   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.170.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.171.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.171.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.171.5.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.171.5 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32245


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32245/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32245/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32245/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32245/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32245/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32245/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32245 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32245/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 33 through 45 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLU    2   13
VAL    3    2
VAL    4    1
GLN    5    9
THR    6    2
ILE    7    5
LYS    8   26
LEU    9    3
LEU   10    3
THR   11    2
GLU   12   15
LYS   13   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    5     12.3185
Cluster     1 =   2   5
2 clashing residues after turn 
Residue clashes:
2-5
cluster 1 has 2 members and 1.100e+01 combinations:
 5  2 
Energy     12.3185
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 1.100e+01 - Sending to search
6.374005 < 12.318486: keeping 
0.000000 < 6.439815: keeping 
Solved cluster 1: residual clashing  0.30
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.171.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.172.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.172.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.172.5.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.172.5 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29577


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29577/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29577/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29577/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29577/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29577/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29577/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29577 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29577/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 32 through 44 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
VAL    2    1
VAL    3    2
GLN    4    7
THR    5    1
ILE    6    2
LYS    7   23
LEU    8    2
LEU    9    3
LYS   12   24
THR   13    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    8.84286
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.172.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.173.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.173.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.173.5.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.173.5 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32709


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32709/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32709/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32709/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32709/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32709/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32709/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32709 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32709/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 31 through 43 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
VAL    2    3
GLN    3   12
ILE    5    3
LYS    6   26
LEU    7    2
GLU   10   15
LYS   11   24
THR   12    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    7     22.3885
Cluster     1 =   4   7
2 clashing residues after turn 
Residue clashes:
4-7
cluster 1 has 2 members and 1.210e+02 combinations:
 7  4 
Energy     23.3692
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 1.210e+02 - Sending to search
7.669165 < 23.369211: keeping 
0.000000 < 8.715668: keeping 
0.000000 < 1.284768: keeping 
Solved cluster 1: residual clashing  1.01
Still clashes at these sidechain pairs:
Residual clashes =    7.66566
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.173.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.175.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.175.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.175.5.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.175.5 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22306


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22306/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22306/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22306/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22306/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22306/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22306/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22306 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22306/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 31 through 42 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
THR    2    3
ILE    3    3
LYS    4   19
LEU    5    2
LEU    6    2
THR    7    1
GLU    8   11
LYS    9   24
THR   10    2
ARG   12   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    7     18.3441
Cluster     1 =   4   7
2 clashing residues after turn 
Residue clashes:
4-7
cluster 1 has 2 members and 3.000e+00 combinations:
 7  4 
Energy     23.2359
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 3.000e+00 - Sending to search
Solved cluster 1: residual clashing 23.24
Still clashes at these sidechain pairs:
ires=    4 irot=    1 jres=    7 jrot=    1      18.3441
Residual clashes =   18.34408
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.175.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.177.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.177.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.177.0.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.177.0 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13356


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13356/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13356/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13356/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13356/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13356/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13356/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13356 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13356/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 31 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
LYS    2   25
LEU    4    3
THR    5    2
GLU    6   12
LYS    7   16
THR    8    2
ARG   10   27
TYR   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.66067
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.177.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.178.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.178.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.178.1.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.178.1 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32547


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32547/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32547/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32547/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32547/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32547/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32547/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32547 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32547/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 30 through 40 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   32
LEU    2    4
LEU    3    3
THR    4    2
GLU    5   13
LYS    6   17
THR    7    1
ARG    9   24
TYR   10    3
GLN   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.11127
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.178.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.179.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.179.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.179.1.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.179.1 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9010


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9010/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9010/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9010/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9010/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9010/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9010/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9010 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9010/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 29 through 39 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
THR    3    2
GLU    4   15
LYS    5   26
ARG    8   21
TYR    9    2
GLN   10   12
GLN   11   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    9     25.1583
turnclash      9   11   11    0     68.9743
Cluster     1 =   6   9  11
3 clashing residues after turn 
Residue clashes:
6-9
9-11
cluster 1 has 3 members and 2.178e+03 combinations:
 11  9  6 
Energy     26.4418
Searching cluster 6
Combinations for 3 members in cluster 1 OK: 2.178e+03 - Sending to search
0.000000 < 26.441835: keeping 
0.000000 < 1.615898: keeping 
Solved cluster 1: residual clashing  1.42
Still clashes at these sidechain pairs:
Residual clashes =    5.65285
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.179.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.180.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.180.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.180.0.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.180.0 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30072


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30072/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30072/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30072/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30072/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30072/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30072/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30072 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30072/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 28 through 37 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
THR    2    2
GLU    3   16
LYS    4   28
THR    5    3
ARG    7   28
TYR    8    2
GLN    9   13
GLN   10    9
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.180.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.181.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.181.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.181.0.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.181.0 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28941


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28941/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28941/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28941/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28941/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28941/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28941/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28941 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28941/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 27 through 37 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
GLU    2   13
LYS    3   15
THR    4    3
ARG    6   30
TYR    7    3
GLN    8   10
GLN    9    7
LYS   10   26
LEU   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.181.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.182.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.182.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.182.1.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.182.1 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31693


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31693/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31693/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31693/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31693/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31693/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31693/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31693 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31693/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 26 through 36 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    2   24
THR    3    2
ARG    5   32
TYR    6    2
GLN    7   14
GLN    8   12
LYS    9   19
LEU   10    2
GLU   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     9   12     17.8370
turnclash      9    4    7    0     49.8372
Cluster     1 =   7   9  12
3 clashing residues after turn 
Residue clashes:
9-12
9-7
cluster 1 has 3 members and 1.100e+02 combinations:
 7  12  9 
Energy     18.5959
Searching cluster 7
Combinations for 3 members in cluster 1 OK: 1.100e+02 - Sending to search
8.442619 < 18.595861: keeping 
5.330055 < 9.267317: keeping 
0.000000 < 6.163525: keeping 
Solved cluster 1: residual clashing  0.90
Still clashes at these sidechain pairs:
Residual clashes =    1.04451
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.182.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dcs.183.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dcs.183.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dcs.183.3.a2m \
	-target T0124 -template 1dcs \
	-out T0124-1dcs.183.3 -outdir und
Skipped atom 866, because occupancy 0.5 <= existing 0.500001
Skipped atom 868, because occupancy 0.5 <= existing 0.500001
Skipped atom 870, because occupancy 0.5 <= existing 0.500001
Skipped atom 872, because occupancy 0.5 <= existing 0.500001
Skipped atom 874, because occupancy 0.5 <= existing 0.500001
Skipped atom 904, because occupancy 0.5 <= existing 0.500001
Skipped atom 906, because occupancy 0.5 <= existing 0.500001
Skipped atom 1429, because occupancy 0.5 <= existing 0.500001
Skipped atom 1431, because occupancy 0.5 <= existing 0.500001
Skipped atom 1433, because occupancy 0.5 <= existing 0.500001
Skipped atom 1435, because occupancy 0.5 <= existing 0.500001
Skipped atom 1437, because occupancy 0.5 <= existing 0.500001
Skipped atom 1439, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
Skipped atom 1457, because occupancy 0.5 <= existing 0.500001
Skipped atom 1459, because occupancy 0.5 <= existing 0.500001
Skipped atom 1461, because occupancy 0.5 <= existing 0.500001
Skipped atom 1463, because occupancy 0.5 <= existing 0.500001
Skipped atom 1465, because occupancy 0.5 <= existing 0.500001
Skipped atom 1467, because occupancy 0.5 <= existing 0.500001
Skipped atom 1469, because occupancy 0.5 <= existing 0.500001
Skipped atom 1471, because occupancy 0.5 <= existing 0.500001
Skipped atom 1473, because occupancy 0.5 <= existing 0.500001
Skipped atom 2084, because occupancy 0.5 <= existing 0.500001
Skipped atom 2086, because occupancy 0.5 <= existing 0.500001
Skipped atom 2088, because occupancy 0.5 <= existing 0.500001
Skipped atom 2090, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dcs-orig.a2m
Writing a2m file: tmp/1dcs-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-416


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-416/tmp -alignfile tmp/1dcs-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dcs-orig.a2m (1 sequences, 311 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-416/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-416/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-416/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-416/tmp.a2m (1 sequences, 311 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-416/tmp.mod tmp/1dcs-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-416 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dcs-align.mod
tmp/1dcs-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-416/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dcs-orig.a2m tmp/1dcs-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dcs-align.mod
Running w0.5 tmp/1dcs-orig.a2m tmp/1dcs-align.mod
Running align2model tmp/1dcs-align -i tmp/1dcs-align.mod -db tmp/1dcs-orig.a2m -db tmp/1dcs-pdb.a2m
partial PDB gets fragment 25 through 35 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
THR    2    2
ARG    4   27
TYR    5    2
GLN    6   17
GLN    7   12
LYS    8   25
GLU   10   16
GLU   11    7
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue Y 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dcs.183.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dekA.123.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dekA.123.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dekA.123.4.a2m \
	-target T0124 -template 1dekA \
	-out T0124-1dekA.123.4 -outdir und
Skipped atom 1140, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1192, because occupancy 0.5 <= existing 0.500001
Skipped atom 1194, because occupancy 0.5 <= existing 0.500001
Skipped atom 1196, because occupancy 0.5 <= existing 0.500001
Skipped atom 1198, because occupancy 0.5 <= existing 0.500001
Skipped atom 1200, because occupancy 0.5 <= existing 0.500001
Skipped atom 1345, because occupancy 0.4 <= existing 0.600001
Skipped atom 1347, because occupancy 0.4 <= existing 0.600001
Skipped atom 1349, because occupancy 0.4 <= existing 0.600001
Skipped atom 1446, because occupancy 0.5 <= existing 0.500001
Skipped atom 1448, because occupancy 0.5 <= existing 0.500001
Skipped atom 1450, because occupancy 0.5 <= existing 0.500001
Skipped atom 1452, because occupancy 0.5 <= existing 0.500001
Skipped atom 1454, because occupancy 0.5 <= existing 0.500001
Skipped atom 1456, because occupancy 0.5 <= existing 0.500001
Skipped atom 1458, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dekA-orig.a2m
Writing a2m file: tmp/1dekA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21502


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21502/tmp -alignfile tmp/1dekA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dekA-orig.a2m (1 sequences, 241 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21502/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21502/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21502/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21502/tmp.a2m (1 sequences, 241 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21502/tmp.mod tmp/1dekA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21502 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dekA-align.mod
tmp/1dekA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21502/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dekA-orig.a2m tmp/1dekA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dekA-align.mod
Running w0.5 tmp/1dekA-orig.a2m tmp/1dekA-align.mod
Running align2model tmp/1dekA-align -i tmp/1dekA-align.mod -db tmp/1dekA-orig.a2m -db tmp/1dekA-pdb.a2m
partial PDB gets fragment 63 through 72 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   17
GLU    2   13
SER    3    2
SER    4    2
SER    6    3
ILE    8    4
LYS    9   22
ASP   10    6
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     9   11     32.3377
Cluster     1 =   9  11
2 clashing residues after turn 
Residue clashes:
9-11
cluster 1 has 2 members and 1.500e+01 combinations:
 9  11 
Energy     34.8262
Searching cluster 9
Combinations for 2 members in cluster 1 OK: 1.500e+01 - Sending to search
0.000000 < 34.826202: keeping 
Solved cluster 1: residual clashing  1.83
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dekA.123.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dekA.124.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dekA.124.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dekA.124.2.a2m \
	-target T0124 -template 1dekA \
	-out T0124-1dekA.124.2 -outdir und
Skipped atom 1140, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1192, because occupancy 0.5 <= existing 0.500001
Skipped atom 1194, because occupancy 0.5 <= existing 0.500001
Skipped atom 1196, because occupancy 0.5 <= existing 0.500001
Skipped atom 1198, because occupancy 0.5 <= existing 0.500001
Skipped atom 1200, because occupancy 0.5 <= existing 0.500001
Skipped atom 1345, because occupancy 0.4 <= existing 0.600001
Skipped atom 1347, because occupancy 0.4 <= existing 0.600001
Skipped atom 1349, because occupancy 0.4 <= existing 0.600001
Skipped atom 1446, because occupancy 0.5 <= existing 0.500001
Skipped atom 1448, because occupancy 0.5 <= existing 0.500001
Skipped atom 1450, because occupancy 0.5 <= existing 0.500001
Skipped atom 1452, because occupancy 0.5 <= existing 0.500001
Skipped atom 1454, because occupancy 0.5 <= existing 0.500001
Skipped atom 1456, because occupancy 0.5 <= existing 0.500001
Skipped atom 1458, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dekA-orig.a2m
Writing a2m file: tmp/1dekA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28485


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28485/tmp -alignfile tmp/1dekA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dekA-orig.a2m (1 sequences, 241 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28485/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28485/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28485/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28485/tmp.a2m (1 sequences, 241 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28485/tmp.mod tmp/1dekA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28485 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dekA-align.mod
tmp/1dekA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28485/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dekA-orig.a2m tmp/1dekA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dekA-align.mod
Running w0.5 tmp/1dekA-orig.a2m tmp/1dekA-align.mod
Running align2model tmp/1dekA-align -i tmp/1dekA-align.mod -db tmp/1dekA-orig.a2m -db tmp/1dekA-pdb.a2m
partial PDB gets fragment 62 through 71 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
SER    2    2
SER    3    2
GLU    4   12
SER    5    2
ASN    6    4
ILE    7    4
LYS    8   27
ASP    9    4
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dekA.124.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dekA.125.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dekA.125.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dekA.125.3.a2m \
	-target T0124 -template 1dekA \
	-out T0124-1dekA.125.3 -outdir und
Skipped atom 1140, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1192, because occupancy 0.5 <= existing 0.500001
Skipped atom 1194, because occupancy 0.5 <= existing 0.500001
Skipped atom 1196, because occupancy 0.5 <= existing 0.500001
Skipped atom 1198, because occupancy 0.5 <= existing 0.500001
Skipped atom 1200, because occupancy 0.5 <= existing 0.500001
Skipped atom 1345, because occupancy 0.4 <= existing 0.600001
Skipped atom 1347, because occupancy 0.4 <= existing 0.600001
Skipped atom 1349, because occupancy 0.4 <= existing 0.600001
Skipped atom 1446, because occupancy 0.5 <= existing 0.500001
Skipped atom 1448, because occupancy 0.5 <= existing 0.500001
Skipped atom 1450, because occupancy 0.5 <= existing 0.500001
Skipped atom 1452, because occupancy 0.5 <= existing 0.500001
Skipped atom 1454, because occupancy 0.5 <= existing 0.500001
Skipped atom 1456, because occupancy 0.5 <= existing 0.500001
Skipped atom 1458, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dekA-orig.a2m
Writing a2m file: tmp/1dekA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31588


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31588/tmp -alignfile tmp/1dekA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dekA-orig.a2m (1 sequences, 241 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31588/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31588/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31588/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31588/tmp.a2m (1 sequences, 241 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31588/tmp.mod tmp/1dekA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31588 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dekA-align.mod
tmp/1dekA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31588/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dekA-orig.a2m tmp/1dekA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dekA-align.mod
Running w0.5 tmp/1dekA-orig.a2m tmp/1dekA-align.mod
Running align2model tmp/1dekA-align -i tmp/1dekA-align.mod -db tmp/1dekA-orig.a2m -db tmp/1dekA-pdb.a2m
partial PDB gets fragment 61 through 70 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
SER    2    3
GLU    3    8
SER    4    2
ASN    5    4
ILE    6    3
LYS    7   21
ASP    8    5
ILE    9    3
LYS   10   21
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dekA.125.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dekA.126.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dekA.126.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dekA.126.3.a2m \
	-target T0124 -template 1dekA \
	-out T0124-1dekA.126.3 -outdir und
Skipped atom 1140, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1192, because occupancy 0.5 <= existing 0.500001
Skipped atom 1194, because occupancy 0.5 <= existing 0.500001
Skipped atom 1196, because occupancy 0.5 <= existing 0.500001
Skipped atom 1198, because occupancy 0.5 <= existing 0.500001
Skipped atom 1200, because occupancy 0.5 <= existing 0.500001
Skipped atom 1345, because occupancy 0.4 <= existing 0.600001
Skipped atom 1347, because occupancy 0.4 <= existing 0.600001
Skipped atom 1349, because occupancy 0.4 <= existing 0.600001
Skipped atom 1446, because occupancy 0.5 <= existing 0.500001
Skipped atom 1448, because occupancy 0.5 <= existing 0.500001
Skipped atom 1450, because occupancy 0.5 <= existing 0.500001
Skipped atom 1452, because occupancy 0.5 <= existing 0.500001
Skipped atom 1454, because occupancy 0.5 <= existing 0.500001
Skipped atom 1456, because occupancy 0.5 <= existing 0.500001
Skipped atom 1458, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dekA-orig.a2m
Writing a2m file: tmp/1dekA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21609


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21609/tmp -alignfile tmp/1dekA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dekA-orig.a2m (1 sequences, 241 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21609/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21609/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21609/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21609/tmp.a2m (1 sequences, 241 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21609/tmp.mod tmp/1dekA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21609 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dekA-align.mod
tmp/1dekA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21609/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dekA-orig.a2m tmp/1dekA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dekA-align.mod
Running w0.5 tmp/1dekA-orig.a2m tmp/1dekA-align.mod
Running align2model tmp/1dekA-align -i tmp/1dekA-align.mod -db tmp/1dekA-orig.a2m -db tmp/1dekA-pdb.a2m
partial PDB gets fragment 60 through 69 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
GLU    2   11
SER    3    3
ASN    4    4
ILE    5    4
LYS    6   24
ASP    7    4
ILE    8    2
LYS    9   28
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7    9     15.4851
Cluster     1 =   7   9
2 clashing residues after turn 
Residue clashes:
7-9
cluster 1 has 2 members and 4.600e+01 combinations:
 9  7 
Energy     15.4851
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 4.600e+01 - Sending to search
0.000000 < 15.485062: keeping 
Solved cluster 1: residual clashing  0.42
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dekA.126.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dfmA.152.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dfmA.152.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dfmA.152.4.a2m \
	-target T0124 -template 1dfmA \
	-out T0124-1dfmA.152.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dfmA-orig.a2m
Writing a2m file: tmp/1dfmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28666


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28666/tmp -alignfile tmp/1dfmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dfmA-orig.a2m (1 sequences, 224 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28666/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28666/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28666/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28666/tmp.a2m (1 sequences, 224 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28666/tmp.mod tmp/1dfmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28666 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dfmA-align.mod
tmp/1dfmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28666/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dfmA-orig.a2m tmp/1dfmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dfmA-align.mod
Running w0.5 tmp/1dfmA-orig.a2m tmp/1dfmA-align.mod
Running align2model tmp/1dfmA-align -i tmp/1dfmA-align.mod -db tmp/1dfmA-orig.a2m -db tmp/1dfmA-pdb.a2m
partial PDB gets fragment 21 through 27 extending start extending end
partial PDB gets fragment 28 through 29 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
SER    2    3
ASP    3    4
LYS    4   24
GLN    7   11
ARG   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 11 rotamers of residue Q 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 26 rotamers of residue R 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dfmA.152.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dfmA.153.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dfmA.153.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dfmA.153.1.a2m \
	-target T0124 -template 1dfmA \
	-out T0124-1dfmA.153.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dfmA-orig.a2m
Writing a2m file: tmp/1dfmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-808


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-808/tmp -alignfile tmp/1dfmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dfmA-orig.a2m (1 sequences, 224 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-808/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-808/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-808/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-808/tmp.a2m (1 sequences, 224 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-808/tmp.mod tmp/1dfmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-808 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dfmA-align.mod
tmp/1dfmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-808/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dfmA-orig.a2m tmp/1dfmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dfmA-align.mod
Running w0.5 tmp/1dfmA-orig.a2m tmp/1dfmA-align.mod
Running align2model tmp/1dfmA-align -i tmp/1dfmA-align.mod -db tmp/1dfmA-orig.a2m -db tmp/1dfmA-pdb.a2m
partial PDB gets fragment 20 through 27 extending start extending end
partial PDB gets fragment 28 through 28 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
ASP    2    4
LYS    3   24
GLN    6   12
GLU    7   12
ARG    8   28
LYS   11   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 28 rotamers of residue R 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 25 rotamers of residue K 12 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dfmA.153.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dfmA.154.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dfmA.154.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dfmA.154.0.a2m \
	-target T0124 -template 1dfmA \
	-out T0124-1dfmA.154.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dfmA-orig.a2m
Writing a2m file: tmp/1dfmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27638


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27638/tmp -alignfile tmp/1dfmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dfmA-orig.a2m (1 sequences, 224 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27638/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27638/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27638/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27638/tmp.a2m (1 sequences, 224 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27638/tmp.mod tmp/1dfmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27638 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dfmA-align.mod
tmp/1dfmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27638/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dfmA-orig.a2m tmp/1dfmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dfmA-align.mod
Running w0.5 tmp/1dfmA-orig.a2m tmp/1dfmA-align.mod
Running align2model tmp/1dfmA-align -i tmp/1dfmA-align.mod -db tmp/1dfmA-orig.a2m -db tmp/1dfmA-pdb.a2m
partial PDB gets fragment 19 through 27 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
LYS    2   26
GLN    5   14
GLU    6   12
ARG    7   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dfmA.154.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dfmA.155.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dfmA.155.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dfmA.155.0.a2m \
	-target T0124 -template 1dfmA \
	-out T0124-1dfmA.155.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dfmA-orig.a2m
Writing a2m file: tmp/1dfmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1740


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1740/tmp -alignfile tmp/1dfmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dfmA-orig.a2m (1 sequences, 224 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1740/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1740/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1740/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1740/tmp.a2m (1 sequences, 224 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1740/tmp.mod tmp/1dfmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1740 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dfmA-align.mod
tmp/1dfmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1740/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dfmA-orig.a2m tmp/1dfmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dfmA-align.mod
Running w0.5 tmp/1dfmA-orig.a2m tmp/1dfmA-align.mod
Running align2model tmp/1dfmA-align -i tmp/1dfmA-align.mod -db tmp/1dfmA-orig.a2m -db tmp/1dfmA-pdb.a2m
partial PDB gets fragment 18 through 27 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
GLN    4   12
ARG    6   31
LEU    7    3
LYS    8   26
LYS    9   26
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dfmA.155.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dfmA.156.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dfmA.156.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dfmA.156.0.a2m \
	-target T0124 -template 1dfmA \
	-out T0124-1dfmA.156.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dfmA-orig.a2m
Writing a2m file: tmp/1dfmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-129


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-129/tmp -alignfile tmp/1dfmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dfmA-orig.a2m (1 sequences, 224 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-129/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-129/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-129/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-129/tmp.a2m (1 sequences, 224 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-129/tmp.mod tmp/1dfmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-129 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dfmA-align.mod
tmp/1dfmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-129/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dfmA-orig.a2m tmp/1dfmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dfmA-align.mod
Running w0.5 tmp/1dfmA-orig.a2m tmp/1dfmA-align.mod
Running align2model tmp/1dfmA-align -i tmp/1dfmA-align.mod -db tmp/1dfmA-orig.a2m -db tmp/1dfmA-pdb.a2m
partial PDB gets fragment 17 through 26 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    3   12
ARG    5   28
LEU    6    3
LYS    7   30
LYS    8   24
GLU    9   12
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dfmA.156.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dfmA.157.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dfmA.157.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dfmA.157.0.a2m \
	-target T0124 -template 1dfmA \
	-out T0124-1dfmA.157.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dfmA-orig.a2m
Writing a2m file: tmp/1dfmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18075


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18075/tmp -alignfile tmp/1dfmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dfmA-orig.a2m (1 sequences, 224 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18075/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18075/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18075/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18075/tmp.a2m (1 sequences, 224 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18075/tmp.mod tmp/1dfmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18075 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dfmA-align.mod
tmp/1dfmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18075/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dfmA-orig.a2m tmp/1dfmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dfmA-align.mod
Running w0.5 tmp/1dfmA-orig.a2m tmp/1dfmA-align.mod
Running align2model tmp/1dfmA-align -i tmp/1dfmA-align.mod -db tmp/1dfmA-orig.a2m -db tmp/1dfmA-pdb.a2m
partial PDB gets fragment 16 through 25 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    2   12
GLU    3   12
ARG    4   27
LEU    5    3
LYS    6   26
LYS    7   24
ILE    9    2
ASN   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dfmA.157.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dfmA.158.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dfmA.158.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dfmA.158.0.a2m \
	-target T0124 -template 1dfmA \
	-out T0124-1dfmA.158.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dfmA-orig.a2m
Writing a2m file: tmp/1dfmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7/tmp -alignfile tmp/1dfmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dfmA-orig.a2m (1 sequences, 224 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7/tmp.a2m (1 sequences, 224 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7/tmp.mod tmp/1dfmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dfmA-align.mod
tmp/1dfmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dfmA-orig.a2m tmp/1dfmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dfmA-align.mod
Running w0.5 tmp/1dfmA-orig.a2m tmp/1dfmA-align.mod
Running align2model tmp/1dfmA-align -i tmp/1dfmA-align.mod -db tmp/1dfmA-orig.a2m -db tmp/1dfmA-pdb.a2m
partial PDB gets fragment 15 through 24 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLU    2   12
ARG    3   27
LEU    4    3
LYS    6   23
GLU    7   12
ILE    8    2
ASN    9    4
ASN   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dfmA.158.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dfmA.159.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dfmA.159.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dfmA.159.1.a2m \
	-target T0124 -template 1dfmA \
	-out T0124-1dfmA.159.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dfmA-orig.a2m
Writing a2m file: tmp/1dfmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25484


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25484/tmp -alignfile tmp/1dfmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dfmA-orig.a2m (1 sequences, 224 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25484/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25484/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25484/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25484/tmp.a2m (1 sequences, 224 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25484/tmp.mod tmp/1dfmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25484 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dfmA-align.mod
tmp/1dfmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25484/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dfmA-orig.a2m tmp/1dfmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dfmA-align.mod
Running w0.5 tmp/1dfmA-orig.a2m tmp/1dfmA-align.mod
Running align2model tmp/1dfmA-align -i tmp/1dfmA-align.mod -db tmp/1dfmA-orig.a2m -db tmp/1dfmA-pdb.a2m
partial PDB gets fragment 14 through 23 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
ARG    2   27
LEU    3    3
LYS    4   26
LYS    5   26
GLU    6   12
ILE    7    3
ASN    8    4
ASN    9    4
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dfmA.159.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dfmA.160.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dfmA.160.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dfmA.160.4.a2m \
	-target T0124 -template 1dfmA \
	-out T0124-1dfmA.160.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dfmA-orig.a2m
Writing a2m file: tmp/1dfmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18955


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18955/tmp -alignfile tmp/1dfmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dfmA-orig.a2m (1 sequences, 224 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18955/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18955/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18955/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18955/tmp.a2m (1 sequences, 224 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18955/tmp.mod tmp/1dfmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18955 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dfmA-align.mod
tmp/1dfmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18955/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dfmA-orig.a2m tmp/1dfmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dfmA-align.mod
Running w0.5 tmp/1dfmA-orig.a2m tmp/1dfmA-align.mod
Running align2model tmp/1dfmA-align -i tmp/1dfmA-align.mod -db tmp/1dfmA-orig.a2m -db tmp/1dfmA-pdb.a2m
partial PDB gets fragment 13 through 22 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   29
LEU    2    3
LYS    3   26
LYS    4   26
GLU    5   12
ILE    6    3
ASN    7    4
ASN    8    4
SER    9    3
HIS   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    7     73.2767
Cluster     1 =   2   7
2 clashing residues after turn 
Residue clashes:
2-7
cluster 1 has 2 members and 2.400e+01 combinations:
 7  2 
Energy     74.5731
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 2.400e+01 - Sending to search
60.000000 < 74.573090: keeping 
44.840816 < 61.502167: keeping 
1.531744 < 46.366219: keeping 
0.000000 < 3.335220: keeping 
Solved cluster 1: residual clashing  3.09
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dfmA.160.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dfmA.161.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dfmA.161.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dfmA.161.3.a2m \
	-target T0124 -template 1dfmA \
	-out T0124-1dfmA.161.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dfmA-orig.a2m
Writing a2m file: tmp/1dfmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26543


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26543/tmp -alignfile tmp/1dfmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dfmA-orig.a2m (1 sequences, 224 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26543/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26543/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26543/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26543/tmp.a2m (1 sequences, 224 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26543/tmp.mod tmp/1dfmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26543 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dfmA-align.mod
tmp/1dfmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26543/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dfmA-orig.a2m tmp/1dfmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dfmA-align.mod
Running w0.5 tmp/1dfmA-orig.a2m tmp/1dfmA-align.mod
Running align2model tmp/1dfmA-align -i tmp/1dfmA-align.mod -db tmp/1dfmA-orig.a2m -db tmp/1dfmA-pdb.a2m
partial PDB gets fragment 12 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   28
LYS    3   28
GLU    4   12
ILE    5    3
ASN    6    4
ASN    7    4
SER    8    3
HIS    9    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    8     80.0000
Cluster     1 =   3   8
2 clashing residues after turn 
Residue clashes:
3-8
cluster 1 has 2 members and 1.000e+02 combinations:
 8  3 
Energy     80.0000
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 1.000e+02 - Sending to search
0.000000 < 80.000000: keeping 
Solved cluster 1: residual clashing  0.76
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dfmA.161.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dgyA.228.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dgyA.228.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dgyA.228.5.a2m \
	-target T0124 -template 1dgyA \
	-out T0124-1dgyA.228.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dgyA-orig.a2m
Writing a2m file: tmp/1dgyA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31382


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31382/tmp -alignfile tmp/1dgyA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dgyA-orig.a2m (1 sequences, 363 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31382/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31382/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31382/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31382/tmp.a2m (1 sequences, 363 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31382/tmp.mod tmp/1dgyA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31382 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dgyA-align.mod
tmp/1dgyA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31382/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dgyA-orig.a2m tmp/1dgyA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dgyA-align.mod
Running w0.5 tmp/1dgyA-orig.a2m tmp/1dgyA-align.mod
Running align2model tmp/1dgyA-align -i tmp/1dgyA-align.mod -db tmp/1dgyA-orig.a2m -db tmp/1dgyA-pdb.a2m
partial PDB gets fragment 0 through 2 extending end
Debugging on !
Reading sequence file
Reading input structure 
4 residues read 
Measuring phi and psi 
Getting chi values
TYR    0    3
MET    1   11
LYS    2   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dgyA.228.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dgyA.229.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dgyA.229.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dgyA.229.3.a2m \
	-target T0124 -template 1dgyA \
	-out T0124-1dgyA.229.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dgyA-orig.a2m
Writing a2m file: tmp/1dgyA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-910


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-910/tmp -alignfile tmp/1dgyA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dgyA-orig.a2m (1 sequences, 363 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-910/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-910/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-910/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-910/tmp.a2m (1 sequences, 363 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-910/tmp.mod tmp/1dgyA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-910 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dgyA-align.mod
tmp/1dgyA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-910/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dgyA-orig.a2m tmp/1dgyA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dgyA-align.mod
Running w0.5 tmp/1dgyA-orig.a2m tmp/1dgyA-align.mod
Running align2model tmp/1dgyA-align -i tmp/1dgyA-align.mod -db tmp/1dgyA-orig.a2m -db tmp/1dgyA-pdb.a2m
partial PDB gets fragment 0 through 1 extending end
Debugging on !
Reading sequence file
Reading input structure 
3 residues read 
Measuring phi and psi 
Getting chi values
LYS    0   30
GLU    1   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dgyA.229.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dgyA.230.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dgyA.230.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dgyA.230.2.a2m \
	-target T0124 -template 1dgyA \
	-out T0124-1dgyA.230.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dgyA-orig.a2m
Writing a2m file: tmp/1dgyA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1191


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1191/tmp -alignfile tmp/1dgyA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dgyA-orig.a2m (1 sequences, 363 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1191/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1191/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1191/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1191/tmp.a2m (1 sequences, 363 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1191/tmp.mod tmp/1dgyA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1191 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dgyA-align.mod
tmp/1dgyA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1191/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dgyA-orig.a2m tmp/1dgyA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dgyA-align.mod
Running w0.5 tmp/1dgyA-orig.a2m tmp/1dgyA-align.mod
Running align2model tmp/1dgyA-align -i tmp/1dgyA-align.mod -db tmp/1dgyA-orig.a2m -db tmp/1dgyA-pdb.a2m
partial PDB gets fragment 0 through 1 extending end
Debugging on !
Reading sequence file
Reading input structure 
3 residues read 
Measuring phi and psi 
Getting chi values
VAL    0    2
PHE    1    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dgyA.230.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dgyA.231.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dgyA.231.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dgyA.231.1.a2m \
	-target T0124 -template 1dgyA \
	-out T0124-1dgyA.231.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dgyA-orig.a2m
Writing a2m file: tmp/1dgyA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27025


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27025/tmp -alignfile tmp/1dgyA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dgyA-orig.a2m (1 sequences, 363 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27025/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27025/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27025/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27025/tmp.a2m (1 sequences, 363 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27025/tmp.mod tmp/1dgyA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27025 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dgyA-align.mod
tmp/1dgyA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27025/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dgyA-orig.a2m tmp/1dgyA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dgyA-align.mod
Running w0.5 tmp/1dgyA-orig.a2m tmp/1dgyA-align.mod
Running align2model tmp/1dgyA-align -i tmp/1dgyA-align.mod -db tmp/1dgyA-orig.a2m -db tmp/1dgyA-pdb.a2m
partial PDB gets fragment 0 through 0
sh: 2820 Memory fault
/projects/kestrel/users/karplus/burial/slicer/slicer: ERROR 'scwrl -v -i tmp/T0124-1dgyA.231.1.pdb -o tmp/T0124-1dgyA.231.1.scwrld-pdb -s tmp/T0124-1dgyA.231.1.scwrl-seq' failed.
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dgyA.231.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dozA.124.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dozA.124.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dozA.124.5.a2m \
	-target T0124 -template 1dozA \
	-out T0124-1dozA.124.5 -outdir und
partial PDB gets fragment 88 through 97 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    2    2
SER    3    2
GLU    4   12
SER    5    2
ASN    6    4
ILE    7    3
LYS    8   26
ASP    9    4
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dozA.124.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dozA.25.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dozA.25.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dozA.25.1.a2m \
	-target T0124 -template 1dozA \
	-out T0124-1dozA.25.1 -outdir und
partial PDB gets fragment 282 through 291 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   30
LEU    3    3
LEU    4    3
LYS    5   28
LYS    6   28
GLN    7   12
GLU    8    8
LYS    9   25
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    3.96213
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dozA.25.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dozA.26.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dozA.26.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dozA.26.4.a2m \
	-target T0124 -template 1dozA \
	-out T0124-1dozA.26.4 -outdir und
partial PDB gets fragment 281 through 291 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
LEU    2    3
LEU    3    3
LYS    4   25
LYS    5   30
GLN    6   13
GLU    7   16
LYS    8   25
GLU    9    8
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dozA.26.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dozA.27.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dozA.27.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dozA.27.3.a2m \
	-target T0124 -template 1dozA \
	-out T0124-1dozA.27.3 -outdir und
partial PDB gets fragment 280 through 290 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
LEU    2    3
LYS    3   27
LYS    4   30
GLN    5   13
GLU    6   16
LYS    7   28
GLU    8   16
LEU    9    3
LYS   10   19
GLU   11   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dozA.27.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dp7P.90.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dp7P.90.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dp7P.90.4.a2m \
	-target T0124 -template 1dp7P \
	-out T0124-1dp7P.90.4 -outdir und
partial PDB gets fragment 46 through 55 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
ILE    3    4
ARG    4   26
ARG    5   26
ARG    6   29
LYS    7   16
GLU    8   14
GLN    9   11
HIS   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dp7P.90.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dp7P.91.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dp7P.91.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dp7P.91.2.a2m \
	-target T0124 -template 1dp7P \
	-out T0124-1dp7P.91.2 -outdir und
partial PDB gets fragment 45 through 54 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    4   29
ARG    5   26
LYS    6   27
GLU    7   14
GLN    8    9
HIS    9    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dp7P.91.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dp7P.92.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dp7P.92.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dp7P.92.4.a2m \
	-target T0124 -template 1dp7P \
	-out T0124-1dp7P.92.4 -outdir und
partial PDB gets fragment 44 through 53 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
ARG    2   26
ARG    3   32
LYS    5   25
GLU    6   12
GLN    7   12
HIS    8    4
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dp7P.92.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dp7P.93.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dp7P.93.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dp7P.93.4.a2m \
	-target T0124 -template 1dp7P \
	-out T0124-1dp7P.93.4 -outdir und
partial PDB gets fragment 43 through 52 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
ARG    2   27
ARG    3   26
LYS    4   30
GLU    5   14
GLN    6   12
HIS    7    3
THR    9    2
GLU   10    9
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dp7P.93.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dpo.48.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dpo.48.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dpo.48.3.a2m \
	-target T0124 -template 1dpo \
	-out T0124-1dpo.48.3 -outdir und
Skipped atom 959, because occupancy 0.5 <= existing 0.500001
Skipped atom 961, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.45 <= existing 0.550001
Skipped atom 1078, because occupancy 0.45 <= existing 0.550001
Skipped atom 1080, because occupancy 0.45 <= existing 0.550001
Skipped atom 1239, because occupancy 1 <= existing 1
Skipped atom 1240, because occupancy 1 <= existing 1
Skipped atom 1241, because occupancy 1 <= existing 1
Skipped atom 1242, because occupancy 1 <= existing 1
Skipped atom 1275, because occupancy 1 <= existing 1
Skipped atom 1276, because occupancy 1 <= existing 1
Skipped atom 1277, because occupancy 1 <= existing 1
Skipped atom 1278, because occupancy 1 <= existing 1
Skipped atom 1474, because occupancy 1 <= existing 1
Skipped atom 1475, because occupancy 1 <= existing 1
Skipped atom 1476, because occupancy 1 <= existing 1
Skipped atom 1477, because occupancy 1 <= existing 1
Skipped atom 1478, because occupancy 1 <= existing 1
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dpo-orig.a2m
Writing a2m file: tmp/1dpo-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-616


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-616/tmp -alignfile tmp/1dpo-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dpo-orig.a2m (1 sequences, 223 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-616/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-616/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-616/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-616/tmp.a2m (1 sequences, 223 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-616/tmp.mod tmp/1dpo-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-616 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dpo-align.mod
tmp/1dpo-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-616/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dpo-orig.a2m tmp/1dpo-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dpo-align.mod
Running w0.5 tmp/1dpo-orig.a2m tmp/1dpo-align.mod
Running align2model tmp/1dpo-align -i tmp/1dpo-align.mod -db tmp/1dpo-orig.a2m -db tmp/1dpo-pdb.a2m
partial PDB gets fragment 203 through 212 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
LEU    2    3
LEU    3    3
GLN    4   15
LYS    5   21
SER    7    3
VAL    8    1
LEU    9    3
PHE   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dpo.48.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dpo.49.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dpo.49.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dpo.49.4.a2m \
	-target T0124 -template 1dpo \
	-out T0124-1dpo.49.4 -outdir und
Skipped atom 959, because occupancy 0.5 <= existing 0.500001
Skipped atom 961, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.45 <= existing 0.550001
Skipped atom 1078, because occupancy 0.45 <= existing 0.550001
Skipped atom 1080, because occupancy 0.45 <= existing 0.550001
Skipped atom 1239, because occupancy 1 <= existing 1
Skipped atom 1240, because occupancy 1 <= existing 1
Skipped atom 1241, because occupancy 1 <= existing 1
Skipped atom 1242, because occupancy 1 <= existing 1
Skipped atom 1275, because occupancy 1 <= existing 1
Skipped atom 1276, because occupancy 1 <= existing 1
Skipped atom 1277, because occupancy 1 <= existing 1
Skipped atom 1278, because occupancy 1 <= existing 1
Skipped atom 1474, because occupancy 1 <= existing 1
Skipped atom 1475, because occupancy 1 <= existing 1
Skipped atom 1476, because occupancy 1 <= existing 1
Skipped atom 1477, because occupancy 1 <= existing 1
Skipped atom 1478, because occupancy 1 <= existing 1
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1dpo-orig.a2m
Writing a2m file: tmp/1dpo-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32472


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32472/tmp -alignfile tmp/1dpo-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1dpo-orig.a2m (1 sequences, 223 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32472/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32472/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32472/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32472/tmp.a2m (1 sequences, 223 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32472/tmp.mod tmp/1dpo-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32472 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1dpo-align.mod
tmp/1dpo-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32472/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1dpo-orig.a2m tmp/1dpo-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1dpo-align.mod
Running w0.5 tmp/1dpo-orig.a2m tmp/1dpo-align.mod
Running align2model tmp/1dpo-align -i tmp/1dpo-align.mod -db tmp/1dpo-orig.a2m -db tmp/1dpo-pdb.a2m
partial PDB gets fragment 202 through 211 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LEU    2    3
GLN    3   11
LYS    4   30
TYR    5    3
SER    6    2
VAL    7    1
LEU    8    3
PHE    9    2
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dpo.49.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dugA.211.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dugA.211.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dugA.211.5.a2m \
	-target T0124 -template 1dugA \
	-out T0124-1dugA.211.5 -outdir und
partial PDB gets fragment 12 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   11
GLU    2   12
VAL    4    2
GLU    6   12
TYR    7    2
GLU    8   12
LYS   10   23
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dugA.211.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dugA.212.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dugA.212.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dugA.212.2.a2m \
	-target T0124 -template 1dugA \
	-out T0124-1dugA.212.2 -outdir und
partial PDB gets fragment 11 through 20 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
VAL    3    1
GLU    5   12
TYR    6    3
GLU    7   12
GLU    8   12
LYS    9   26
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.82253
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dugA.212.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1dugA.213.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1dugA.213.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1dugA.213.2.a2m \
	-target T0124 -template 1dugA \
	-out T0124-1dugA.213.2 -outdir und
partial PDB gets fragment 10 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    2    3
GLU    4   12
TYR    5    3
GLU    6   12
GLU    7   12
LYS    8   26
LYS   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1dugA.213.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.76.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.76.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.76.4.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.76.4 -outdir und
partial PDB gets fragment 135 through 144 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
LEU    2    3
GLU    3   12
MET    4   10
GLU    5   15
LEU    6    3
ILE    7    3
HIS    8    4
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.76.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.76.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.76.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.76.5.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.76.5 -outdir und
partial PDB gets fragment 131 through 140 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
LEU    2    3
GLU    3   13
MET    4   11
GLU    5   12
LEU    6    3
ILE    7    3
HIS    8    4
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.76.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.77.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.77.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.77.4.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.77.4 -outdir und
partial PDB gets fragment 134 through 143 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   12
MET    3   12
GLU    4   12
LEU    5    3
ILE    6    4
HIS    7    4
LEU    8    3
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue L 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    7     45.3152
Cluster     1 =   2   7
2 clashing residues after turn 
Residue clashes:
2-7
cluster 1 has 2 members and 3.000e+00 combinations:
 2  7 
Energy    135.0476
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 3.000e+00 - Sending to search
14.521895 < 135.047577: keeping 
Solved cluster 1: residual clashing 38.73
Still clashes at these sidechain pairs:
ires=    2 irot=    2 jres=    7 jrot=    4      14.5219
Residual clashes =   19.14823
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.77.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.77.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.77.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.77.5.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.77.5 -outdir und
partial PDB gets fragment 130 through 139 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   13
MET    3   12
GLU    4   13
LEU    5    3
ILE    6    2
HIS    7    4
LEU    8    3
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.77.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.78.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.78.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.78.2.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.78.2 -outdir und
partial PDB gets fragment 133 through 142 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
MET    2   11
GLU    3   12
LEU    4    3
ILE    5    3
HIS    6    4
LEU    7    3
GLU    9   12
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.78.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.78.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.78.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.78.4.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.78.4 -outdir und
partial PDB gets fragment 129 through 138 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1    7
MET    2    9
GLU    3   13
LEU    4    3
ILE    5    2
HIS    6    3
LEU    7    3
GLU    9   12
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.78.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.79.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.79.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.79.2.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.79.2 -outdir und
partial PDB gets fragment 132 through 141 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   12
GLU    2   13
LEU    3    3
ILE    4    2
HIS    5    4
LEU    6    3
GLU    8   15
GLU    9   15
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.79.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.80.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.80.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.80.2.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.80.2 -outdir und
partial PDB gets fragment 131 through 140 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
LEU    2    3
ILE    3    2
HIS    4    3
LEU    5    3
GLU    7   12
GLU    8   12
TYR    9    3
HIS   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.80.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.80.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.80.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.80.4.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.80.4 -outdir und
partial PDB gets fragment 127 through 136 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    3
ILE    3    3
HIS    4    3
LEU    5    4
GLU    7   13
GLU    8   13
TYR    9    2
HIS   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.80.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.81.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.81.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.81.0.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.81.0 -outdir und
partial PDB gets fragment 130 through 139 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ILE    2    2
HIS    3    4
LEU    4    3
GLU    6   12
GLU    7   15
TYR    8    3
HIS    9    4
ASP   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.81.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.82.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.82.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.82.0.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.82.0 -outdir und
partial PDB gets fragment 129 through 138 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
HIS    2    3
LEU    3    4
GLU    5   13
GLU    6   13
TYR    7    2
HIS    8    4
ASP    9    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.78348
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.82.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.83.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.83.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.83.1.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.83.1 -outdir und
partial PDB gets fragment 128 through 137 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
GLU    4   13
GLU    5   14
TYR    6    3
HIS    7    3
ASP    8    4
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.83.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.84.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.84.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.84.0.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.84.0 -outdir und
partial PDB gets fragment 127 through 136 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    3    7
GLU    4   12
TYR    5    2
HIS    6    4
ASP    7    4
ILE    9    2
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.84.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.85.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.85.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.85.0.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.85.0 -outdir und
partial PDB gets fragment 126 through 135 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    3   12
TYR    4    2
HIS    5    3
ASP    6    5
ILE    8    2
ARG    9   27
ARG   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.85.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.86.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.86.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.86.0.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.86.0 -outdir und
partial PDB gets fragment 125 through 134 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
GLU    2   15
TYR    3    3
HIS    4    3
ASP    5    5
ILE    7    2
ARG    8   29
ARG    9   26
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    8     40.3935
turnclash      3    4   10    0     42.4298
Cluster     1 =   3   8  10
3 clashing residues after turn 
Residue clashes:
3-8
3-10
cluster 1 has 3 members and 2.080e+02 combinations:
 10  8  3 
Energy     40.3935
Searching cluster 3
Combinations for 3 members in cluster 1 OK: 2.080e+02 - Sending to search
23.813131 < 40.393490: keeping 
14.201122 < 25.004169: keeping 
13.526886 < 15.886424: keeping 
0.393489 < 15.249882: keeping 
Solved cluster 1: residual clashing  1.34
Still clashes at these sidechain pairs:
Residual clashes =    0.39349
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.86.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.87.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.87.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.87.0.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.87.0 -outdir und
partial PDB gets fragment 124 through 133 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   16
TYR    2    2
HIS    3    4
ASP    4    4
ILE    6    3
ARG    8   30
ARG    9   29
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.87.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.88.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.88.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.88.0.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.88.0 -outdir und
partial PDB gets fragment 123 through 132 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
HIS    2    4
ASP    3    5
ILE    5    5
ARG    6   30
ARG    7   18
LYS    9   25
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.88.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.89.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.89.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.89.0.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.89.0 -outdir und
partial PDB gets fragment 122 through 131 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
ASP    2    6
ILE    4    3
ARG    5   30
ARG    6   32
ARG    7   30
LYS    8   18
GLU    9   12
GLN   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.89.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.90.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.90.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.90.0.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.90.0 -outdir und
partial PDB gets fragment 121 through 130 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    4   29
ARG    5   27
ARG    6   30
LYS    7   30
GLU    8   15
GLN    9    7
HIS   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.90.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1duzA.91.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1duzA.91.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1duzA.91.3.a2m \
	-target T0124 -template 1duzA \
	-out T0124-1duzA.91.3 -outdir und
partial PDB gets fragment 120 through 129 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    2    4
ARG    3   26
ARG    4   32
ARG    5   32
LYS    6   27
GLU    7   15
GLN    8   14
HIS    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1duzA.91.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ecpA.186.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ecpA.186.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ecpA.186.5.a2m \
	-target T0124 -template 1ecpA \
	-out T0124-1ecpA.186.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ecpA-orig.a2m
Writing a2m file: tmp/1ecpA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-346


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-346/tmp -alignfile tmp/1ecpA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ecpA-orig.a2m (1 sequences, 238 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-346/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-346/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-346/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-346/tmp.a2m (1 sequences, 238 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-346/tmp.mod tmp/1ecpA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-346 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ecpA-align.mod
tmp/1ecpA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-346/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ecpA-orig.a2m tmp/1ecpA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ecpA-align.mod
Running w0.5 tmp/1ecpA-orig.a2m tmp/1ecpA-align.mod
Running align2model tmp/1ecpA-align -i tmp/1ecpA-align.mod -db tmp/1ecpA-orig.a2m -db tmp/1ecpA-pdb.a2m
partial PDB gets fragment 21 through 30 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
TYR    2    3
GLN    3   14
GLN    4   11
LEU    6    3
GLU    7   12
GLU    8   12
LYS    9   29
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ecpA.186.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ek0A.103.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ek0A.103.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ek0A.103.5.a2m \
	-target T0124 -template 1ek0A \
	-out T0124-1ek0A.103.5 -outdir und
Skipped atom 20, because occupancy 0.16 <= existing 0.840001
Skipped atom 22, because occupancy 0.16 <= existing 0.840001
Skipped atom 80, because occupancy 0.46 <= existing 0.540001
Skipped atom 82, because occupancy 0.46 <= existing 0.540001
Skipped atom 84, because occupancy 0.46 <= existing 0.540001
Skipped atom 86, because occupancy 0.46 <= existing 0.540001
Skipped atom 88, because occupancy 0.46 <= existing 0.540001
Skipped atom 608, because occupancy 0.23 <= existing 0.770001
Skipped atom 610, because occupancy 0.23 <= existing 0.770001
Skipped atom 612, because occupancy 0.23 <= existing 0.770001
Skipped atom 614, because occupancy 0.23 <= existing 0.770001
Skipped atom 842, because occupancy 0.4 <= existing 0.610001
Skipped atom 844, because occupancy 0.4 <= existing 0.610001
Skipped atom 846, because occupancy 0.4 <= existing 0.610001
Skipped atom 848, because occupancy 0.4 <= existing 0.610001
Skipped atom 850, because occupancy 0.4 <= existing 0.610001
Skipped atom 852, because occupancy 0.4 <= existing 0.610001
Skipped atom 1074, because occupancy 0.41 <= existing 0.590001
Skipped atom 1076, because occupancy 0.41 <= existing 0.590001
Skipped atom 1078, because occupancy 0.41 <= existing 0.590001
Skipped atom 1080, because occupancy 0.41 <= existing 0.590001
Skipped atom 1082, because occupancy 0.41 <= existing 0.590001
Skipped atom 1084, because occupancy 0.41 <= existing 0.590001
Skipped atom 1086, because occupancy 0.41 <= existing 0.590001
Skipped atom 1331, because occupancy 0.27 <= existing 0.730001
Skipped atom 1333, because occupancy 0.27 <= existing 0.730001
Skipped atom 1335, because occupancy 0.27 <= existing 0.730001
Skipped atom 1337, because occupancy 0.27 <= existing 0.730001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ek0A-orig.a2m
Writing a2m file: tmp/1ek0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23291


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23291/tmp -alignfile tmp/1ek0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ek0A-orig.a2m (1 sequences, 170 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23291/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23291/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23291/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23291/tmp.a2m (1 sequences, 170 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23291/tmp.mod tmp/1ek0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23291 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ek0A-align.mod
tmp/1ek0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23291/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ek0A-orig.a2m tmp/1ek0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ek0A-align.mod
Running w0.5 tmp/1ek0A-orig.a2m tmp/1ek0A-align.mod
Running align2model tmp/1ek0A-align -i tmp/1ek0A-align.mod -db tmp/1ek0A-orig.a2m -db tmp/1ek0A-pdb.a2m
partial PDB gets fragment 79 through 88 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
THR    2    2
LYS    4   27
ILE    5    4
GLU    7   13
LEU    8    3
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   11     55.8214
turnclash     11    6    8    0     36.1655
Cluster     1 =   5   8  11
3 clashing residues after turn 
Residue clashes:
5-11
5-8
11-8
cluster 1 has 3 members and 2.990e+03 combinations:
 8  11  5 
Energy     60.6369
Searching cluster 5
Combinations for 3 members in cluster 1 OK: 2.990e+03 - Sending to search
4.097527 < 60.636936: keeping 
3.638459 < 5.379778: keeping 
0.000000 < 4.922009: keeping 
0.000000 < 2.453443: keeping 
Solved cluster 1: residual clashing  2.43
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ek0A.103.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ek0A.104.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ek0A.104.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ek0A.104.5.a2m \
	-target T0124 -template 1ek0A \
	-out T0124-1ek0A.104.5 -outdir und
Skipped atom 20, because occupancy 0.16 <= existing 0.840001
Skipped atom 22, because occupancy 0.16 <= existing 0.840001
Skipped atom 80, because occupancy 0.46 <= existing 0.540001
Skipped atom 82, because occupancy 0.46 <= existing 0.540001
Skipped atom 84, because occupancy 0.46 <= existing 0.540001
Skipped atom 86, because occupancy 0.46 <= existing 0.540001
Skipped atom 88, because occupancy 0.46 <= existing 0.540001
Skipped atom 608, because occupancy 0.23 <= existing 0.770001
Skipped atom 610, because occupancy 0.23 <= existing 0.770001
Skipped atom 612, because occupancy 0.23 <= existing 0.770001
Skipped atom 614, because occupancy 0.23 <= existing 0.770001
Skipped atom 842, because occupancy 0.4 <= existing 0.610001
Skipped atom 844, because occupancy 0.4 <= existing 0.610001
Skipped atom 846, because occupancy 0.4 <= existing 0.610001
Skipped atom 848, because occupancy 0.4 <= existing 0.610001
Skipped atom 850, because occupancy 0.4 <= existing 0.610001
Skipped atom 852, because occupancy 0.4 <= existing 0.610001
Skipped atom 1074, because occupancy 0.41 <= existing 0.590001
Skipped atom 1076, because occupancy 0.41 <= existing 0.590001
Skipped atom 1078, because occupancy 0.41 <= existing 0.590001
Skipped atom 1080, because occupancy 0.41 <= existing 0.590001
Skipped atom 1082, because occupancy 0.41 <= existing 0.590001
Skipped atom 1084, because occupancy 0.41 <= existing 0.590001
Skipped atom 1086, because occupancy 0.41 <= existing 0.590001
Skipped atom 1331, because occupancy 0.27 <= existing 0.730001
Skipped atom 1333, because occupancy 0.27 <= existing 0.730001
Skipped atom 1335, because occupancy 0.27 <= existing 0.730001
Skipped atom 1337, because occupancy 0.27 <= existing 0.730001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ek0A-orig.a2m
Writing a2m file: tmp/1ek0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3026


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3026/tmp -alignfile tmp/1ek0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ek0A-orig.a2m (1 sequences, 170 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3026/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3026/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3026/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3026/tmp.a2m (1 sequences, 170 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3026/tmp.mod tmp/1ek0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3026 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ek0A-align.mod
tmp/1ek0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3026/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ek0A-orig.a2m tmp/1ek0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ek0A-align.mod
Running w0.5 tmp/1ek0A-orig.a2m tmp/1ek0A-align.mod
Running align2model tmp/1ek0A-align -i tmp/1ek0A-align.mod -db tmp/1ek0A-orig.a2m -db tmp/1ek0A-pdb.a2m
partial PDB gets fragment 78 through 87 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
LYS    3   27
ILE    4    2
THR    5    2
GLU    6   15
LEU    7    2
ARG    9   32
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ek0A.104.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ek0A.107.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ek0A.107.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ek0A.107.5.a2m \
	-target T0124 -template 1ek0A \
	-out T0124-1ek0A.107.5 -outdir und
Skipped atom 20, because occupancy 0.16 <= existing 0.840001
Skipped atom 22, because occupancy 0.16 <= existing 0.840001
Skipped atom 80, because occupancy 0.46 <= existing 0.540001
Skipped atom 82, because occupancy 0.46 <= existing 0.540001
Skipped atom 84, because occupancy 0.46 <= existing 0.540001
Skipped atom 86, because occupancy 0.46 <= existing 0.540001
Skipped atom 88, because occupancy 0.46 <= existing 0.540001
Skipped atom 608, because occupancy 0.23 <= existing 0.770001
Skipped atom 610, because occupancy 0.23 <= existing 0.770001
Skipped atom 612, because occupancy 0.23 <= existing 0.770001
Skipped atom 614, because occupancy 0.23 <= existing 0.770001
Skipped atom 842, because occupancy 0.4 <= existing 0.610001
Skipped atom 844, because occupancy 0.4 <= existing 0.610001
Skipped atom 846, because occupancy 0.4 <= existing 0.610001
Skipped atom 848, because occupancy 0.4 <= existing 0.610001
Skipped atom 850, because occupancy 0.4 <= existing 0.610001
Skipped atom 852, because occupancy 0.4 <= existing 0.610001
Skipped atom 1074, because occupancy 0.41 <= existing 0.590001
Skipped atom 1076, because occupancy 0.41 <= existing 0.590001
Skipped atom 1078, because occupancy 0.41 <= existing 0.590001
Skipped atom 1080, because occupancy 0.41 <= existing 0.590001
Skipped atom 1082, because occupancy 0.41 <= existing 0.590001
Skipped atom 1084, because occupancy 0.41 <= existing 0.590001
Skipped atom 1086, because occupancy 0.41 <= existing 0.590001
Skipped atom 1331, because occupancy 0.27 <= existing 0.730001
Skipped atom 1333, because occupancy 0.27 <= existing 0.730001
Skipped atom 1335, because occupancy 0.27 <= existing 0.730001
Skipped atom 1337, because occupancy 0.27 <= existing 0.730001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ek0A-orig.a2m
Writing a2m file: tmp/1ek0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1453


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1453/tmp -alignfile tmp/1ek0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ek0A-orig.a2m (1 sequences, 170 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1453/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1453/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1453/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1453/tmp.a2m (1 sequences, 170 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1453/tmp.mod tmp/1ek0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1453 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ek0A-align.mod
tmp/1ek0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1453/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ek0A-orig.a2m tmp/1ek0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ek0A-align.mod
Running w0.5 tmp/1ek0A-orig.a2m tmp/1ek0A-align.mod
Running align2model tmp/1ek0A-align -i tmp/1ek0A-align.mod -db tmp/1ek0A-orig.a2m -db tmp/1ek0A-pdb.a2m
partial PDB gets fragment 75 through 84 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    5
THR    2    3
GLU    3   15
ARG    6   28
GLU    7   13
LYS    8   27
GLN    9   15
ILE   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ek0A.107.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ek0A.108.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ek0A.108.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ek0A.108.5.a2m \
	-target T0124 -template 1ek0A \
	-out T0124-1ek0A.108.5 -outdir und
Skipped atom 20, because occupancy 0.16 <= existing 0.840001
Skipped atom 22, because occupancy 0.16 <= existing 0.840001
Skipped atom 80, because occupancy 0.46 <= existing 0.540001
Skipped atom 82, because occupancy 0.46 <= existing 0.540001
Skipped atom 84, because occupancy 0.46 <= existing 0.540001
Skipped atom 86, because occupancy 0.46 <= existing 0.540001
Skipped atom 88, because occupancy 0.46 <= existing 0.540001
Skipped atom 608, because occupancy 0.23 <= existing 0.770001
Skipped atom 610, because occupancy 0.23 <= existing 0.770001
Skipped atom 612, because occupancy 0.23 <= existing 0.770001
Skipped atom 614, because occupancy 0.23 <= existing 0.770001
Skipped atom 842, because occupancy 0.4 <= existing 0.610001
Skipped atom 844, because occupancy 0.4 <= existing 0.610001
Skipped atom 846, because occupancy 0.4 <= existing 0.610001
Skipped atom 848, because occupancy 0.4 <= existing 0.610001
Skipped atom 850, because occupancy 0.4 <= existing 0.610001
Skipped atom 852, because occupancy 0.4 <= existing 0.610001
Skipped atom 1074, because occupancy 0.41 <= existing 0.590001
Skipped atom 1076, because occupancy 0.41 <= existing 0.590001
Skipped atom 1078, because occupancy 0.41 <= existing 0.590001
Skipped atom 1080, because occupancy 0.41 <= existing 0.590001
Skipped atom 1082, because occupancy 0.41 <= existing 0.590001
Skipped atom 1084, because occupancy 0.41 <= existing 0.590001
Skipped atom 1086, because occupancy 0.41 <= existing 0.590001
Skipped atom 1331, because occupancy 0.27 <= existing 0.730001
Skipped atom 1333, because occupancy 0.27 <= existing 0.730001
Skipped atom 1335, because occupancy 0.27 <= existing 0.730001
Skipped atom 1337, because occupancy 0.27 <= existing 0.730001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ek0A-orig.a2m
Writing a2m file: tmp/1ek0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1470


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1470/tmp -alignfile tmp/1ek0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ek0A-orig.a2m (1 sequences, 170 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1470/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1470/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1470/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1470/tmp.a2m (1 sequences, 170 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1470/tmp.mod tmp/1ek0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1470 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ek0A-align.mod
tmp/1ek0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1470/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ek0A-orig.a2m tmp/1ek0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ek0A-align.mod
Running w0.5 tmp/1ek0A-orig.a2m tmp/1ek0A-align.mod
Running align2model tmp/1ek0A-align -i tmp/1ek0A-align.mod -db tmp/1ek0A-orig.a2m -db tmp/1ek0A-pdb.a2m
partial PDB gets fragment 74 through 83 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
GLU    2   14
LEU    3    5
ARG    5   26
GLU    6   12
LYS    7   27
GLN    8   11
ILE    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ek0A.108.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ek0A.109.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ek0A.109.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ek0A.109.4.a2m \
	-target T0124 -template 1ek0A \
	-out T0124-1ek0A.109.4 -outdir und
Skipped atom 20, because occupancy 0.16 <= existing 0.840001
Skipped atom 22, because occupancy 0.16 <= existing 0.840001
Skipped atom 80, because occupancy 0.46 <= existing 0.540001
Skipped atom 82, because occupancy 0.46 <= existing 0.540001
Skipped atom 84, because occupancy 0.46 <= existing 0.540001
Skipped atom 86, because occupancy 0.46 <= existing 0.540001
Skipped atom 88, because occupancy 0.46 <= existing 0.540001
Skipped atom 608, because occupancy 0.23 <= existing 0.770001
Skipped atom 610, because occupancy 0.23 <= existing 0.770001
Skipped atom 612, because occupancy 0.23 <= existing 0.770001
Skipped atom 614, because occupancy 0.23 <= existing 0.770001
Skipped atom 842, because occupancy 0.4 <= existing 0.610001
Skipped atom 844, because occupancy 0.4 <= existing 0.610001
Skipped atom 846, because occupancy 0.4 <= existing 0.610001
Skipped atom 848, because occupancy 0.4 <= existing 0.610001
Skipped atom 850, because occupancy 0.4 <= existing 0.610001
Skipped atom 852, because occupancy 0.4 <= existing 0.610001
Skipped atom 1074, because occupancy 0.41 <= existing 0.590001
Skipped atom 1076, because occupancy 0.41 <= existing 0.590001
Skipped atom 1078, because occupancy 0.41 <= existing 0.590001
Skipped atom 1080, because occupancy 0.41 <= existing 0.590001
Skipped atom 1082, because occupancy 0.41 <= existing 0.590001
Skipped atom 1084, because occupancy 0.41 <= existing 0.590001
Skipped atom 1086, because occupancy 0.41 <= existing 0.590001
Skipped atom 1331, because occupancy 0.27 <= existing 0.730001
Skipped atom 1333, because occupancy 0.27 <= existing 0.730001
Skipped atom 1335, because occupancy 0.27 <= existing 0.730001
Skipped atom 1337, because occupancy 0.27 <= existing 0.730001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ek0A-orig.a2m
Writing a2m file: tmp/1ek0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-521


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-521/tmp -alignfile tmp/1ek0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ek0A-orig.a2m (1 sequences, 170 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-521/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-521/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-521/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-521/tmp.a2m (1 sequences, 170 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-521/tmp.mod tmp/1ek0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-521 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ek0A-align.mod
tmp/1ek0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-521/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ek0A-orig.a2m tmp/1ek0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ek0A-align.mod
Running w0.5 tmp/1ek0A-orig.a2m tmp/1ek0A-align.mod
Running align2model tmp/1ek0A-align -i tmp/1ek0A-align.mod -db tmp/1ek0A-orig.a2m -db tmp/1ek0A-pdb.a2m
partial PDB gets fragment 73 through 82 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   10
LEU    2    3
ARG    4   32
GLU    5   15
LYS    6   26
GLN    7   12
ILE    8    4
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ek0A.109.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ek0A.110.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ek0A.110.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ek0A.110.4.a2m \
	-target T0124 -template 1ek0A \
	-out T0124-1ek0A.110.4 -outdir und
Skipped atom 20, because occupancy 0.16 <= existing 0.840001
Skipped atom 22, because occupancy 0.16 <= existing 0.840001
Skipped atom 80, because occupancy 0.46 <= existing 0.540001
Skipped atom 82, because occupancy 0.46 <= existing 0.540001
Skipped atom 84, because occupancy 0.46 <= existing 0.540001
Skipped atom 86, because occupancy 0.46 <= existing 0.540001
Skipped atom 88, because occupancy 0.46 <= existing 0.540001
Skipped atom 608, because occupancy 0.23 <= existing 0.770001
Skipped atom 610, because occupancy 0.23 <= existing 0.770001
Skipped atom 612, because occupancy 0.23 <= existing 0.770001
Skipped atom 614, because occupancy 0.23 <= existing 0.770001
Skipped atom 842, because occupancy 0.4 <= existing 0.610001
Skipped atom 844, because occupancy 0.4 <= existing 0.610001
Skipped atom 846, because occupancy 0.4 <= existing 0.610001
Skipped atom 848, because occupancy 0.4 <= existing 0.610001
Skipped atom 850, because occupancy 0.4 <= existing 0.610001
Skipped atom 852, because occupancy 0.4 <= existing 0.610001
Skipped atom 1074, because occupancy 0.41 <= existing 0.590001
Skipped atom 1076, because occupancy 0.41 <= existing 0.590001
Skipped atom 1078, because occupancy 0.41 <= existing 0.590001
Skipped atom 1080, because occupancy 0.41 <= existing 0.590001
Skipped atom 1082, because occupancy 0.41 <= existing 0.590001
Skipped atom 1084, because occupancy 0.41 <= existing 0.590001
Skipped atom 1086, because occupancy 0.41 <= existing 0.590001
Skipped atom 1331, because occupancy 0.27 <= existing 0.730001
Skipped atom 1333, because occupancy 0.27 <= existing 0.730001
Skipped atom 1335, because occupancy 0.27 <= existing 0.730001
Skipped atom 1337, because occupancy 0.27 <= existing 0.730001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ek0A-orig.a2m
Writing a2m file: tmp/1ek0A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31973


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31973/tmp -alignfile tmp/1ek0A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ek0A-orig.a2m (1 sequences, 170 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31973/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31973/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31973/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31973/tmp.a2m (1 sequences, 170 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31973/tmp.mod tmp/1ek0A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31973 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ek0A-align.mod
tmp/1ek0A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31973/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ek0A-orig.a2m tmp/1ek0A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ek0A-align.mod
Running w0.5 tmp/1ek0A-orig.a2m tmp/1ek0A-align.mod
Running align2model tmp/1ek0A-align -i tmp/1ek0A-align.mod -db tmp/1ek0A-orig.a2m -db tmp/1ek0A-pdb.a2m
partial PDB gets fragment 72 through 81 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ARG    3   30
GLU    4   14
LYS    5   32
GLN    6   14
ILE    7    2
GLU    9   13
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ek0A.110.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elkA.59.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elkA.59.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elkA.59.2.a2m \
	-target T0124 -template 1elkA \
	-out T0124-1elkA.59.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elkA-orig.a2m
Writing a2m file: tmp/1elkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32101


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32101/tmp -alignfile tmp/1elkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elkA-orig.a2m (1 sequences, 157 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32101/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32101/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32101/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32101/tmp.a2m (1 sequences, 157 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32101/tmp.mod tmp/1elkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32101 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elkA-align.mod
tmp/1elkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32101/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elkA-orig.a2m tmp/1elkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elkA-align.mod
Running w0.5 tmp/1elkA-orig.a2m tmp/1elkA-align.mod
Running align2model tmp/1elkA-align -i tmp/1elkA-align.mod -db tmp/1elkA-orig.a2m -db tmp/1elkA-pdb.a2m
partial PDB gets fragment 120 through 129 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
PRO    2    2
VAL    3    2
TYR    4    3
PRO    5    2
ARG    6   27
LEU    8    2
ASP    9    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    9     68.1685
Cluster     1 =   5   9
2 clashing residues after turn 
Residue clashes:
5-9
cluster 1 has 2 members and 2.000e+00 combinations:
 9  5 
Energy     68.1684
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search
0.000000 < 68.168449: keeping 
Solved cluster 1: residual clashing  2.18
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elkA.59.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.21.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.21.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.21.2.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.21.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27874


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27874/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27874/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27874/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27874/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27874/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27874/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27874 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27874/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 119 through 127 extending start
Debugging on !
Reading sequence file
Reading input structure 
10 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
LYS    2   26
LEU    3    3
PHE    4    3
LEU    5    3
LYS    6   25
LEU    7    3
LEU    8    3
LYS    9   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.46354
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.21.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.22.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.22.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.22.0.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.22.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29289


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29289/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29289/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29289/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29289/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29289/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29289/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29289 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29289/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 118 through 127 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LEU    2    3
PHE    3    3
LEU    4    3
LEU    6    3
LYS    9   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.22.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.23.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.23.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.23.0.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.23.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18905


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18905/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18905/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18905/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18905/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18905/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18905/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18905 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18905/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 117 through 126 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
PHE    2    3
LEU    3    3
LYS    4   26
LEU    5    3
LEU    6    3
LYS    7   26
LYS    8   25
GLN    9   13
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.38656
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.23.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.24.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.24.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.24.0.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.24.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2826


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2826/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2826/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2826/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2826/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2826/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2826/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2826 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2826/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 116 through 125 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PHE    1    3
LEU    2    3
LYS    3   26
LEU    4    3
LEU    5    3
LYS    6   26
GLN    8   13
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.11262
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.24.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.25.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.25.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.25.0.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.25.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31273


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31273/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31273/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31273/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31273/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31273/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31273/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31273 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31273/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 115 through 124 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LEU    3    3
LEU    4    3
LYS    5   24
LYS    6   26
GLN    7   12
GLU    8   12
LYS    9   26
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.25.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.25.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.25.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.25.4.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.25.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25412


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25412/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25412/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25412/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25412/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25412/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25412/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25412 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25412/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 113 through 123 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   26
LEU    3    3
LEU    4    3
LYS    5   26
LYS    6   26
GLU    8   13
LYS    9   26
GLU   10   12
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.25.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.26.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.26.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.26.3.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.26.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1586


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1586/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1586/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1586/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1586/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1586/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1586/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1586 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1586/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 112 through 123 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LEU    2    3
GLN    6   13
GLU    7   12
LYS    8   24
GLU    9   12
LEU   10    3
GLU   12   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.26.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.27.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.27.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.27.4.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.27.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-19510


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-19510/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-19510/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-19510/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-19510/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19510/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-19510/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-19510 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19510/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 111 through 122 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LEU    2    3
LYS    3   26
LYS    4   26
GLN    5   11
GLU    6   12
LYS    7   26
GLU    8   12
LEU    9    3
LYS   10   26
LEU   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.27.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.29.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.29.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.29.0.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.29.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32406


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32406/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32406/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32406/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32406/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32406/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32406/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32406 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32406/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 111 through 121 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LYS    2   26
GLN    3   12
GLU    4   12
GLU    6   13
LEU    7    3
LYS    8   26
GLU    9   12
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.29.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.30.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.30.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.30.0.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.30.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1934


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1934/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1934/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1934/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1934/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1934/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1934/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1934 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1934/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 110 through 120 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   31
GLN    2   12
GLU    3   12
LYS    4   26
GLU    5   12
LEU    6    3
GLU    8   13
LEU    9    3
GLU   10   12
ARG   11   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.30.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.31.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.31.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.31.1.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.31.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2215


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2215/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2215/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2215/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2215/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2215/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2215/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2215 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2215/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 109 through 119 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLU    2   16
LYS    3   26
GLU    4   12
LEU    5    3
LYS    6   26
GLU    7   12
LEU    8    3
GLU    9   12
ARG   10   27
LYS   11   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    7     40.2223
turnclash      7   21   11    0     36.3742
Cluster     1 =   2   7  11
3 clashing residues after turn 
Residue clashes:
2-7
7-11
cluster 1 has 3 members and 7.776e+03 combinations:
 11  2  7 
Energy     40.2223
Searching cluster 2
Combinations for 3 members in cluster 1 OK: 7.776e+03 - Sending to search
0.000000 < 40.222286: keeping 
Solved cluster 1: residual clashing  0.01
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.31.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.32.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.32.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.32.5.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.32.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28049


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28049/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28049/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28049/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28049/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28049/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28049/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28049 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28049/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 108 through 118 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    2   26
GLU    3   16
LEU    4    3
LYS    5   26
GLU    6   12
GLU    8   13
ARG    9   27
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.32.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1elrA.34.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1elrA.34.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1elrA.34.2.a2m \
	-target T0124 -template 1elrA \
	-out T0124-1elrA.34.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1elrA-orig.a2m
Writing a2m file: tmp/1elrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22231


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22231/tmp -alignfile tmp/1elrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1elrA-orig.a2m (1 sequences, 131 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22231/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22231/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22231/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22231/tmp.a2m (1 sequences, 131 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22231/tmp.mod tmp/1elrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22231 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1elrA-align.mod
tmp/1elrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22231/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1elrA-orig.a2m tmp/1elrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1elrA-align.mod
Running w0.5 tmp/1elrA-orig.a2m tmp/1elrA-align.mod
Running align2model tmp/1elrA-align -i tmp/1elrA-align.mod -db tmp/1elrA-orig.a2m -db tmp/1elrA-pdb.a2m
partial PDB gets fragment 112 through 121 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    2    3
LYS    3   26
GLU    4   12
LEU    5    3
GLU    6   12
ARG    7   27
LYS    8   24
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1elrA.34.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1et9A.156.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1et9A.156.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1et9A.156.5.a2m \
	-target T0124 -template 1et9A \
	-out T0124-1et9A.156.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1et9A-orig.a2m
Writing a2m file: tmp/1et9A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18370


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18370/tmp -alignfile tmp/1et9A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1et9A-orig.a2m (1 sequences, 204 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18370/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18370/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18370/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18370/tmp.a2m (1 sequences, 204 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18370/tmp.mod tmp/1et9A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18370 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1et9A-align.mod
tmp/1et9A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18370/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1et9A-orig.a2m tmp/1et9A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1et9A-align.mod
Running w0.5 tmp/1et9A-orig.a2m tmp/1et9A-align.mod
Running align2model tmp/1et9A-align -i tmp/1et9A-align.mod -db tmp/1et9A-orig.a2m -db tmp/1et9A-pdb.a2m
partial PDB gets fragment 63 through 72 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    3   13
GLU    4   13
ARG    5   29
LYS    7   24
LYS    8   31
GLU    9   12
ILE   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1et9A.156.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1et9A.160.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1et9A.160.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1et9A.160.5.a2m \
	-target T0124 -template 1et9A \
	-out T0124-1et9A.160.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1et9A-orig.a2m
Writing a2m file: tmp/1et9A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-506


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-506/tmp -alignfile tmp/1et9A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1et9A-orig.a2m (1 sequences, 204 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-506/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-506/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-506/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-506/tmp.a2m (1 sequences, 204 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-506/tmp.mod tmp/1et9A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-506 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1et9A-align.mod
tmp/1et9A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-506/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1et9A-orig.a2m tmp/1et9A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1et9A-align.mod
Running w0.5 tmp/1et9A-orig.a2m tmp/1et9A-align.mod
Running align2model tmp/1et9A-align -i tmp/1et9A-align.mod -db tmp/1et9A-orig.a2m -db tmp/1et9A-pdb.a2m
partial PDB gets fragment 62 through 71 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
LEU    2    2
LYS    3   27
LYS    4   27
GLU    5   13
ILE    6    4
ASN    7    6
ASN    8    6
SER    9    3
HIS   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1et9A.160.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ezm.137.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ezm.137.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ezm.137.1.a2m \
	-target T0124 -template 1ezm \
	-out T0124-1ezm.137.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ezm-orig.a2m
Writing a2m file: tmp/1ezm-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3044


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3044/tmp -alignfile tmp/1ezm-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ezm-orig.a2m (1 sequences, 301 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3044/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3044/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3044/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3044/tmp.a2m (1 sequences, 301 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3044/tmp.mod tmp/1ezm-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3044 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ezm-align.mod
tmp/1ezm-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3044/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ezm-orig.a2m tmp/1ezm-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ezm-align.mod
Running w0.5 tmp/1ezm-orig.a2m tmp/1ezm-align.mod
Running align2model tmp/1ezm-align -i tmp/1ezm-align.mod -db tmp/1ezm-orig.a2m -db tmp/1ezm-pdb.a2m
partial PDB gets fragment 36 through 45 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   13
LYS    4   27
ARG    5   28
LEU    6    2
ASP    7    4
ARG    8   21
ILE    9    5
GLN   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ezm.137.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ezm.138.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ezm.138.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ezm.138.0.a2m \
	-target T0124 -template 1ezm \
	-out T0124-1ezm.138.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ezm-orig.a2m
Writing a2m file: tmp/1ezm-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-16280


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-16280/tmp -alignfile tmp/1ezm-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ezm-orig.a2m (1 sequences, 301 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-16280/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16280/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16280/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16280/tmp.a2m (1 sequences, 301 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16280/tmp.mod tmp/1ezm-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16280 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ezm-align.mod
tmp/1ezm-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16280/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ezm-orig.a2m tmp/1ezm-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ezm-align.mod
Running w0.5 tmp/1ezm-orig.a2m tmp/1ezm-align.mod
Running align2model tmp/1ezm-align -i tmp/1ezm-align.mod -db tmp/1ezm-orig.a2m -db tmp/1ezm-pdb.a2m
partial PDB gets fragment 35 through 44 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    3   26
ARG    4   27
LEU    5    3
ARG    7   32
ILE    8    3
GLN    9   11
VAL   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ezm.138.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ezm.139.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ezm.139.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ezm.139.0.a2m \
	-target T0124 -template 1ezm \
	-out T0124-1ezm.139.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ezm-orig.a2m
Writing a2m file: tmp/1ezm-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23888


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23888/tmp -alignfile tmp/1ezm-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ezm-orig.a2m (1 sequences, 301 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23888/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23888/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23888/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23888/tmp.a2m (1 sequences, 301 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23888/tmp.mod tmp/1ezm-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23888 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ezm-align.mod
tmp/1ezm-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23888/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ezm-orig.a2m tmp/1ezm-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ezm-align.mod
Running w0.5 tmp/1ezm-orig.a2m tmp/1ezm-align.mod
Running align2model tmp/1ezm-align -i tmp/1ezm-align.mod -db tmp/1ezm-orig.a2m -db tmp/1ezm-pdb.a2m
partial PDB gets fragment 34 through 43 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   25
ARG    3   30
LEU    4    3
ASP    5    5
ARG    6   27
ILE    7    2
GLN    8   14
VAL    9    2
MET   10    8
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ezm.139.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ezm.140.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ezm.140.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ezm.140.0.a2m \
	-target T0124 -template 1ezm \
	-out T0124-1ezm.140.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ezm-orig.a2m
Writing a2m file: tmp/1ezm-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-333


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-333/tmp -alignfile tmp/1ezm-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ezm-orig.a2m (1 sequences, 301 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-333/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-333/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-333/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-333/tmp.a2m (1 sequences, 301 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-333/tmp.mod tmp/1ezm-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-333 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ezm-align.mod
tmp/1ezm-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-333/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ezm-orig.a2m tmp/1ezm-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ezm-align.mod
Running w0.5 tmp/1ezm-orig.a2m tmp/1ezm-align.mod
Running align2model tmp/1ezm-align -i tmp/1ezm-align.mod -db tmp/1ezm-orig.a2m -db tmp/1ezm-pdb.a2m
partial PDB gets fragment 33 through 42 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   20
ARG    2   30
LEU    3    3
ASP    4    7
ARG    5   27
ILE    6    3
GLN    7   13
VAL    8    1
MET   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.95029
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ezm.140.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ezm.141.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ezm.141.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ezm.141.0.a2m \
	-target T0124 -template 1ezm \
	-out T0124-1ezm.141.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ezm-orig.a2m
Writing a2m file: tmp/1ezm-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31314


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31314/tmp -alignfile tmp/1ezm-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ezm-orig.a2m (1 sequences, 301 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31314/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31314/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31314/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31314/tmp.a2m (1 sequences, 301 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31314/tmp.mod tmp/1ezm-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31314 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ezm-align.mod
tmp/1ezm-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31314/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ezm-orig.a2m tmp/1ezm-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ezm-align.mod
Running w0.5 tmp/1ezm-orig.a2m tmp/1ezm-align.mod
Running align2model tmp/1ezm-align -i tmp/1ezm-align.mod -db tmp/1ezm-orig.a2m -db tmp/1ezm-pdb.a2m
partial PDB gets fragment 32 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   29
LEU    2    2
ASP    3    4
ARG    4   25
ILE    5    4
GLN    6   12
VAL    7    1
MET    8   10
MET    9   10
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ezm.141.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ezm.142.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ezm.142.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ezm.142.2.a2m \
	-target T0124 -template 1ezm \
	-out T0124-1ezm.142.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ezm-orig.a2m
Writing a2m file: tmp/1ezm-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1632


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1632/tmp -alignfile tmp/1ezm-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ezm-orig.a2m (1 sequences, 301 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1632/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1632/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1632/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1632/tmp.a2m (1 sequences, 301 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1632/tmp.mod tmp/1ezm-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1632 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ezm-align.mod
tmp/1ezm-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1632/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ezm-orig.a2m tmp/1ezm-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ezm-align.mod
Running w0.5 tmp/1ezm-orig.a2m tmp/1ezm-align.mod
Running align2model tmp/1ezm-align -i tmp/1ezm-align.mod -db tmp/1ezm-orig.a2m -db tmp/1ezm-pdb.a2m
partial PDB gets fragment 31 through 40 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ARG    3   21
ILE    4    4
GLN    5   12
MET    7   10
MET    8   10
ARG    9   27
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ezm.142.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ezm.64.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ezm.64.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ezm.64.5.a2m \
	-target T0124 -template 1ezm \
	-out T0124-1ezm.64.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ezm-orig.a2m
Writing a2m file: tmp/1ezm-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28942


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28942/tmp -alignfile tmp/1ezm-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ezm-orig.a2m (1 sequences, 301 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28942/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28942/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28942/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28942/tmp.a2m (1 sequences, 301 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28942/tmp.mod tmp/1ezm-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28942 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ezm-align.mod
tmp/1ezm-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28942/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ezm-orig.a2m tmp/1ezm-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ezm-align.mod
Running w0.5 tmp/1ezm-orig.a2m tmp/1ezm-align.mod
Running align2model tmp/1ezm-align -i tmp/1ezm-align.mod -db tmp/1ezm-orig.a2m -db tmp/1ezm-pdb.a2m
partial PDB gets fragment 91 through 100 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   19
LEU    3    3
ASP    4    4
SER    5    3
GLN    6   12
VAL    7    1
VAL    8    3
GLU    9   13
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ezm.64.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ezm.67.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ezm.67.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ezm.67.2.a2m \
	-target T0124 -template 1ezm \
	-out T0124-1ezm.67.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ezm-orig.a2m
Writing a2m file: tmp/1ezm-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2216


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2216/tmp -alignfile tmp/1ezm-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ezm-orig.a2m (1 sequences, 301 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2216/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2216/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2216/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2216/tmp.a2m (1 sequences, 301 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2216/tmp.mod tmp/1ezm-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2216 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ezm-align.mod
tmp/1ezm-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2216/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ezm-orig.a2m tmp/1ezm-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ezm-align.mod
Running w0.5 tmp/1ezm-orig.a2m tmp/1ezm-align.mod
Running align2model tmp/1ezm-align -i tmp/1ezm-align.mod -db tmp/1ezm-orig.a2m -db tmp/1ezm-pdb.a2m
partial PDB gets fragment 91 through 100 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    5
SER    2    3
GLN    3   14
VAL    4    3
VAL    5    2
GLU    6   12
LEU    7    4
GLU    9   12
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ezm.67.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ezm.68.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ezm.68.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ezm.68.3.a2m \
	-target T0124 -template 1ezm \
	-out T0124-1ezm.68.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ezm-orig.a2m
Writing a2m file: tmp/1ezm-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21831


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21831/tmp -alignfile tmp/1ezm-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ezm-orig.a2m (1 sequences, 301 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21831/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21831/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21831/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21831/tmp.a2m (1 sequences, 301 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21831/tmp.mod tmp/1ezm-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21831 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ezm-align.mod
tmp/1ezm-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21831/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ezm-orig.a2m tmp/1ezm-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ezm-align.mod
Running w0.5 tmp/1ezm-orig.a2m tmp/1ezm-align.mod
Running align2model tmp/1ezm-align -i tmp/1ezm-align.mod -db tmp/1ezm-orig.a2m -db tmp/1ezm-pdb.a2m
partial PDB gets fragment 90 through 99 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
GLN    2    7
VAL    3    1
VAL    4    2
GLU    5   15
LYS    7   32
GLU    8   13
ARG    9   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.23961
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ezm.68.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.187.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.187.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.187.5.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.187.5 -outdir und
partial PDB gets fragment 36 through 45 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    2
GLN    2   11
GLN    3   13
LYS    4   28
GLU    6   13
GLU    7   13
LYS    8   31
GLN    9   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue Y 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    7     82.7336
Cluster     1 =   2   7
2 clashing residues after turn 
Residue clashes:
2-7
cluster 1 has 2 members and 1.600e+01 combinations:
 2  7 
Energy    193.2578
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 1.600e+01 - Sending to search
82.733566 < 193.257812: keeping 
79.492149 < 193.257797: keeping 
71.593529 < 191.550064: keeping 
16.525093 < 182.649750: keeping 
0.000000 < 128.195251: keeping 
Solved cluster 1: residual clashing 21.06
Still clashes at these sidechain pairs:
ires=    2 irot=    2 jres=    4 jrot=    1      13.7260
Residual clashes =   13.72598
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.187.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.188.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.188.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.188.1.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.188.1 -outdir und
partial PDB gets fragment 35 through 44 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLN    2   16
LYS    3   24
LEU    4    3
GLU    5   13
GLU    6   11
LYS    7   26
GLN    8   12
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.188.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.189.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.189.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.189.0.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.189.0 -outdir und
partial PDB gets fragment 34 through 43 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
LYS    2   26
LEU    3    5
GLU    4   12
LYS    6   29
GLN    7   11
GLU    9   13
ASN   10    6
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.189.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.190.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.190.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.190.1.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.190.1 -outdir und
partial PDB gets fragment 33 through 42 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
LEU    2    2
GLU    3   12
GLU    4   15
LYS    5   24
GLN    6   13
GLU    8   11
ASN    9    4
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.06228
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.190.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.191.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.191.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.191.1.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.191.1 -outdir und
partial PDB gets fragment 32 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   14
GLU    3   15
LYS    4   26
GLN    5   16
ASN    8    3
ARG   10   28
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.92830
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.191.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.192.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.192.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.192.1.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.192.1 -outdir und
partial PDB gets fragment 31 through 40 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   10
GLU    2   13
LYS    3   27
GLN    4   13
GLU    6   15
ASN    7    4
LEU    8    3
ARG    9   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.192.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.193.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.193.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.193.2.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.193.2 -outdir und
partial PDB gets fragment 30 through 39 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    2   17
GLN    3   12
GLU    5   15
ASN    6    4
LEU    7    5
ARG    8   26
ILE   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.193.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.194.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.194.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.194.2.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.194.2 -outdir und
partial PDB gets fragment 29 through 38 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   29
GLU    4   13
ASN    5    5
LEU    6    2
ARG    7   27
GLN   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.194.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.195.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.195.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.195.4.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.195.4 -outdir und
partial PDB gets fragment 28 through 37 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
GLU    3   12
ASN    4    4
LEU    5    3
ARG    6   29
ILE    8    3
GLN    9   16
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.195.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.196.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.196.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.196.4.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.196.4 -outdir und
partial PDB gets fragment 27 through 36 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   15
ASN    3    5
LEU    4    2
ARG    5   25
ILE    7    4
GLN    8   13
GLU    9   12
LYS   10   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.196.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.197.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.197.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.197.4.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.197.4 -outdir und
partial PDB gets fragment 26 through 35 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
ASN    2    5
LEU    3    2
ARG    4   32
ILE    6    2
GLN    7   12
GLU    8   14
LYS    9   24
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.10383
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.197.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fce.198.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fce.198.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fce.198.4.a2m \
	-target T0124 -template 1fce \
	-out T0124-1fce.198.4 -outdir und
partial PDB gets fragment 25 through 34 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
LEU    2    3
ARG    3   25
ILE    5    4
GLU    7   10
LYS    8   27
GLU    9   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fce.198.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fdr.167.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fdr.167.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fdr.167.5.a2m \
	-target T0124 -template 1fdr \
	-out T0124-1fdr.167.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fdr-orig.a2m
Writing a2m file: tmp/1fdr-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29742


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29742/tmp -alignfile tmp/1fdr-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fdr-orig.a2m (1 sequences, 248 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29742/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29742/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29742/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29742/tmp.a2m (1 sequences, 248 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29742/tmp.mod tmp/1fdr-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29742 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fdr-align.mod
tmp/1fdr-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29742/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fdr-orig.a2m tmp/1fdr-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fdr-align.mod
Running w0.5 tmp/1fdr-orig.a2m tmp/1fdr-align.mod
Running align2model tmp/1fdr-align -i tmp/1fdr-align.mod -db tmp/1fdr-orig.a2m -db tmp/1fdr-pdb.a2m
partial PDB gets fragment 29 through 38 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    5
SER    2    3
HIS    3    3
ILE    4    5
GLU    6   16
VAL    7    1
VAL    8    2
GLN    9   14
THR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fdr.167.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fdr.87.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fdr.87.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fdr.87.3.a2m \
	-target T0124 -template 1fdr \
	-out T0124-1fdr.87.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fdr-orig.a2m
Writing a2m file: tmp/1fdr-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31418


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31418/tmp -alignfile tmp/1fdr-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fdr-orig.a2m (1 sequences, 248 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31418/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31418/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31418/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31418/tmp.a2m (1 sequences, 248 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31418/tmp.mod tmp/1fdr-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31418 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fdr-align.mod
tmp/1fdr-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31418/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fdr-orig.a2m tmp/1fdr-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fdr-align.mod
Running w0.5 tmp/1fdr-orig.a2m tmp/1fdr-align.mod
Running align2model tmp/1fdr-align -i tmp/1fdr-align.mod -db tmp/1fdr-orig.a2m -db tmp/1fdr-pdb.a2m
partial PDB gets fragment 68 through 77 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
TYR    2    3
HIS    3    3
ASP    4    4
ILE    6    3
ARG    7   32
ARG    8   32
ARG    9   24
LYS   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fdr.87.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fdr.89.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fdr.89.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fdr.89.4.a2m \
	-target T0124 -template 1fdr \
	-out T0124-1fdr.89.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fdr-orig.a2m
Writing a2m file: tmp/1fdr-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1668


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1668/tmp -alignfile tmp/1fdr-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fdr-orig.a2m (1 sequences, 248 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1668/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1668/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1668/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1668/tmp.a2m (1 sequences, 248 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1668/tmp.mod tmp/1fdr-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1668 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fdr-align.mod
tmp/1fdr-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1668/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fdr-orig.a2m tmp/1fdr-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fdr-align.mod
Running w0.5 tmp/1fdr-orig.a2m tmp/1fdr-align.mod
Running align2model tmp/1fdr-align -i tmp/1fdr-align.mod -db tmp/1fdr-orig.a2m -db tmp/1fdr-pdb.a2m
partial PDB gets fragment 66 through 75 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
ILE    4    4
ARG    5   30
ARG    6   27
ARG    7   32
LYS    8   26
GLU    9   15
GLN   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fdr.89.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fdr.89.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fdr.89.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fdr.89.5.a2m \
	-target T0124 -template 1fdr \
	-out T0124-1fdr.89.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fdr-orig.a2m
Writing a2m file: tmp/1fdr-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2207


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2207/tmp -alignfile tmp/1fdr-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fdr-orig.a2m (1 sequences, 248 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2207/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2207/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2207/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2207/tmp.a2m (1 sequences, 248 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2207/tmp.mod tmp/1fdr-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2207 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fdr-align.mod
tmp/1fdr-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2207/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fdr-orig.a2m tmp/1fdr-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fdr-align.mod
Running w0.5 tmp/1fdr-orig.a2m tmp/1fdr-align.mod
Running align2model tmp/1fdr-align -i tmp/1fdr-align.mod -db tmp/1fdr-orig.a2m -db tmp/1fdr-pdb.a2m
partial PDB gets fragment 70 through 79 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
ASP    2    4
ILE    4    3
ARG    5   32
ARG    6   32
ARG    7   24
LYS    8   29
GLU    9   13
GLN   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fdr.89.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fdr.90.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fdr.90.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fdr.90.5.a2m \
	-target T0124 -template 1fdr \
	-out T0124-1fdr.90.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fdr-orig.a2m
Writing a2m file: tmp/1fdr-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27929


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27929/tmp -alignfile tmp/1fdr-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fdr-orig.a2m (1 sequences, 248 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27929/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27929/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27929/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27929/tmp.a2m (1 sequences, 248 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27929/tmp.mod tmp/1fdr-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27929 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fdr-align.mod
tmp/1fdr-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27929/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fdr-orig.a2m tmp/1fdr-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fdr-align.mod
Running w0.5 tmp/1fdr-orig.a2m tmp/1fdr-align.mod
Running align2model tmp/1fdr-align -i tmp/1fdr-align.mod -db tmp/1fdr-orig.a2m -db tmp/1fdr-pdb.a2m
partial PDB gets fragment 69 through 78 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
ILE    3    3
ARG    4   32
ARG    6   28
LYS    7   29
GLU    8   12
GLN    9   13
HIS   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fdr.90.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fds.11.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fds.11.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fds.11.2.a2m \
	-target T0124 -template 1fds \
	-out T0124-1fds.11.2 -outdir und
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 336, because occupancy 0.5 <= existing 0.500001
Skipped atom 338, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 506, because occupancy 0.5 <= existing 0.500001
Skipped atom 508, because occupancy 0.5 <= existing 0.500001
Skipped atom 510, because occupancy 0.5 <= existing 0.500001
Skipped atom 512, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 986, because occupancy 0.5 <= existing 0.500001
Skipped atom 988, because occupancy 0.5 <= existing 0.500001
Skipped atom 990, because occupancy 0.5 <= existing 0.500001
Skipped atom 992, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1673, because occupancy 0.5 <= existing 0.500001
Skipped atom 1675, because occupancy 0.5 <= existing 0.500001
Skipped atom 1677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1679, because occupancy 0.5 <= existing 0.500001
Skipped atom 1681, because occupancy 0.5 <= existing 0.500001
Skipped atom 1683, because occupancy 0.5 <= existing 0.500001
Skipped atom 1685, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
Skipped atom 1804, because occupancy 0.5 <= existing 0.500001
Skipped atom 1806, because occupancy 0.5 <= existing 0.500001
Skipped atom 1808, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fds-orig.a2m
Writing a2m file: tmp/1fds-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2631


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2631/tmp -alignfile tmp/1fds-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fds-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2631/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2631/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2631/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2631/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2631/tmp.mod tmp/1fds-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2631 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fds-align.mod
tmp/1fds-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2631/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fds-orig.a2m tmp/1fds-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fds-align.mod
Running w0.5 tmp/1fds-orig.a2m tmp/1fds-align.mod
Running align2model tmp/1fds-align -i tmp/1fds-align.mod -db tmp/1fds-orig.a2m -db tmp/1fds-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fds.11.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fds.14.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fds.14.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fds.14.3.a2m \
	-target T0124 -template 1fds \
	-out T0124-1fds.14.3 -outdir und
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 336, because occupancy 0.5 <= existing 0.500001
Skipped atom 338, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 506, because occupancy 0.5 <= existing 0.500001
Skipped atom 508, because occupancy 0.5 <= existing 0.500001
Skipped atom 510, because occupancy 0.5 <= existing 0.500001
Skipped atom 512, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 986, because occupancy 0.5 <= existing 0.500001
Skipped atom 988, because occupancy 0.5 <= existing 0.500001
Skipped atom 990, because occupancy 0.5 <= existing 0.500001
Skipped atom 992, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1673, because occupancy 0.5 <= existing 0.500001
Skipped atom 1675, because occupancy 0.5 <= existing 0.500001
Skipped atom 1677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1679, because occupancy 0.5 <= existing 0.500001
Skipped atom 1681, because occupancy 0.5 <= existing 0.500001
Skipped atom 1683, because occupancy 0.5 <= existing 0.500001
Skipped atom 1685, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
Skipped atom 1804, because occupancy 0.5 <= existing 0.500001
Skipped atom 1806, because occupancy 0.5 <= existing 0.500001
Skipped atom 1808, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fds-orig.a2m
Writing a2m file: tmp/1fds-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-261


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-261/tmp -alignfile tmp/1fds-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fds-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-261/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-261/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-261/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-261/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-261/tmp.mod tmp/1fds-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-261 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fds-align.mod
tmp/1fds-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-261/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fds-orig.a2m tmp/1fds-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fds-align.mod
Running w0.5 tmp/1fds-orig.a2m tmp/1fds-align.mod
Running align2model tmp/1fds-align -i tmp/1fds-align.mod -db tmp/1fds-orig.a2m -db tmp/1fds-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fds.14.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fds.15.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fds.15.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fds.15.4.a2m \
	-target T0124 -template 1fds \
	-out T0124-1fds.15.4 -outdir und
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 336, because occupancy 0.5 <= existing 0.500001
Skipped atom 338, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 506, because occupancy 0.5 <= existing 0.500001
Skipped atom 508, because occupancy 0.5 <= existing 0.500001
Skipped atom 510, because occupancy 0.5 <= existing 0.500001
Skipped atom 512, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 986, because occupancy 0.5 <= existing 0.500001
Skipped atom 988, because occupancy 0.5 <= existing 0.500001
Skipped atom 990, because occupancy 0.5 <= existing 0.500001
Skipped atom 992, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1673, because occupancy 0.5 <= existing 0.500001
Skipped atom 1675, because occupancy 0.5 <= existing 0.500001
Skipped atom 1677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1679, because occupancy 0.5 <= existing 0.500001
Skipped atom 1681, because occupancy 0.5 <= existing 0.500001
Skipped atom 1683, because occupancy 0.5 <= existing 0.500001
Skipped atom 1685, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
Skipped atom 1804, because occupancy 0.5 <= existing 0.500001
Skipped atom 1806, because occupancy 0.5 <= existing 0.500001
Skipped atom 1808, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fds-orig.a2m
Writing a2m file: tmp/1fds-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3864


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3864/tmp -alignfile tmp/1fds-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fds-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3864/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3864/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3864/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3864/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3864/tmp.mod tmp/1fds-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3864 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fds-align.mod
tmp/1fds-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3864/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fds-orig.a2m tmp/1fds-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fds-align.mod
Running w0.5 tmp/1fds-orig.a2m tmp/1fds-align.mod
Running align2model tmp/1fds-align -i tmp/1fds-align.mod -db tmp/1fds-orig.a2m -db tmp/1fds-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fds.15.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fds.16.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fds.16.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fds.16.3.a2m \
	-target T0124 -template 1fds \
	-out T0124-1fds.16.3 -outdir und
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 336, because occupancy 0.5 <= existing 0.500001
Skipped atom 338, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 506, because occupancy 0.5 <= existing 0.500001
Skipped atom 508, because occupancy 0.5 <= existing 0.500001
Skipped atom 510, because occupancy 0.5 <= existing 0.500001
Skipped atom 512, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 986, because occupancy 0.5 <= existing 0.500001
Skipped atom 988, because occupancy 0.5 <= existing 0.500001
Skipped atom 990, because occupancy 0.5 <= existing 0.500001
Skipped atom 992, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1673, because occupancy 0.5 <= existing 0.500001
Skipped atom 1675, because occupancy 0.5 <= existing 0.500001
Skipped atom 1677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1679, because occupancy 0.5 <= existing 0.500001
Skipped atom 1681, because occupancy 0.5 <= existing 0.500001
Skipped atom 1683, because occupancy 0.5 <= existing 0.500001
Skipped atom 1685, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
Skipped atom 1804, because occupancy 0.5 <= existing 0.500001
Skipped atom 1806, because occupancy 0.5 <= existing 0.500001
Skipped atom 1808, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fds-orig.a2m
Writing a2m file: tmp/1fds-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4177


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4177/tmp -alignfile tmp/1fds-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fds-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4177/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4177/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4177/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4177/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4177/tmp.mod tmp/1fds-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4177 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fds-align.mod
tmp/1fds-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4177/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fds-orig.a2m tmp/1fds-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fds-align.mod
Running w0.5 tmp/1fds-orig.a2m tmp/1fds-align.mod
Running align2model tmp/1fds-align -i tmp/1fds-align.mod -db tmp/1fds-orig.a2m -db tmp/1fds-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fds.16.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fds.17.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fds.17.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fds.17.3.a2m \
	-target T0124 -template 1fds \
	-out T0124-1fds.17.3 -outdir und
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 336, because occupancy 0.5 <= existing 0.500001
Skipped atom 338, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 506, because occupancy 0.5 <= existing 0.500001
Skipped atom 508, because occupancy 0.5 <= existing 0.500001
Skipped atom 510, because occupancy 0.5 <= existing 0.500001
Skipped atom 512, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 986, because occupancy 0.5 <= existing 0.500001
Skipped atom 988, because occupancy 0.5 <= existing 0.500001
Skipped atom 990, because occupancy 0.5 <= existing 0.500001
Skipped atom 992, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1673, because occupancy 0.5 <= existing 0.500001
Skipped atom 1675, because occupancy 0.5 <= existing 0.500001
Skipped atom 1677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1679, because occupancy 0.5 <= existing 0.500001
Skipped atom 1681, because occupancy 0.5 <= existing 0.500001
Skipped atom 1683, because occupancy 0.5 <= existing 0.500001
Skipped atom 1685, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
Skipped atom 1804, because occupancy 0.5 <= existing 0.500001
Skipped atom 1806, because occupancy 0.5 <= existing 0.500001
Skipped atom 1808, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fds-orig.a2m
Writing a2m file: tmp/1fds-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28579


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28579/tmp -alignfile tmp/1fds-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fds-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28579/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28579/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28579/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28579/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28579/tmp.mod tmp/1fds-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28579 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fds-align.mod
tmp/1fds-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28579/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fds-orig.a2m tmp/1fds-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fds-align.mod
Running w0.5 tmp/1fds-orig.a2m tmp/1fds-align.mod
Running align2model tmp/1fds-align -i tmp/1fds-align.mod -db tmp/1fds-orig.a2m -db tmp/1fds-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fds.17.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fds.18.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fds.18.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fds.18.2.a2m \
	-target T0124 -template 1fds \
	-out T0124-1fds.18.2 -outdir und
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 336, because occupancy 0.5 <= existing 0.500001
Skipped atom 338, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 506, because occupancy 0.5 <= existing 0.500001
Skipped atom 508, because occupancy 0.5 <= existing 0.500001
Skipped atom 510, because occupancy 0.5 <= existing 0.500001
Skipped atom 512, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 986, because occupancy 0.5 <= existing 0.500001
Skipped atom 988, because occupancy 0.5 <= existing 0.500001
Skipped atom 990, because occupancy 0.5 <= existing 0.500001
Skipped atom 992, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1673, because occupancy 0.5 <= existing 0.500001
Skipped atom 1675, because occupancy 0.5 <= existing 0.500001
Skipped atom 1677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1679, because occupancy 0.5 <= existing 0.500001
Skipped atom 1681, because occupancy 0.5 <= existing 0.500001
Skipped atom 1683, because occupancy 0.5 <= existing 0.500001
Skipped atom 1685, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
Skipped atom 1804, because occupancy 0.5 <= existing 0.500001
Skipped atom 1806, because occupancy 0.5 <= existing 0.500001
Skipped atom 1808, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fds-orig.a2m
Writing a2m file: tmp/1fds-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27551


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27551/tmp -alignfile tmp/1fds-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fds-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27551/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27551/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27551/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27551/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27551/tmp.mod tmp/1fds-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27551 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fds-align.mod
tmp/1fds-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27551/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fds-orig.a2m tmp/1fds-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fds-align.mod
Running w0.5 tmp/1fds-orig.a2m tmp/1fds-align.mod
Running align2model tmp/1fds-align -i tmp/1fds-align.mod -db tmp/1fds-orig.a2m -db tmp/1fds-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fds.18.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fds.19.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fds.19.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fds.19.2.a2m \
	-target T0124 -template 1fds \
	-out T0124-1fds.19.2 -outdir und
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 336, because occupancy 0.5 <= existing 0.500001
Skipped atom 338, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 506, because occupancy 0.5 <= existing 0.500001
Skipped atom 508, because occupancy 0.5 <= existing 0.500001
Skipped atom 510, because occupancy 0.5 <= existing 0.500001
Skipped atom 512, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 986, because occupancy 0.5 <= existing 0.500001
Skipped atom 988, because occupancy 0.5 <= existing 0.500001
Skipped atom 990, because occupancy 0.5 <= existing 0.500001
Skipped atom 992, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1673, because occupancy 0.5 <= existing 0.500001
Skipped atom 1675, because occupancy 0.5 <= existing 0.500001
Skipped atom 1677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1679, because occupancy 0.5 <= existing 0.500001
Skipped atom 1681, because occupancy 0.5 <= existing 0.500001
Skipped atom 1683, because occupancy 0.5 <= existing 0.500001
Skipped atom 1685, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
Skipped atom 1804, because occupancy 0.5 <= existing 0.500001
Skipped atom 1806, because occupancy 0.5 <= existing 0.500001
Skipped atom 1808, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fds-orig.a2m
Writing a2m file: tmp/1fds-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11301


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11301/tmp -alignfile tmp/1fds-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fds-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11301/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11301/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11301/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11301/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11301/tmp.mod tmp/1fds-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-11301 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fds-align.mod
tmp/1fds-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11301/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fds-orig.a2m tmp/1fds-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fds-align.mod
Running w0.5 tmp/1fds-orig.a2m tmp/1fds-align.mod
Running align2model tmp/1fds-align -i tmp/1fds-align.mod -db tmp/1fds-orig.a2m -db tmp/1fds-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fds.19.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fds.20.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fds.20.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fds.20.4.a2m \
	-target T0124 -template 1fds \
	-out T0124-1fds.20.4 -outdir und
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 336, because occupancy 0.5 <= existing 0.500001
Skipped atom 338, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 506, because occupancy 0.5 <= existing 0.500001
Skipped atom 508, because occupancy 0.5 <= existing 0.500001
Skipped atom 510, because occupancy 0.5 <= existing 0.500001
Skipped atom 512, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 986, because occupancy 0.5 <= existing 0.500001
Skipped atom 988, because occupancy 0.5 <= existing 0.500001
Skipped atom 990, because occupancy 0.5 <= existing 0.500001
Skipped atom 992, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1673, because occupancy 0.5 <= existing 0.500001
Skipped atom 1675, because occupancy 0.5 <= existing 0.500001
Skipped atom 1677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1679, because occupancy 0.5 <= existing 0.500001
Skipped atom 1681, because occupancy 0.5 <= existing 0.500001
Skipped atom 1683, because occupancy 0.5 <= existing 0.500001
Skipped atom 1685, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
Skipped atom 1804, because occupancy 0.5 <= existing 0.500001
Skipped atom 1806, because occupancy 0.5 <= existing 0.500001
Skipped atom 1808, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fds-orig.a2m
Writing a2m file: tmp/1fds-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31820


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31820/tmp -alignfile tmp/1fds-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fds-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31820/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31820/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31820/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31820/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31820/tmp.mod tmp/1fds-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31820 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fds-align.mod
tmp/1fds-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31820/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fds-orig.a2m tmp/1fds-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fds-align.mod
Running w0.5 tmp/1fds-orig.a2m tmp/1fds-align.mod
Running align2model tmp/1fds-align -i tmp/1fds-align.mod -db tmp/1fds-orig.a2m -db tmp/1fds-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fds.20.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fds.8.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fds.8.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fds.8.3.a2m \
	-target T0124 -template 1fds \
	-out T0124-1fds.8.3 -outdir und
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 336, because occupancy 0.5 <= existing 0.500001
Skipped atom 338, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 506, because occupancy 0.5 <= existing 0.500001
Skipped atom 508, because occupancy 0.5 <= existing 0.500001
Skipped atom 510, because occupancy 0.5 <= existing 0.500001
Skipped atom 512, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 986, because occupancy 0.5 <= existing 0.500001
Skipped atom 988, because occupancy 0.5 <= existing 0.500001
Skipped atom 990, because occupancy 0.5 <= existing 0.500001
Skipped atom 992, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1673, because occupancy 0.5 <= existing 0.500001
Skipped atom 1675, because occupancy 0.5 <= existing 0.500001
Skipped atom 1677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1679, because occupancy 0.5 <= existing 0.500001
Skipped atom 1681, because occupancy 0.5 <= existing 0.500001
Skipped atom 1683, because occupancy 0.5 <= existing 0.500001
Skipped atom 1685, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
Skipped atom 1804, because occupancy 0.5 <= existing 0.500001
Skipped atom 1806, because occupancy 0.5 <= existing 0.500001
Skipped atom 1808, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fds-orig.a2m
Writing a2m file: tmp/1fds-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29707


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29707/tmp -alignfile tmp/1fds-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fds-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29707/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29707/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29707/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29707/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29707/tmp.mod tmp/1fds-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29707 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fds-align.mod
tmp/1fds-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29707/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fds-orig.a2m tmp/1fds-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fds-align.mod
Running w0.5 tmp/1fds-orig.a2m tmp/1fds-align.mod
Running align2model tmp/1fds-align -i tmp/1fds-align.mod -db tmp/1fds-orig.a2m -db tmp/1fds-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fds.8.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fds.9.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fds.9.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fds.9.4.a2m \
	-target T0124 -template 1fds \
	-out T0124-1fds.9.4 -outdir und
Skipped atom 334, because occupancy 0.5 <= existing 0.500001
Skipped atom 336, because occupancy 0.5 <= existing 0.500001
Skipped atom 338, because occupancy 0.5 <= existing 0.500001
Skipped atom 340, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 506, because occupancy 0.5 <= existing 0.500001
Skipped atom 508, because occupancy 0.5 <= existing 0.500001
Skipped atom 510, because occupancy 0.5 <= existing 0.500001
Skipped atom 512, because occupancy 0.5 <= existing 0.500001
Skipped atom 514, because occupancy 0.5 <= existing 0.500001
Skipped atom 986, because occupancy 0.5 <= existing 0.500001
Skipped atom 988, because occupancy 0.5 <= existing 0.500001
Skipped atom 990, because occupancy 0.5 <= existing 0.500001
Skipped atom 992, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1673, because occupancy 0.5 <= existing 0.500001
Skipped atom 1675, because occupancy 0.5 <= existing 0.500001
Skipped atom 1677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1679, because occupancy 0.5 <= existing 0.500001
Skipped atom 1681, because occupancy 0.5 <= existing 0.500001
Skipped atom 1683, because occupancy 0.5 <= existing 0.500001
Skipped atom 1685, because occupancy 0.5 <= existing 0.500001
Skipped atom 1802, because occupancy 0.5 <= existing 0.500001
Skipped atom 1804, because occupancy 0.5 <= existing 0.500001
Skipped atom 1806, because occupancy 0.5 <= existing 0.500001
Skipped atom 1808, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fds-orig.a2m
Writing a2m file: tmp/1fds-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1139


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1139/tmp -alignfile tmp/1fds-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fds-orig.a2m (1 sequences, 327 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1139/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1139/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1139/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1139/tmp.a2m (1 sequences, 327 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1139/tmp.mod tmp/1fds-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1139 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fds-align.mod
tmp/1fds-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1139/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fds-orig.a2m tmp/1fds-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fds-align.mod
Running w0.5 tmp/1fds-orig.a2m tmp/1fds-align.mod
Running align2model tmp/1fds-align -i tmp/1fds-align.mod -db tmp/1fds-orig.a2m -db tmp/1fds-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fds.9.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fmb.59.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fmb.59.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fmb.59.5.a2m \
	-target T0124 -template 1fmb \
	-out T0124-1fmb.59.5 -outdir und
Skipped atom 424, because occupancy 0.5 <= existing 0.500001
Skipped atom 426, because occupancy 0.5 <= existing 0.500001
Skipped atom 428, because occupancy 0.5 <= existing 0.500001
Skipped atom 430, because occupancy 0.5 <= existing 0.500001
Skipped atom 432, because occupancy 0.5 <= existing 0.500001
Skipped atom 434, because occupancy 0.5 <= existing 0.500001
Skipped atom 436, because occupancy 0.5 <= existing 0.500001
Skipped atom 438, because occupancy 0.5 <= existing 0.500001
Skipped atom 440, because occupancy 0.5 <= existing 0.500001
Skipped atom 442, because occupancy 0.5 <= existing 0.500001
Skipped atom 444, because occupancy 0.5 <= existing 0.500001
Skipped atom 446, because occupancy 0.5 <= existing 0.500001
Skipped atom 448, because occupancy 0.5 <= existing 0.500001
Skipped atom 450, because occupancy 0.5 <= existing 0.500001
Skipped atom 452, because occupancy 0.5 <= existing 0.500001
Skipped atom 779, because occupancy 0.5 <= existing 0.500001
Skipped atom 781, because occupancy 0.5 <= existing 0.500001
Skipped atom 783, because occupancy 0.5 <= existing 0.500001
Skipped atom 785, because occupancy 0.5 <= existing 0.500001
Skipped atom 787, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 77 through 86 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
PRO    2    2
VAL    3    3
TYR    4    3
PRO    5    2
ARG    6   32
LEU    8    2
ASP    9    5
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7    9     47.6880
Cluster     1 =   7   9
2 clashing residues after turn 
Residue clashes:
7-9
cluster 1 has 2 members and 2.800e+01 combinations:
 9  7 
Energy     47.6880
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 2.800e+01 - Sending to search
29.067137 < 47.688019: keeping 
0.000000 < 29.501787: keeping 
Solved cluster 1: residual clashing  0.71
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fmb.59.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1frpA.19.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1frpA.19.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1frpA.19.4.a2m \
	-target T0124 -template 1frpA \
	-out T0124-1frpA.19.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1frpA-orig.a2m
Writing a2m file: tmp/1frpA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20413


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20413/tmp -alignfile tmp/1frpA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1frpA-orig.a2m (1 sequences, 335 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20413/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20413/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20413/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20413/tmp.a2m (1 sequences, 335 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20413/tmp.mod tmp/1frpA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20413 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1frpA-align.mod
tmp/1frpA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20413/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1frpA-orig.a2m tmp/1frpA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1frpA-align.mod
Running w0.5 tmp/1frpA-orig.a2m tmp/1frpA-align.mod
Running align2model tmp/1frpA-align -i tmp/1frpA-align.mod -db tmp/1frpA-orig.a2m -db tmp/1frpA-pdb.a2m
partial PDB gets fragment 299 through 308 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   17
GLN    2   14
MET    3   13
LYS    4   29
PHE    6    2
LEU    7    3
LYS    8   25
LEU    9    3
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7   11     14.2779
Cluster     1 =   7  11
2 clashing residues after turn 
Residue clashes:
7-11
cluster 1 has 2 members and 3.000e+00 combinations:
 7  11 
Energy     15.5407
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 3.000e+00 - Sending to search
0.000000 < 15.540699: keeping 
Solved cluster 1: residual clashing  2.28
Still clashes at these sidechain pairs:
Residual clashes =    7.28756
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1frpA.19.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fvkA.189.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fvkA.189.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fvkA.189.4.a2m \
	-target T0124 -template 1fvkA \
	-out T0124-1fvkA.189.4 -outdir und
Skipped atom 1033, because occupancy 0.5 <= existing 0.500001
Skipped atom 1035, because occupancy 0.5 <= existing 0.500001
Skipped atom 1350, because occupancy 0.5 <= existing 0.500001
Skipped atom 1352, because occupancy 0.5 <= existing 0.500001
Skipped atom 1354, because occupancy 0.5 <= existing 0.500001
Skipped atom 1356, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fvkA-orig.a2m
Writing a2m file: tmp/1fvkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27671


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27671/tmp -alignfile tmp/1fvkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fvkA-orig.a2m (1 sequences, 189 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27671/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27671/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27671/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27671/tmp.a2m (1 sequences, 189 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27671/tmp.mod tmp/1fvkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27671 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fvkA-align.mod
tmp/1fvkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27671/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fvkA-orig.a2m tmp/1fvkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fvkA-align.mod
Running w0.5 tmp/1fvkA-orig.a2m tmp/1fvkA-align.mod
Running align2model tmp/1fvkA-align -i tmp/1fvkA-align.mod -db tmp/1fvkA-orig.a2m -db tmp/1fvkA-pdb.a2m
partial PDB gets fragment 30 through 39 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   11
LYS    2   30
LEU    3    3
GLU    4   12
GLU    5   12
LYS    6   25
GLN    7   12
GLU    9   12
ASN   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fvkA.189.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fvkA.190.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fvkA.190.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fvkA.190.0.a2m \
	-target T0124 -template 1fvkA \
	-out T0124-1fvkA.190.0 -outdir und
Skipped atom 1033, because occupancy 0.5 <= existing 0.500001
Skipped atom 1035, because occupancy 0.5 <= existing 0.500001
Skipped atom 1350, because occupancy 0.5 <= existing 0.500001
Skipped atom 1352, because occupancy 0.5 <= existing 0.500001
Skipped atom 1354, because occupancy 0.5 <= existing 0.500001
Skipped atom 1356, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fvkA-orig.a2m
Writing a2m file: tmp/1fvkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-16887


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-16887/tmp -alignfile tmp/1fvkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fvkA-orig.a2m (1 sequences, 189 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-16887/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16887/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16887/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16887/tmp.a2m (1 sequences, 189 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16887/tmp.mod tmp/1fvkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16887 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fvkA-align.mod
tmp/1fvkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16887/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fvkA-orig.a2m tmp/1fvkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fvkA-align.mod
Running w0.5 tmp/1fvkA-orig.a2m tmp/1fvkA-align.mod
Running align2model tmp/1fvkA-align -i tmp/1fvkA-align.mod -db tmp/1fvkA-orig.a2m -db tmp/1fvkA-pdb.a2m
partial PDB gets fragment 29 through 38 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
LEU    2    3
GLU    3   15
GLU    4   12
LYS    5   24
ASN    9    6
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.02848
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fvkA.190.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fvkA.191.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fvkA.191.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fvkA.191.0.a2m \
	-target T0124 -template 1fvkA \
	-out T0124-1fvkA.191.0 -outdir und
Skipped atom 1033, because occupancy 0.5 <= existing 0.500001
Skipped atom 1035, because occupancy 0.5 <= existing 0.500001
Skipped atom 1350, because occupancy 0.5 <= existing 0.500001
Skipped atom 1352, because occupancy 0.5 <= existing 0.500001
Skipped atom 1354, because occupancy 0.5 <= existing 0.500001
Skipped atom 1356, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fvkA-orig.a2m
Writing a2m file: tmp/1fvkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2174


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2174/tmp -alignfile tmp/1fvkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fvkA-orig.a2m (1 sequences, 189 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2174/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2174/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2174/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2174/tmp.a2m (1 sequences, 189 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2174/tmp.mod tmp/1fvkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2174 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fvkA-align.mod
tmp/1fvkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2174/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fvkA-orig.a2m tmp/1fvkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fvkA-align.mod
Running w0.5 tmp/1fvkA-orig.a2m tmp/1fvkA-align.mod
Running align2model tmp/1fvkA-align -i tmp/1fvkA-align.mod -db tmp/1fvkA-orig.a2m -db tmp/1fvkA-pdb.a2m
partial PDB gets fragment 28 through 37 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
GLU    2   12
GLU    3   12
LYS    4   30
GLN    5   12
GLU    7   12
ASN    8    4
LEU    9    3
ARG   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    6     19.7613
Cluster     1 =   3   6
2 clashing residues after turn 
Residue clashes:
3-6
cluster 1 has 2 members and 8.800e+01 combinations:
 6  3 
Energy     22.1077
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 8.800e+01 - Sending to search
15.943876 < 22.107746: keeping 
3.643276 < 18.784637: keeping 
0.000000 < 6.597930: keeping 
0.000000 < 3.551712: keeping 
Solved cluster 1: residual clashing  0.58
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fvkA.191.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1fvkA.192.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1fvkA.192.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1fvkA.192.5.a2m \
	-target T0124 -template 1fvkA \
	-out T0124-1fvkA.192.5 -outdir und
Skipped atom 1033, because occupancy 0.5 <= existing 0.500001
Skipped atom 1035, because occupancy 0.5 <= existing 0.500001
Skipped atom 1350, because occupancy 0.5 <= existing 0.500001
Skipped atom 1352, because occupancy 0.5 <= existing 0.500001
Skipped atom 1354, because occupancy 0.5 <= existing 0.500001
Skipped atom 1356, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1449, because occupancy 0.5 <= existing 0.500001
Skipped atom 1451, because occupancy 0.5 <= existing 0.500001
Skipped atom 1453, because occupancy 0.5 <= existing 0.500001
Skipped atom 1455, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fvkA-orig.a2m
Writing a2m file: tmp/1fvkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17780


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17780/tmp -alignfile tmp/1fvkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fvkA-orig.a2m (1 sequences, 189 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17780/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17780/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17780/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17780/tmp.a2m (1 sequences, 189 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17780/tmp.mod tmp/1fvkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17780 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fvkA-align.mod
tmp/1fvkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17780/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fvkA-orig.a2m tmp/1fvkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fvkA-align.mod
Running w0.5 tmp/1fvkA-orig.a2m tmp/1fvkA-align.mod
Running align2model tmp/1fvkA-align -i tmp/1fvkA-align.mod -db tmp/1fvkA-orig.a2m -db tmp/1fvkA-pdb.a2m
partial PDB gets fragment 27 through 36 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
GLU    2   12
LYS    3   25
GLN    4   11
GLU    6   12
ASN    7    4
LEU    8    3
ARG    9   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    7     13.7460
Cluster     1 =   4   7
2 clashing residues after turn 
Residue clashes:
4-7
cluster 1 has 2 members and 8.400e+01 combinations:
 7  4 
Energy     16.9371
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 8.400e+01 - Sending to search
0.000000 < 16.937084: keeping 
0.000000 < 3.647177: keeping 
Solved cluster 1: residual clashing  1.54
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1fvkA.192.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1garA.147.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1garA.147.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1garA.147.4.a2m \
	-target T0124 -template 1garA \
	-out T0124-1garA.147.4 -outdir und
Skipped atom 780, because occupancy 0.5 <= existing 0.500001
Skipped atom 782, because occupancy 0.5 <= existing 0.500001
Skipped atom 784, because occupancy 0.5 <= existing 0.500001
Skipped atom 786, because occupancy 0.5 <= existing 0.500001
Skipped atom 788, because occupancy 0.5 <= existing 0.500001
Skipped atom 790, because occupancy 0.5 <= existing 0.500001
Skipped atom 792, because occupancy 0.5 <= existing 0.500001
Skipped atom 830, because occupancy 0.5 <= existing 0.500001
Skipped atom 832, because occupancy 0.5 <= existing 0.500001
Skipped atom 834, because occupancy 0.5 <= existing 0.500001
Skipped atom 836, because occupancy 0.5 <= existing 0.500001
Skipped atom 838, because occupancy 0.5 <= existing 0.500001
Skipped atom 840, because occupancy 0.5 <= existing 0.500001
Skipped atom 1228, because occupancy 0.5 <= existing 0.500001
Skipped atom 1230, because occupancy 0.5 <= existing 0.500001
Skipped atom 1232, because occupancy 0.5 <= existing 0.500001
Skipped atom 1234, because occupancy 0.5 <= existing 0.500001
Skipped atom 1236, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1garA-orig.a2m
Writing a2m file: tmp/1garA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3152


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3152/tmp -alignfile tmp/1garA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1garA-orig.a2m (1 sequences, 212 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3152/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3152/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3152/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3152/tmp.a2m (1 sequences, 212 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3152/tmp.mod tmp/1garA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3152 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1garA-align.mod
tmp/1garA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3152/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1garA-orig.a2m tmp/1garA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1garA-align.mod
Running w0.5 tmp/1garA-orig.a2m tmp/1garA-align.mod
Running align2model tmp/1garA-align -i tmp/1garA-align.mod -db tmp/1garA-orig.a2m -db tmp/1garA-pdb.a2m
partial PDB gets fragment 38 through 47 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
MET    2   12
MET    3   12
ARG    4   32
SER    5    2
THR    6    2
SER    7    3
ASP    8    4
LYS    9   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1garA.147.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1garA.148.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1garA.148.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1garA.148.2.a2m \
	-target T0124 -template 1garA \
	-out T0124-1garA.148.2 -outdir und
Skipped atom 780, because occupancy 0.5 <= existing 0.500001
Skipped atom 782, because occupancy 0.5 <= existing 0.500001
Skipped atom 784, because occupancy 0.5 <= existing 0.500001
Skipped atom 786, because occupancy 0.5 <= existing 0.500001
Skipped atom 788, because occupancy 0.5 <= existing 0.500001
Skipped atom 790, because occupancy 0.5 <= existing 0.500001
Skipped atom 792, because occupancy 0.5 <= existing 0.500001
Skipped atom 830, because occupancy 0.5 <= existing 0.500001
Skipped atom 832, because occupancy 0.5 <= existing 0.500001
Skipped atom 834, because occupancy 0.5 <= existing 0.500001
Skipped atom 836, because occupancy 0.5 <= existing 0.500001
Skipped atom 838, because occupancy 0.5 <= existing 0.500001
Skipped atom 840, because occupancy 0.5 <= existing 0.500001
Skipped atom 1228, because occupancy 0.5 <= existing 0.500001
Skipped atom 1230, because occupancy 0.5 <= existing 0.500001
Skipped atom 1232, because occupancy 0.5 <= existing 0.500001
Skipped atom 1234, because occupancy 0.5 <= existing 0.500001
Skipped atom 1236, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1garA-orig.a2m
Writing a2m file: tmp/1garA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2096


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2096/tmp -alignfile tmp/1garA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1garA-orig.a2m (1 sequences, 212 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2096/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2096/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2096/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2096/tmp.a2m (1 sequences, 212 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2096/tmp.mod tmp/1garA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2096 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1garA-align.mod
tmp/1garA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2096/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1garA-orig.a2m tmp/1garA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1garA-align.mod
Running w0.5 tmp/1garA-orig.a2m tmp/1garA-align.mod
Running align2model tmp/1garA-align -i tmp/1garA-align.mod -db tmp/1garA-orig.a2m -db tmp/1garA-pdb.a2m
partial PDB gets fragment 37 through 46 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
MET    2    8
ARG    3   26
SER    4    2
THR    5    2
SER    6    2
ASP    7    4
LYS    8   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1garA.148.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1garA.154.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1garA.154.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1garA.154.3.a2m \
	-target T0124 -template 1garA \
	-out T0124-1garA.154.3 -outdir und
Skipped atom 780, because occupancy 0.5 <= existing 0.500001
Skipped atom 782, because occupancy 0.5 <= existing 0.500001
Skipped atom 784, because occupancy 0.5 <= existing 0.500001
Skipped atom 786, because occupancy 0.5 <= existing 0.500001
Skipped atom 788, because occupancy 0.5 <= existing 0.500001
Skipped atom 790, because occupancy 0.5 <= existing 0.500001
Skipped atom 792, because occupancy 0.5 <= existing 0.500001
Skipped atom 830, because occupancy 0.5 <= existing 0.500001
Skipped atom 832, because occupancy 0.5 <= existing 0.500001
Skipped atom 834, because occupancy 0.5 <= existing 0.500001
Skipped atom 836, because occupancy 0.5 <= existing 0.500001
Skipped atom 838, because occupancy 0.5 <= existing 0.500001
Skipped atom 840, because occupancy 0.5 <= existing 0.500001
Skipped atom 1228, because occupancy 0.5 <= existing 0.500001
Skipped atom 1230, because occupancy 0.5 <= existing 0.500001
Skipped atom 1232, because occupancy 0.5 <= existing 0.500001
Skipped atom 1234, because occupancy 0.5 <= existing 0.500001
Skipped atom 1236, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1garA-orig.a2m
Writing a2m file: tmp/1garA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22399


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22399/tmp -alignfile tmp/1garA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1garA-orig.a2m (1 sequences, 212 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22399/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22399/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22399/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22399/tmp.a2m (1 sequences, 212 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22399/tmp.mod tmp/1garA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22399 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1garA-align.mod
tmp/1garA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22399/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1garA-orig.a2m tmp/1garA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1garA-align.mod
Running w0.5 tmp/1garA-orig.a2m tmp/1garA-align.mod
Running align2model tmp/1garA-align -i tmp/1garA-align.mod -db tmp/1garA-orig.a2m -db tmp/1garA-pdb.a2m
partial PDB gets fragment 37 through 46 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
LYS    2   19
GLN    5   14
GLU    6   15
ARG    7   32
LEU    8    3
LYS    9   24
LYS   10   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1garA.154.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1garA.156.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1garA.156.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1garA.156.3.a2m \
	-target T0124 -template 1garA \
	-out T0124-1garA.156.3 -outdir und
Skipped atom 780, because occupancy 0.5 <= existing 0.500001
Skipped atom 782, because occupancy 0.5 <= existing 0.500001
Skipped atom 784, because occupancy 0.5 <= existing 0.500001
Skipped atom 786, because occupancy 0.5 <= existing 0.500001
Skipped atom 788, because occupancy 0.5 <= existing 0.500001
Skipped atom 790, because occupancy 0.5 <= existing 0.500001
Skipped atom 792, because occupancy 0.5 <= existing 0.500001
Skipped atom 830, because occupancy 0.5 <= existing 0.500001
Skipped atom 832, because occupancy 0.5 <= existing 0.500001
Skipped atom 834, because occupancy 0.5 <= existing 0.500001
Skipped atom 836, because occupancy 0.5 <= existing 0.500001
Skipped atom 838, because occupancy 0.5 <= existing 0.500001
Skipped atom 840, because occupancy 0.5 <= existing 0.500001
Skipped atom 1228, because occupancy 0.5 <= existing 0.500001
Skipped atom 1230, because occupancy 0.5 <= existing 0.500001
Skipped atom 1232, because occupancy 0.5 <= existing 0.500001
Skipped atom 1234, because occupancy 0.5 <= existing 0.500001
Skipped atom 1236, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1garA-orig.a2m
Writing a2m file: tmp/1garA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1579


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1579/tmp -alignfile tmp/1garA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1garA-orig.a2m (1 sequences, 212 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1579/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1579/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1579/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1579/tmp.a2m (1 sequences, 212 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1579/tmp.mod tmp/1garA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1579 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1garA-align.mod
tmp/1garA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1579/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1garA-orig.a2m tmp/1garA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1garA-align.mod
Running w0.5 tmp/1garA-orig.a2m tmp/1garA-align.mod
Running align2model tmp/1garA-align -i tmp/1garA-align.mod -db tmp/1garA-orig.a2m -db tmp/1garA-pdb.a2m
partial PDB gets fragment 37 through 46 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    3   12
GLU    4   15
ARG    5   32
LYS    7   28
LYS    8   25
GLU    9   12
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    3.82220
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1garA.156.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.147.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.147.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.147.2.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.147.2 -outdir und
partial PDB gets fragment 88 through 97 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
MET    2   13
MET    3   10
ARG    4   26
SER    5    2
THR    6    1
ASP    8    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.147.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.147.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.147.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.147.5.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.147.5 -outdir und
partial PDB gets fragment 86 through 96 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
MET    2   10
MET    3   10
ARG    4   31
SER    5    3
THR    6    1
SER    7    2
ASP    8    6
LYS    9   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.147.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.149.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.149.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.149.1.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.149.1 -outdir und
partial PDB gets fragment 86 through 95 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
ARG    2   24
SER    3    3
THR    4    3
SER    5    3
ASP    6    4
LYS    7   24
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.149.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.149.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.149.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.149.2.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.149.2 -outdir und
partial PDB gets fragment 84 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
ARG    2   32
SER    3    2
THR    4    1
SER    5    3
ASP    6    8
LYS    7   23
GLN   10   13
GLU   11   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.149.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.150.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.150.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.150.3.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.150.3 -outdir und
partial PDB gets fragment 83 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   16
SER    2    3
THR    3    3
SER    4    2
ASP    5    4
LYS    6   27
GLN    9   12
ARG   11   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7   12     18.1923
Cluster     1 =   7  12
2 clashing residues after turn 
Residue clashes:
7-12
cluster 1 has 2 members and 6.510e+02 combinations:
 7  12 
Energy     18.1923
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 6.510e+02 - Sending to search
16.011702 < 18.192329: keeping 
3.569817 < 16.366179: keeping 
0.000000 < 5.358459: keeping 
0.000000 < 2.284504: keeping 
0.000000 < 1.051167: keeping 
Solved cluster 1: residual clashing  0.98
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.150.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.151.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.151.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.151.2.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.151.2 -outdir und
partial PDB gets fragment 82 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
THR    2    2
SER    3    3
ASP    4    6
LYS    5   26
GLN    8   15
GLU    9   11
ARG   10   26
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.151.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.152.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.152.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.152.2.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.152.2 -outdir und
partial PDB gets fragment 81 through 91 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
SER    2    2
ASP    3    4
LYS    4   27
GLN    7   11
GLU    8   14
ARG    9   31
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.152.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.154.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.154.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.154.2.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.154.2 -outdir und
partial PDB gets fragment 81 through 90 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
LYS    2   18
GLN    5   14
GLU    6   13
ARG    7   24
LEU    8    3
LYS    9   31
LYS   10   23
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.154.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.155.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.155.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.155.3.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.155.3 -outdir und
partial PDB gets fragment 80 through 89 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
GLN    4    7
GLU    5   13
ARG    6   32
LEU    7    3
LYS    8   26
LYS    9   27
GLU   10   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.155.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.231.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.231.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.231.3.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.231.3 -outdir und
partial PDB gets fragment 4 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   11
VAL    2    1
LYS    3   29
ASN    4    5
TYR    5    3
MET    6   10
GLU    8   16
VAL    9    2
PHE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.231.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gca.232.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gca.232.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gca.232.2.a2m \
	-target T0124 -template 1gca \
	-out T0124-1gca.232.2 -outdir und
partial PDB gets fragment 3 through 12 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
LYS    2   27
ASN    3    5
TYR    4    3
MET    5   11
LYS    6   27
GLU    7   15
VAL    8    2
PHE    9    3
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gca.232.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gof.48.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gof.48.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gof.48.5.a2m \
	-target T0124 -template 1gof \
	-out T0124-1gof.48.5 -outdir und
partial PDB gets fragment 620 through 629 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
LEU    2    3
LEU    3    3
GLN    4    9
LYS    5   30
TYR    6    3
SER    7    2
LEU    9    4
PHE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4   10     26.2707
Cluster     1 =   4  10
2 clashing residues after turn 
Residue clashes:
4-10
cluster 1 has 2 members and 2.000e+00 combinations:
 4  10 
Energy     28.2210
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search
6.848528 < 28.220982: keeping 
Solved cluster 1: residual clashing 10.75
Still clashes at these sidechain pairs:
Residual clashes =    6.84853
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gof.48.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gof.49.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gof.49.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gof.49.2.a2m \
	-target T0124 -template 1gof \
	-out T0124-1gof.49.2 -outdir und
partial PDB gets fragment 619 through 628 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    3
GLN    3   14
LYS    4   28
TYR    5    3
VAL    7    3
LEU    8    2
PHE    9    3
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   11     18.5490
keepclash     8   10     10.5931
Cluster     1 =   5  11
Cluster     2 =   8  10
4 clashing residues after turn 
Residue clashes:
5-11
8-10
cluster 1 has 2 members and 2.800e+01 combinations:
 11  5 
Energy     18.5490
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 2.800e+01 - Sending to search
0.000000 < 18.549021: keeping 
Solved cluster 1: residual clashing  2.22
cluster 2 has 2 members and 9.000e+00 combinations:
 8  10 
Energy     12.1211
Searching cluster 8
Combinations for 2 members in cluster 2 OK: 9.000e+00 - Sending to search
0.000000 < 12.121120: keeping 
Solved cluster 2: residual clashing  0.10
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gof.49.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gof.50.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gof.50.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gof.50.2.a2m \
	-target T0124 -template 1gof \
	-out T0124-1gof.50.2 -outdir und
partial PDB gets fragment 618 through 627 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLN    2   12
LYS    3   28
TYR    4    3
SER    5    3
VAL    6    2
LEU    7    3
PHE    8    4
LEU    9    2
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    5     26.6288
Cluster     1 =   3   5
2 clashing residues after turn 
Residue clashes:
3-5
cluster 1 has 2 members and 3.600e+01 combinations:
 5  3 
Energy     26.6288
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 3.600e+01 - Sending to search
0.000000 < 26.628799: keeping 
Solved cluster 1: residual clashing  0.07
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gof.50.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gof.51.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gof.51.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gof.51.2.a2m \
	-target T0124 -template 1gof \
	-out T0124-1gof.51.2 -outdir und
partial PDB gets fragment 617 through 626 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   15
LYS    2   27
TYR    3    3
SER    4    3
LEU    6    3
PHE    7    3
LEU    8    3
GLU    9   15
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gof.51.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gox.143.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gox.143.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gox.143.2.a2m \
	-target T0124 -template 1gox \
	-out T0124-1gox.143.2 -outdir und
Bad short name: ACE for alphabet: ExtAA
Replacing ACE with X
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gox-orig.a2m
Writing a2m file: tmp/1gox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6395


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6395/tmp -alignfile tmp/1gox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gox-orig.a2m (1 sequences, 369 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6395/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6395/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6395/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6395/tmp.a2m (1 sequences, 369 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6395/tmp.mod tmp/1gox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6395 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gox-align.mod
tmp/1gox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6395/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gox-orig.a2m tmp/1gox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gox-align.mod
Running w0.5 tmp/1gox-orig.a2m tmp/1gox-align.mod
Running align2model tmp/1gox-align -i tmp/1gox-align.mod -db tmp/1gox-orig.a2m -db tmp/1gox-pdb.a2m
partial PDB gets fragment 31 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   32
ILE    3    2
GLN    4   14
VAL    5    1
MET    6   10
MET    7   10
ARG    8   27
SER    9    3
THR   10    2
SER   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gox.143.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gox.145.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gox.145.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gox.145.4.a2m \
	-target T0124 -template 1gox \
	-out T0124-1gox.145.4 -outdir und
Bad short name: ACE for alphabet: ExtAA
Replacing ACE with X
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gox-orig.a2m
Writing a2m file: tmp/1gox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2988


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2988/tmp -alignfile tmp/1gox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gox-orig.a2m (1 sequences, 369 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2988/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2988/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2988/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2988/tmp.a2m (1 sequences, 369 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2988/tmp.mod tmp/1gox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2988 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gox-align.mod
tmp/1gox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2988/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gox-orig.a2m tmp/1gox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gox-align.mod
Running w0.5 tmp/1gox-orig.a2m tmp/1gox-align.mod
Running align2model tmp/1gox-align -i tmp/1gox-align.mod -db tmp/1gox-orig.a2m -db tmp/1gox-pdb.a2m
partial PDB gets fragment 31 through 40 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
VAL    3    1
MET    4   10
MET    5   10
ARG    6   26
SER    7    2
THR    8    2
SER    9    3
ASP   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    4     12.0575
Cluster     1 =   2   4
2 clashing residues after turn 
Residue clashes:
2-4
cluster 1 has 2 members and 2.000e+00 combinations:
 4  2 
Energy     12.0575
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search
6.600213 < 12.057493: keeping 
Solved cluster 1: residual clashing  8.80
Still clashes at these sidechain pairs:
Residual clashes =    6.60021
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gox.145.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gox.146.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gox.146.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gox.146.4.a2m \
	-target T0124 -template 1gox \
	-out T0124-1gox.146.4 -outdir und
Bad short name: ACE for alphabet: ExtAA
Replacing ACE with X
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gox-orig.a2m
Writing a2m file: tmp/1gox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20097


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20097/tmp -alignfile tmp/1gox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gox-orig.a2m (1 sequences, 369 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20097/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20097/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20097/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20097/tmp.a2m (1 sequences, 369 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20097/tmp.mod tmp/1gox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20097 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gox-align.mod
tmp/1gox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20097/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gox-orig.a2m tmp/1gox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gox-align.mod
Running w0.5 tmp/1gox-orig.a2m tmp/1gox-align.mod
Running align2model tmp/1gox-align -i tmp/1gox-align.mod -db tmp/1gox-orig.a2m -db tmp/1gox-pdb.a2m
partial PDB gets fragment 30 through 39 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
VAL    2    2
MET    3    6
MET    4   10
ARG    5   32
SER    6    3
THR    7    1
SER    8    2
ASP    9    4
LYS   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gox.146.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.0.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.0.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.0.5.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.0.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4544


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4544/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4544/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4544/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4544/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4544/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4544/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4544 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4544/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 175 through 183 extending start
sh: 21981 Floating exception
/projects/kestrel/users/karplus/burial/slicer/slicer: ERROR 'scwrl -v -i tmp/T0124-1gp1A.0.5.pdb -o tmp/T0124-1gp1A.0.5.scwrld-pdb -s tmp/T0124-1gp1A.0.5.scwrl-seq' failed.
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.0.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.143.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.143.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.143.5.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.143.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4323


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4323/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4323/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4323/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4323/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4323/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4323/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4323 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4323/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 28 through 34 extending start extending end
partial PDB gets fragment 35 through 37 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    5
ARG    2   29
ILE    3    2
GLN    4   11
VAL    5    3
MET    6   11
MET    7   10
SER   10    2
SER   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 10 rotamers of residue M 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue S 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.143.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.148.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.148.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.148.5.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.148.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5074


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5074/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5074/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5074/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5074/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5074/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5074/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5074 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5074/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 25 through 34 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
MET    2   10
ARG    3   24
SER    4    3
THR    5    3
SER    6    3
ASP    7    5
LYS    8   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.148.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.157.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.157.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.157.4.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.157.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3501


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3501/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3501/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3501/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3501/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3501/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3501/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3501 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3501/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 14 through 23 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    2   12
GLU    3   13
ARG    4   28
LYS    6   25
LYS    7   30
GLU    8   12
ILE    9    4
ASN   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.157.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.158.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.158.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.158.2.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.158.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3518


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3518/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3518/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3518/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3518/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3518/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3518/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3518 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3518/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 13 through 22 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   15
ARG    3   26
LEU    4    3
LYS    5   27
LYS    6   31
GLU    7   15
ILE    8    5
ASN    9    5
ASN   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.158.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.159.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.159.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.159.4.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.159.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2569


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2569/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2569/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2569/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2569/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2569/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2569/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2569 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2569/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 12 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
ARG    2   32
LEU    3    3
LYS    4   24
LYS    5   26
GLU    6   13
ILE    7    4
ASN    8    5
ASN    9    4
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.159.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.160.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.160.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.160.3.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.160.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1253


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1253/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1253/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1253/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1253/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1253/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1253/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1253 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1253/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 11 through 20 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   32
LEU    2    5
LYS    3   30
LYS    4   25
GLU    5   12
ILE    6    3
ASN    8    5
HIS   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   11     15.6150
Cluster     1 =   8  11
2 clashing residues after turn 
Residue clashes:
8-11
cluster 1 has 2 members and 0.000e+00 combinations:
 8  11 
Energy     15.6150
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
0.000000 < 15.615028: keeping 
Solved cluster 1: residual clashing  1.37
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.160.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.161.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.161.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.161.4.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.161.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1043


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1043/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1043/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1043/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1043/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1043/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1043/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1043 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1043/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 10 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   30
LYS    3   25
GLU    4   14
ILE    5    2
ASN    6    5
ASN    7    5
SER    8    3
HIS    9    4
ILE   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.161.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.161.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.161.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.161.5.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.161.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30300


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30300/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30300/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30300/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30300/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30300/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30300/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30300 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30300/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 14 through 23 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   24
LYS    3   26
GLU    4   13
ILE    5    4
ASN    6    5
ASN    7    4
SER    8    2
HIS    9    3
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.161.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.162.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.162.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.162.3.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.162.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3201


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3201/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3201/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3201/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3201/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3201/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3201/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3201 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3201/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 13 through 22 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
LYS    2   25
GLU    3   12
ILE    4    3
ASN    6    5
HIS    8    3
ILE    9    2
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue I 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    9     15.6150
Cluster     1 =   6   9
2 clashing residues after turn 
Residue clashes:
6-9
cluster 1 has 2 members and 0.000e+00 combinations:
 6  9 
Energy     15.6150
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
0.000000 < 15.615028: keeping 
Solved cluster 1: residual clashing  1.37
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.162.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.163.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.163.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.163.0.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.163.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9593


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9593/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9593/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9593/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9593/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9593/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9593/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9593 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9593/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 12 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
GLU    2   14
ILE    3    2
ASN    4    5
ASN    5    5
SER    6    3
HIS    7    4
ILE    8    4
GLN    9   14
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.163.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1gp1A.164.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1gp1A.164.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1gp1A.164.0.a2m \
	-target T0124 -template 1gp1A \
	-out T0124-1gp1A.164.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1gp1A-orig.a2m
Writing a2m file: tmp/1gp1A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4874


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4874/tmp -alignfile tmp/1gp1A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1gp1A-orig.a2m (1 sequences, 198 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4874/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4874/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4874/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4874/tmp.a2m (1 sequences, 198 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4874/tmp.mod tmp/1gp1A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4874 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1gp1A-align.mod
tmp/1gp1A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4874/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1gp1A-orig.a2m tmp/1gp1A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1gp1A-align.mod
Running w0.5 tmp/1gp1A-orig.a2m tmp/1gp1A-align.mod
Running align2model tmp/1gp1A-align -i tmp/1gp1A-align.mod -db tmp/1gp1A-orig.a2m -db tmp/1gp1A-pdb.a2m
partial PDB gets fragment 11 through 20 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
ILE    2    3
ASN    3    6
ASN    4    5
SER    5    2
HIS    6    3
ILE    7    3
GLN    8   15
GLU    9   15
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1gp1A.164.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.10.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.10.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.10.3.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.10.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3964


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3964/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3964/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3964/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3964/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3964/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3964/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3964 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3964/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 150 through 156 extending start
Debugging on !
Reading sequence file
Reading input structure 
8 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
GLN    2   15
THR    3    2
SER    5    3
LEU    6    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.10.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.11.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.11.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.11.5.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.11.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-83


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-83/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-83/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-83/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-83/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-83/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-83/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-83 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-83/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 149 through 156 extending start
Debugging on !
Reading sequence file
Reading input structure 
9 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
THR    2    2
SER    4    3
LEU    5    2
GLU    7   15
LEU    8    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.11.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.12.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.12.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.12.3.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.12.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1954


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1954/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1954/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1954/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1954/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1954/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1954/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1954 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1954/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 148 through 156 extending start
Debugging on !
Reading sequence file
Reading input structure 
10 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
SER    3    2
LEU    4    3
GLU    6   13
LEU    7    2
GLN    8   13
GLN    9   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.12.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.61.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.61.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.61.1.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.61.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8265


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8265/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8265/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8265/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8265/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8265/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8265/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8265 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8265/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 63 through 73 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
TYR    2    2
PRO    3    2
ARG    4   32
LEU    6    2
ASP    7    4
SER    8    3
GLN    9   12
VAL   10    2
VAL   11    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.86983
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.61.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.61.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.61.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.61.3.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.61.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3088


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3088/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3088/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3088/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3088/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3088/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3088/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3088 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3088/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 65 through 74 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
TYR    2    2
PRO    3    2
ARG    4   21
LEU    6    3
ASP    7    5
SER    8    3
GLN    9   12
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.43482
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.61.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.61.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.61.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.61.5.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.61.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1489


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1489/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1489/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1489/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1489/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1489/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1489/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1489 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1489/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 61 through 70 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
TYR    2    2
PRO    3    2
ARG    4   21
LEU    6    3
ASP    7    6
SER    8    2
GLN    9   10
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue L 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.39700
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.61.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.62.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.62.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.62.3.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.62.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26824


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26824/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26824/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26824/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26824/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26824/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26824/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26824 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26824/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 60 through 69 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    2
PRO    2    2
LEU    5    2
ASP    6    3
SER    7    3
GLN    8   15
VAL    9    1
VAL   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 3 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.62.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.63.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.63.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.63.3.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.63.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-350


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-350/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-350/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-350/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-350/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-350/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-350/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-350 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-350/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 59 through 68 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
ARG    2   26
LEU    4    2
SER    6    2
GLN    7   13
VAL    8    3
VAL    9    2
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue V 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.58106
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.63.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.86.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.86.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.86.5.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.86.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4889


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4889/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4889/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4889/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4889/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4889/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4889/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4889 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4889/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 44 through 53 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
GLU    2   15
TYR    3    3
HIS    4    4
ASP    5    5
ILE    7    4
ARG    8   27
ARG    9   25
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.16789
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.86.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.88.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.88.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.88.3.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.88.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28652


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28652/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28652/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28652/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28652/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28652/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28652/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28652 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28652/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 46 through 55 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
HIS    2    4
ASP    3    5
ILE    5    4
ARG    6   27
ARG    7   25
ARG    8   27
LYS    9   27
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.88.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.89.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.89.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.89.1.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.89.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5105


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5105/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5105/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5105/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5105/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5105/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5105/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5105 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5105/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 45 through 54 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
ASP    2    5
ILE    4    3
ARG    5   27
ARG    6   26
ARG    7   27
LYS    8   27
GLU    9   13
GLN   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.89.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.89.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.89.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.89.3.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.89.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3113


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3113/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3113/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3113/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3113/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3113/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3113/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3113 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3113/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 43 through 53 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
ASP    2    5
ILE    4    4
ARG    5   32
ARG    6   26
ARG    7   27
LYS    8   23
GLU    9   12
GLN   10   12
HIS   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.89.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.90.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.90.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.90.3.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.90.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5340


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5340/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5340/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5340/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5340/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5340/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5340/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5340 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5340/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 42 through 52 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    7
ILE    3    3
ARG    4   28
ARG    5   24
ARG    6   32
LYS    7   20
GLU    8   12
GLN    9   11
HIS   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.90.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.91.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.91.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.91.1.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.91.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20814


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20814/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20814/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20814/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20814/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20814/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20814/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20814 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20814/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 41 through 51 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ILE    2    4
ARG    3   27
ARG    4   26
ARG    5   28
LYS    6   21
GLN    8   11
HIS    9    3
THR   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.91.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.92.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.92.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.92.2.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.92.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5405


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5405/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5405/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5405/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5405/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5405/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5405/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5405 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5405/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 40 through 50 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    5
ARG    2   31
ARG    3   30
ARG    4   27
GLU    6   15
GLN    7   12
HIS    8    4
THR   10    2
GLU   11   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.92.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1hfc.93.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1hfc.93.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1hfc.93.3.a2m \
	-target T0124 -template 1hfc \
	-out T0124-1hfc.93.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1hfc-orig.a2m
Writing a2m file: tmp/1hfc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27824


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27824/tmp -alignfile tmp/1hfc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1hfc-orig.a2m (1 sequences, 169 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27824/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27824/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27824/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27824/tmp.a2m (1 sequences, 169 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27824/tmp.mod tmp/1hfc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27824 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1hfc-align.mod
tmp/1hfc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27824/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1hfc-orig.a2m tmp/1hfc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1hfc-align.mod
Running w0.5 tmp/1hfc-orig.a2m tmp/1hfc-align.mod
Running align2model tmp/1hfc-align -i tmp/1hfc-align.mod -db tmp/1hfc-orig.a2m -db tmp/1hfc-pdb.a2m
partial PDB gets fragment 39 through 49 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   24
ARG    2   32
ARG    3   31
LYS    4   28
GLU    5   12
GLN    6   12
HIS    7    3
THR    9    2
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1hfc.93.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1htrB.223.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1htrB.223.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1htrB.223.2.a2m \
	-target T0124 -template 1htrB \
	-out T0124-1htrB.223.2 -outdir und
Skipped atom 1114, because occupancy 0.4 <= existing 0.600001
Skipped atom 1116, because occupancy 0.4 <= existing 0.600001
Skipped atom 1118, because occupancy 0.4 <= existing 0.600001
Skipped atom 1189, because occupancy 0.4 <= existing 0.600001
Skipped atom 1191, because occupancy 0.4 <= existing 0.600001
Skipped atom 1193, because occupancy 0.4 <= existing 0.600001
Skipped atom 1195, because occupancy 0.4 <= existing 0.600001
Skipped atom 1297, because occupancy 0.4 <= existing 0.600001
Skipped atom 2036, because occupancy 0.4 <= existing 0.600001
Skipped atom 2396, because occupancy 0.3 <= existing 0.700001
Skipped atom 2398, because occupancy 0.3 <= existing 0.700001
Skipped atom 2400, because occupancy 0.3 <= existing 0.700001
Skipped atom 2402, because occupancy 0.3 <= existing 0.700001
Skipped atom 2820, because occupancy 0.4 <= existing 0.600001
Skipped atom 2822, because occupancy 0.4 <= existing 0.600001
Skipped atom 2824, because occupancy 0.4 <= existing 0.600001
partial PDB gets fragment 5 through 14 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
LEU    2    3
THR    3    2
VAL    4    2
GLU    5   15
VAL    6    2
GLN    7   14
GLU    8   14
MET    9   10
VAL   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1htrB.223.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1htrB.224.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1htrB.224.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1htrB.224.4.a2m \
	-target T0124 -template 1htrB \
	-out T0124-1htrB.224.4 -outdir und
Skipped atom 1114, because occupancy 0.4 <= existing 0.600001
Skipped atom 1116, because occupancy 0.4 <= existing 0.600001
Skipped atom 1118, because occupancy 0.4 <= existing 0.600001
Skipped atom 1189, because occupancy 0.4 <= existing 0.600001
Skipped atom 1191, because occupancy 0.4 <= existing 0.600001
Skipped atom 1193, because occupancy 0.4 <= existing 0.600001
Skipped atom 1195, because occupancy 0.4 <= existing 0.600001
Skipped atom 1297, because occupancy 0.4 <= existing 0.600001
Skipped atom 2036, because occupancy 0.4 <= existing 0.600001
Skipped atom 2396, because occupancy 0.3 <= existing 0.700001
Skipped atom 2398, because occupancy 0.3 <= existing 0.700001
Skipped atom 2400, because occupancy 0.3 <= existing 0.700001
Skipped atom 2402, because occupancy 0.3 <= existing 0.700001
Skipped atom 2820, because occupancy 0.4 <= existing 0.600001
Skipped atom 2822, because occupancy 0.4 <= existing 0.600001
Skipped atom 2824, because occupancy 0.4 <= existing 0.600001
partial PDB gets fragment 4 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
THR    2    2
VAL    3    3
GLU    4   15
VAL    5    2
GLN    6   14
GLU    7   12
MET    8   12
VAL    9    2
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    4     12.7491
Cluster     1 =   2   4
2 clashing residues after turn 
Residue clashes:
2-4
cluster 1 has 2 members and 6.000e+00 combinations:
 2  4 
Energy     12.7491
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 6.000e+00 - Sending to search
7.680861 < 12.749142: keeping 
0.000000 < 7.949042: keeping 
Solved cluster 1: residual clashing  0.34
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1htrB.224.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1htrB.225.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1htrB.225.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1htrB.225.0.a2m \
	-target T0124 -template 1htrB \
	-out T0124-1htrB.225.0 -outdir und
Skipped atom 1114, because occupancy 0.4 <= existing 0.600001
Skipped atom 1116, because occupancy 0.4 <= existing 0.600001
Skipped atom 1118, because occupancy 0.4 <= existing 0.600001
Skipped atom 1189, because occupancy 0.4 <= existing 0.600001
Skipped atom 1191, because occupancy 0.4 <= existing 0.600001
Skipped atom 1193, because occupancy 0.4 <= existing 0.600001
Skipped atom 1195, because occupancy 0.4 <= existing 0.600001
Skipped atom 1297, because occupancy 0.4 <= existing 0.600001
Skipped atom 2036, because occupancy 0.4 <= existing 0.600001
Skipped atom 2396, because occupancy 0.3 <= existing 0.700001
Skipped atom 2398, because occupancy 0.3 <= existing 0.700001
Skipped atom 2400, because occupancy 0.3 <= existing 0.700001
Skipped atom 2402, because occupancy 0.3 <= existing 0.700001
Skipped atom 2820, because occupancy 0.4 <= existing 0.600001
Skipped atom 2822, because occupancy 0.4 <= existing 0.600001
Skipped atom 2824, because occupancy 0.4 <= existing 0.600001
partial PDB gets fragment 3 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
VAL    2    1
GLU    3   13
VAL    4    3
GLN    5   14
GLU    6   10
VAL    8    3
LYS    9   30
ASN   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.13880
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1htrB.225.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1htrB.226.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1htrB.226.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1htrB.226.0.a2m \
	-target T0124 -template 1htrB \
	-out T0124-1htrB.226.0 -outdir und
Skipped atom 1114, because occupancy 0.4 <= existing 0.600001
Skipped atom 1116, because occupancy 0.4 <= existing 0.600001
Skipped atom 1118, because occupancy 0.4 <= existing 0.600001
Skipped atom 1189, because occupancy 0.4 <= existing 0.600001
Skipped atom 1191, because occupancy 0.4 <= existing 0.600001
Skipped atom 1193, because occupancy 0.4 <= existing 0.600001
Skipped atom 1195, because occupancy 0.4 <= existing 0.600001
Skipped atom 1297, because occupancy 0.4 <= existing 0.600001
Skipped atom 2036, because occupancy 0.4 <= existing 0.600001
Skipped atom 2396, because occupancy 0.3 <= existing 0.700001
Skipped atom 2398, because occupancy 0.3 <= existing 0.700001
Skipped atom 2400, because occupancy 0.3 <= existing 0.700001
Skipped atom 2402, because occupancy 0.3 <= existing 0.700001
Skipped atom 2820, because occupancy 0.4 <= existing 0.600001
Skipped atom 2822, because occupancy 0.4 <= existing 0.600001
Skipped atom 2824, because occupancy 0.4 <= existing 0.600001
partial PDB gets fragment 2 through 12 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
GLU    2   15
VAL    3    1
GLN    4   13
GLU    5   15
MET    6   11
VAL    7    2
LYS    8   30
ASN    9    4
TYR   10    2
MET   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue Y 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1htrB.226.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1htrB.227.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1htrB.227.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1htrB.227.0.a2m \
	-target T0124 -template 1htrB \
	-out T0124-1htrB.227.0 -outdir und
Skipped atom 1114, because occupancy 0.4 <= existing 0.600001
Skipped atom 1116, because occupancy 0.4 <= existing 0.600001
Skipped atom 1118, because occupancy 0.4 <= existing 0.600001
Skipped atom 1189, because occupancy 0.4 <= existing 0.600001
Skipped atom 1191, because occupancy 0.4 <= existing 0.600001
Skipped atom 1193, because occupancy 0.4 <= existing 0.600001
Skipped atom 1195, because occupancy 0.4 <= existing 0.600001
Skipped atom 1297, because occupancy 0.4 <= existing 0.600001
Skipped atom 2036, because occupancy 0.4 <= existing 0.600001
Skipped atom 2396, because occupancy 0.3 <= existing 0.700001
Skipped atom 2398, because occupancy 0.3 <= existing 0.700001
Skipped atom 2400, because occupancy 0.3 <= existing 0.700001
Skipped atom 2402, because occupancy 0.3 <= existing 0.700001
Skipped atom 2820, because occupancy 0.4 <= existing 0.600001
Skipped atom 2822, because occupancy 0.4 <= existing 0.600001
Skipped atom 2824, because occupancy 0.4 <= existing 0.600001
partial PDB gets fragment 1 through 11 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
VAL    2    3
GLN    3   15
MET    5    6
VAL    6    3
LYS    7   27
ASN    8    5
TYR    9    3
MET   10    8
LYS   11   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1htrB.227.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1htrB.228.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1htrB.228.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1htrB.228.1.a2m \
	-target T0124 -template 1htrB \
	-out T0124-1htrB.228.1 -outdir und
Skipped atom 1114, because occupancy 0.4 <= existing 0.600001
Skipped atom 1116, because occupancy 0.4 <= existing 0.600001
Skipped atom 1118, because occupancy 0.4 <= existing 0.600001
Skipped atom 1189, because occupancy 0.4 <= existing 0.600001
Skipped atom 1191, because occupancy 0.4 <= existing 0.600001
Skipped atom 1193, because occupancy 0.4 <= existing 0.600001
Skipped atom 1195, because occupancy 0.4 <= existing 0.600001
Skipped atom 1297, because occupancy 0.4 <= existing 0.600001
Skipped atom 2036, because occupancy 0.4 <= existing 0.600001
Skipped atom 2396, because occupancy 0.3 <= existing 0.700001
Skipped atom 2398, because occupancy 0.3 <= existing 0.700001
Skipped atom 2400, because occupancy 0.3 <= existing 0.700001
Skipped atom 2402, because occupancy 0.3 <= existing 0.700001
Skipped atom 2820, because occupancy 0.4 <= existing 0.600001
Skipped atom 2822, because occupancy 0.4 <= existing 0.600001
Skipped atom 2824, because occupancy 0.4 <= existing 0.600001
partial PDB gets fragment 0 through 10 extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    0    2
GLN    1   13
GLU    2   15
MET    3   12
VAL    4    1
LYS    5   27
ASN    6    5
TYR    7    3
MET    8    6
LYS    9   30
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.07024
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1htrB.228.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1htrB.230.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1htrB.230.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1htrB.230.3.a2m \
	-target T0124 -template 1htrB \
	-out T0124-1htrB.230.3 -outdir und
Skipped atom 1114, because occupancy 0.4 <= existing 0.600001
Skipped atom 1116, because occupancy 0.4 <= existing 0.600001
Skipped atom 1118, because occupancy 0.4 <= existing 0.600001
Skipped atom 1189, because occupancy 0.4 <= existing 0.600001
Skipped atom 1191, because occupancy 0.4 <= existing 0.600001
Skipped atom 1193, because occupancy 0.4 <= existing 0.600001
Skipped atom 1195, because occupancy 0.4 <= existing 0.600001
Skipped atom 1297, because occupancy 0.4 <= existing 0.600001
Skipped atom 2036, because occupancy 0.4 <= existing 0.600001
Skipped atom 2396, because occupancy 0.3 <= existing 0.700001
Skipped atom 2398, because occupancy 0.3 <= existing 0.700001
Skipped atom 2400, because occupancy 0.3 <= existing 0.700001
Skipped atom 2402, because occupancy 0.3 <= existing 0.700001
Skipped atom 2820, because occupancy 0.4 <= existing 0.600001
Skipped atom 2822, because occupancy 0.4 <= existing 0.600001
Skipped atom 2824, because occupancy 0.4 <= existing 0.600001
partial PDB gets fragment 0 through 9 extending end
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
GLU    0   16
MET    1   12
VAL    2    3
LYS    3   28
ASN    4    4
TYR    5    3
LYS    7   26
GLU    8   10
VAL    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1htrB.230.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1huw.221.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1huw.221.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1huw.221.4.a2m \
	-target T0124 -template 1huw \
	-out T0124-1huw.221.4 -outdir und
Skipped atom 238, because occupancy 0.5 <= existing 0.500001
Skipped atom 240, because occupancy 0.5 <= existing 0.500001
Skipped atom 242, because occupancy 0.5 <= existing 0.500001
Skipped atom 244, because occupancy 0.5 <= existing 0.500001
Skipped atom 246, because occupancy 0.5 <= existing 0.500001
Skipped atom 331, because occupancy 0.5 <= existing 0.500001
Skipped atom 333, because occupancy 0.5 <= existing 0.500001
Skipped atom 335, because occupancy 0.5 <= existing 0.500001
Skipped atom 337, because occupancy 0.5 <= existing 0.500001
Skipped atom 339, because occupancy 0.5 <= existing 0.500001
Skipped atom 962, because occupancy 0.5 <= existing 0.500001
Skipped atom 964, because occupancy 0.5 <= existing 0.500001
Skipped atom 966, because occupancy 0.5 <= existing 0.500001
Skipped atom 968, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 3 through 12 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   29
THR    3    2
LEU    4    3
THR    5    2
VAL    6    1
GLU    7   15
VAL    8    1
GLN    9   12
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1huw.221.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ixh.121.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ixh.121.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ixh.121.5.a2m \
	-target T0124 -template 1ixh \
	-out T0124-1ixh.121.5 -outdir und
Skipped atom 9, because occupancy 0.35 <= existing 0.650001
Skipped atom 11, because occupancy 0.35 <= existing 0.650001
Skipped atom 2419, because occupancy 0.5 <= existing 0.500001
Skipped atom 2421, because occupancy 0.5 <= existing 0.500001
Skipped atom 3487, because occupancy 0.28 <= existing 0.720001
Skipped atom 3662, because occupancy 0.31 <= existing 0.690001
Skipped atom 3664, because occupancy 0.31 <= existing 0.690001
Skipped atom 3666, because occupancy 0.31 <= existing 0.690001
partial PDB gets fragment 92 through 101 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    3
LYS    3   24
GLU    4   14
SER    5    3
SER    6    3
GLU    7   12
SER    8    3
ASN    9    4
ILE   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ixh.121.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ixh.122.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ixh.122.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ixh.122.4.a2m \
	-target T0124 -template 1ixh \
	-out T0124-1ixh.122.4 -outdir und
Skipped atom 9, because occupancy 0.35 <= existing 0.650001
Skipped atom 11, because occupancy 0.35 <= existing 0.650001
Skipped atom 2419, because occupancy 0.5 <= existing 0.500001
Skipped atom 2421, because occupancy 0.5 <= existing 0.500001
Skipped atom 3487, because occupancy 0.28 <= existing 0.720001
Skipped atom 3662, because occupancy 0.31 <= existing 0.690001
Skipped atom 3664, because occupancy 0.31 <= existing 0.690001
Skipped atom 3666, because occupancy 0.31 <= existing 0.690001
partial PDB gets fragment 91 through 100 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   27
GLU    3   13
SER    4    3
SER    5    2
GLU    6   12
SER    7    3
ASN    8    4
ILE    9    3
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.24754
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ixh.122.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1kapP.139.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1kapP.139.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1kapP.139.4.a2m \
	-target T0124 -template 1kapP \
	-out T0124-1kapP.139.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1kapP-orig.a2m
Writing a2m file: tmp/1kapP-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7133


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7133/tmp -alignfile tmp/1kapP-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1kapP-orig.a2m (1 sequences, 479 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7133/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7133/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7133/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7133/tmp.a2m (1 sequences, 479 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7133/tmp.mod tmp/1kapP-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7133 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1kapP-align.mod
tmp/1kapP-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7133/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1kapP-orig.a2m tmp/1kapP-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1kapP-align.mod
Running w0.5 tmp/1kapP-orig.a2m tmp/1kapP-align.mod
Running align2model tmp/1kapP-align -i tmp/1kapP-align.mod -db tmp/1kapP-orig.a2m -db tmp/1kapP-pdb.a2m
partial PDB gets fragment 15 through 24 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   30
LEU    4    4
ASP    5    5
ARG    6   19
ILE    7    5
GLN    8   13
MET   10    6
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1kapP.139.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1kveB.57.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1kveB.57.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1kveB.57.5.a2m \
	-target T0124 -template 1kveB \
	-out T0124-1kveB.57.5 -outdir und
partial PDB gets fragment 59 through 69 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    3
GLU    3   12
PRO    4    2
VAL    5    2
TYR    6    2
PRO    7    2
ARG    8   30
LEU   10    3
ASP   11    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3   11     11.4643
Cluster     1 =   3  11
2 clashing residues after turn 
Residue clashes:
3-11
cluster 1 has 2 members and 2.000e+00 combinations:
 11  3 
Energy     15.0202
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search
10.000000 < 15.020214: keeping 
Solved cluster 1: residual clashing 14.26
Still clashes at these sidechain pairs:
Residual clashes =   10.18758
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1kveB.57.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1kveB.58.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1kveB.58.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1kveB.58.5.a2m \
	-target T0124 -template 1kveB \
	-out T0124-1kveB.58.5 -outdir und
partial PDB gets fragment 58 through 68 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   13
PRO    3    2
VAL    4    1
TYR    5    2
PRO    6    2
ARG    7   26
LEU    9    3
SER   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1kveB.58.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1kveB.60.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1kveB.60.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1kveB.60.2.a2m \
	-target T0124 -template 1kveB \
	-out T0124-1kveB.60.2 -outdir und
partial PDB gets fragment 58 through 67 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
VAL    2    1
TYR    3    3
PRO    4    2
ARG    5   26
LEU    7    3
ASP    8    5
SER    9    3
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   10     21.7249
Cluster     1 =   8  10
2 clashing residues after turn 
Residue clashes:
8-10
cluster 1 has 2 members and 6.000e+00 combinations:
 8  10 
Energy     21.7249
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 6.000e+00 - Sending to search
0.000000 < 21.724892: keeping 
Solved cluster 1: residual clashing  0.29
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1kveB.60.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lid.81.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lid.81.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lid.81.5.a2m \
	-target T0124 -template 1lid \
	-out T0124-1lid.81.5 -outdir und
partial PDB gets fragment 65 through 74 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    2    4
HIS    3    3
LEU    4    3
GLU    6   14
TYR    8    2
HIS    9    4
ASP   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    3     15.6233
Cluster     1 =   2   3
2 clashing residues after turn 
Residue clashes:
2-3
cluster 1 has 2 members and 0.000e+00 combinations:
 2  3 
Energy     15.6233
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
15.623260 < 15.623260: keeping 
10.000000 < 15.623260: keeping 
0.000000 < 11.300347: keeping 
Solved cluster 1: residual clashing  1.85
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lid.81.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lid.82.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lid.82.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lid.82.3.a2m \
	-target T0124 -template 1lid \
	-out T0124-1lid.82.3 -outdir und
partial PDB gets fragment 64 through 73 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    4
HIS    2    3
LEU    3    3
GLU    6   14
TYR    7    3
HIS    8    4
ASP    9    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lid.82.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lid.83.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lid.83.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lid.83.3.a2m \
	-target T0124 -template 1lid \
	-out T0124-1lid.83.3 -outdir und
partial PDB gets fragment 63 through 72 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
LEU    2    3
GLU    4   14
GLU    5   13
TYR    6    3
HIS    7    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lid.83.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lid.84.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lid.84.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lid.84.3.a2m \
	-target T0124 -template 1lid \
	-out T0124-1lid.84.3 -outdir und
partial PDB gets fragment 62 through 71 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    3   14
GLU    4   12
TYR    5    3
HIS    6    3
ASP    7    5
ILE    9    4
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lid.84.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lid.85.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lid.85.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lid.85.4.a2m \
	-target T0124 -template 1lid \
	-out T0124-1lid.85.4 -outdir und
partial PDB gets fragment 61 through 70 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   13
GLU    3   14
TYR    4    3
HIS    5    3
ASP    6    4
ILE    8    4
ARG    9   29
ARG   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   20.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lid.85.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lldA.119.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lldA.119.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lldA.119.2.a2m \
	-target T0124 -template 1lldA \
	-out T0124-1lldA.119.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1lldA-orig.a2m
Writing a2m file: tmp/1lldA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22415


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22415/tmp -alignfile tmp/1lldA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1lldA-orig.a2m (1 sequences, 319 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22415/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22415/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22415/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22415/tmp.a2m (1 sequences, 319 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22415/tmp.mod tmp/1lldA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22415 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1lldA-align.mod
tmp/1lldA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22415/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1lldA-orig.a2m tmp/1lldA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1lldA-align.mod
Running w0.5 tmp/1lldA-orig.a2m tmp/1lldA-align.mod
Running align2model tmp/1lldA-align -i tmp/1lldA-align.mod -db tmp/1lldA-orig.a2m -db tmp/1lldA-pdb.a2m
partial PDB gets fragment 49 through 59 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   31
LEU    4    3
LYS    5   31
GLU    6   11
SER    7    2
GLU    9   13
SER   10    3
ASN   11    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lldA.119.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lldA.120.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lldA.120.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lldA.120.3.a2m \
	-target T0124 -template 1lldA \
	-out T0124-1lldA.120.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1lldA-orig.a2m
Writing a2m file: tmp/1lldA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2390


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2390/tmp -alignfile tmp/1lldA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1lldA-orig.a2m (1 sequences, 319 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2390/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2390/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2390/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2390/tmp.a2m (1 sequences, 319 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2390/tmp.mod tmp/1lldA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2390 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1lldA-align.mod
tmp/1lldA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2390/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1lldA-orig.a2m tmp/1lldA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1lldA-align.mod
Running w0.5 tmp/1lldA-orig.a2m tmp/1lldA-align.mod
Running align2model tmp/1lldA-align -i tmp/1lldA-align.mod -db tmp/1lldA-orig.a2m -db tmp/1lldA-pdb.a2m
partial PDB gets fragment 48 through 58 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   20
LEU    3    3
LYS    4   19
GLU    5   15
SER    6    2
SER    7    2
GLU    8   12
ASN   10    5
ILE   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.58508
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lldA.120.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lldA.121.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lldA.121.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lldA.121.2.a2m \
	-target T0124 -template 1lldA \
	-out T0124-1lldA.121.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1lldA-orig.a2m
Writing a2m file: tmp/1lldA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5486


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5486/tmp -alignfile tmp/1lldA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1lldA-orig.a2m (1 sequences, 319 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5486/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5486/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5486/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5486/tmp.a2m (1 sequences, 319 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5486/tmp.mod tmp/1lldA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5486 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1lldA-align.mod
tmp/1lldA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5486/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1lldA-orig.a2m tmp/1lldA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1lldA-align.mod
Running w0.5 tmp/1lldA-orig.a2m tmp/1lldA-align.mod
Running align2model tmp/1lldA-align -i tmp/1lldA-align.mod -db tmp/1lldA-orig.a2m -db tmp/1lldA-pdb.a2m
partial PDB gets fragment 47 through 57 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    2
LYS    3   27
GLU    4   15
SER    5    2
SER    6    3
GLU    7   15
SER    8    2
ASN    9    5
ILE   10    3
LYS   11   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.36491
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lldA.121.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lldA.123.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lldA.123.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lldA.123.1.a2m \
	-target T0124 -template 1lldA \
	-out T0124-1lldA.123.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1lldA-orig.a2m
Writing a2m file: tmp/1lldA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20733


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20733/tmp -alignfile tmp/1lldA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1lldA-orig.a2m (1 sequences, 319 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20733/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20733/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20733/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20733/tmp.a2m (1 sequences, 319 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20733/tmp.mod tmp/1lldA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20733 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1lldA-align.mod
tmp/1lldA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20733/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1lldA-orig.a2m tmp/1lldA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1lldA-align.mod
Running w0.5 tmp/1lldA-orig.a2m tmp/1lldA-align.mod
Running align2model tmp/1lldA-align -i tmp/1lldA-align.mod -db tmp/1lldA-orig.a2m -db tmp/1lldA-pdb.a2m
partial PDB gets fragment 47 through 56 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
GLU    2   11
GLU    5   12
SER    6    3
ASN    7    5
ILE    8    2
LYS    9   27
ASP   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lldA.123.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lopA.61.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lopA.61.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lopA.61.2.a2m \
	-target T0124 -template 1lopA \
	-out T0124-1lopA.61.2 -outdir und
partial PDB gets fragment 96 through 105 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
TYR    2    2
PRO    3    2
ARG    4   26
LEU    6    2
ASP    7    5
SER    8    2
GLN    9   13
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lopA.61.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lopA.62.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lopA.62.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lopA.62.4.a2m \
	-target T0124 -template 1lopA \
	-out T0124-1lopA.62.4 -outdir und
partial PDB gets fragment 95 through 104 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
PRO    2    2
ARG    3   24
LEU    5    3
ASP    6    4
SER    7    2
GLN    8   14
VAL    9    1
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lopA.62.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lopA.63.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lopA.63.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lopA.63.5.a2m \
	-target T0124 -template 1lopA \
	-out T0124-1lopA.63.5 -outdir und
partial PDB gets fragment 94 through 103 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
ARG    2   27
LEU    4    3
ASP    5    8
SER    6    2
GLN    7   12
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   10     11.7136
Cluster     1 =   8  10
2 clashing residues after turn 
Residue clashes:
8-10
cluster 1 has 2 members and 0.000e+00 combinations:
 10  8 
Energy     11.7794
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
0.000000 < 11.779369: keeping 
Solved cluster 1: residual clashing  0.73
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lopA.63.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lopA.65.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lopA.65.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lopA.65.3.a2m \
	-target T0124 -template 1lopA \
	-out T0124-1lopA.65.3 -outdir und
partial PDB gets fragment 92 through 101 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    3
ASP    3    5
SER    4    2
VAL    6    2
VAL    7    3
GLU    8   13
LEU    9    3
LYS   10   21
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lopA.65.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1louA.159.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1louA.159.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1louA.159.3.a2m \
	-target T0124 -template 1louA \
	-out T0124-1louA.159.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1louA-orig.a2m
Writing a2m file: tmp/1louA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2389


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2389/tmp -alignfile tmp/1louA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1louA-orig.a2m (1 sequences, 101 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2389/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2389/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2389/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2389/tmp.a2m (1 sequences, 101 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2389/tmp.mod tmp/1louA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2389 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1louA-align.mod
tmp/1louA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2389/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1louA-orig.a2m tmp/1louA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1louA-align.mod
Running w0.5 tmp/1louA-orig.a2m tmp/1louA-align.mod
Running align2model tmp/1louA-align -i tmp/1louA-align.mod -db tmp/1louA-orig.a2m -db tmp/1louA-pdb.a2m
partial PDB gets fragment 13 through 22 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
ARG    2   30
LEU    3    3
LYS    4   24
LYS    5   26
GLU    6   12
ILE    7    3
ASN    8    4
ASN    9    4
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1louA.159.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lst.100.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lst.100.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lst.100.0.a2m \
	-target T0124 -template 1lst \
	-out T0124-1lst.100.0 -outdir und
partial PDB gets fragment 96 through 105 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    2    1
GLU    3   13
GLN    4   13
THR    5    1
LYS    7   25
ILE    8    3
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lst.100.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lst.100.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lst.100.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lst.100.2.a2m \
	-target T0124 -template 1lst \
	-out T0124-1lst.100.2 -outdir und
partial PDB gets fragment 94 through 104 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
THR    2    2
GLU    3   15
GLN    4   15
THR    5    1
LYS    7   28
THR    9    2
GLU   10   12
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lst.100.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lst.101.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lst.101.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lst.101.2.a2m \
	-target T0124 -template 1lst \
	-out T0124-1lst.101.2 -outdir und
partial PDB gets fragment 93 through 103 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
THR    1    3
GLU    2   14
GLN    3   10
THR    4    3
LYS    6   25
ILE    7    4
THR    8    1
GLU    9   13
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    8     11.7295
Cluster     1 =   4   8
2 clashing residues after turn 
Residue clashes:
4-8
cluster 1 has 2 members and 3.000e+00 combinations:
 8  4 
Energy     16.1154
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 3.000e+00 - Sending to search
Solved cluster 1: residual clashing 16.12
Still clashes at these sidechain pairs:
ires=    4 irot=    4 jres=    8 jrot=    4      11.7295
Residual clashes =   11.72950
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lst.101.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lst.102.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lst.102.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lst.102.4.a2m \
	-target T0124 -template 1lst \
	-out T0124-1lst.102.4 -outdir und
partial PDB gets fragment 92 through 102 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
GLN    2   14
THR    3    3
LYS    5   31
ILE    6    4
THR    7    1
GLU    8   14
LEU    9    3
ARG   11   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lst.102.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lst.104.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lst.104.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lst.104.2.a2m \
	-target T0124 -template 1lst \
	-out T0124-1lst.104.2 -outdir und
partial PDB gets fragment 92 through 101 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    3
LYS    3   26
ILE    4    4
THR    5    3
GLU    6   15
LEU    7    3
ARG    9   30
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 4 rotamers of residue I 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   11     12.8235
Cluster     1 =   5  11
2 clashing residues after turn 
Residue clashes:
5-11
cluster 1 has 2 members and 4.800e+01 combinations:
 5  11 
Energy     26.3970
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 4.800e+01 - Sending to search
5.648117 < 26.397007: keeping 
0.000000 < 19.715864: keeping 
3.051773 < 14.719385: keeping 
0.000000 < 10.568267: keeping 
0.000000 < 8.010771: keeping 
Solved cluster 1: residual clashing  7.35
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lst.104.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lst.105.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lst.105.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lst.105.3.a2m \
	-target T0124 -template 1lst \
	-out T0124-1lst.105.3 -outdir und
partial PDB gets fragment 91 through 100 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   31
ILE    3    5
THR    4    3
GLU    5   11
LEU    6    3
ARG    8   26
GLU    9   14
LYS   10   28
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lst.105.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lst.106.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lst.106.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lst.106.4.a2m \
	-target T0124 -template 1lst \
	-out T0124-1lst.106.4 -outdir und
partial PDB gets fragment 90 through 99 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   20
ILE    2    5
THR    3    3
GLU    4   15
LEU    5    3
ARG    7   32
GLU    8   15
LYS    9   25
GLN   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lst.106.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1lst.99.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1lst.99.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1lst.99.0.a2m \
	-target T0124 -template 1lst \
	-out T0124-1lst.99.0 -outdir und
partial PDB gets fragment 97 through 106 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
THR    3    1
GLU    4   15
GLN    5   12
THR    6    2
LYS    8   25
ILE    9    3
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1lst.99.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mdl.45.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mdl.45.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mdl.45.2.a2m \
	-target T0124 -template 1mdl \
	-out T0124-1mdl.45.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mdl-orig.a2m
Writing a2m file: tmp/1mdl-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4530


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4530/tmp -alignfile tmp/1mdl-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mdl-orig.a2m (1 sequences, 359 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4530/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4530/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4530/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4530/tmp.a2m (1 sequences, 359 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4530/tmp.mod tmp/1mdl-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4530 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mdl-align.mod
tmp/1mdl-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4530/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mdl-orig.a2m tmp/1mdl-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mdl-align.mod
Running w0.5 tmp/1mdl-orig.a2m tmp/1mdl-align.mod
Running align2model tmp/1mdl-align -i tmp/1mdl-align.mod -db tmp/1mdl-orig.a2m -db tmp/1mdl-pdb.a2m
partial PDB gets fragment 333 through 342 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   30
ARG    2   29
GLU    3   12
GLU    4   15
LEU    5    2
LEU    6    3
GLN    7   15
LYS    8   30
TYR    9    2
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mdl.45.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mdl.46.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mdl.46.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mdl.46.1.a2m \
	-target T0124 -template 1mdl \
	-out T0124-1mdl.46.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mdl-orig.a2m
Writing a2m file: tmp/1mdl-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26902


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26902/tmp -alignfile tmp/1mdl-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mdl-orig.a2m (1 sequences, 359 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26902/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26902/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26902/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26902/tmp.a2m (1 sequences, 359 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26902/tmp.mod tmp/1mdl-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26902 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mdl-align.mod
tmp/1mdl-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26902/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mdl-orig.a2m tmp/1mdl-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mdl-align.mod
Running w0.5 tmp/1mdl-orig.a2m tmp/1mdl-align.mod
Running align2model tmp/1mdl-align -i tmp/1mdl-align.mod -db tmp/1mdl-orig.a2m -db tmp/1mdl-pdb.a2m
partial PDB gets fragment 332 through 345 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
16 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
GLU    2   14
GLU    3   14
LEU    4    3
LEU    5    3
GLN    6   11
LYS    7   23
TYR    8    3
SER    9    3
VAL   10    2
LEU   11    2
PHE   12    2
LEU   13    3
GLU   14   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue F 13 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     9   13     10.1161
Cluster     1 =   9  13
2 clashing residues after turn 
Residue clashes:
9-13
cluster 1 has 2 members and 4.000e+00 combinations:
 13  9 
Energy    150.5712
Searching cluster 9
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
0.000000 < 150.571243: keeping 
Solved cluster 1: residual clashing 141.88
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mdl.46.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mdl.47.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mdl.47.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mdl.47.2.a2m \
	-target T0124 -template 1mdl \
	-out T0124-1mdl.47.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mdl-orig.a2m
Writing a2m file: tmp/1mdl-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5676


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5676/tmp -alignfile tmp/1mdl-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mdl-orig.a2m (1 sequences, 359 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5676/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5676/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5676/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5676/tmp.a2m (1 sequences, 359 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5676/tmp.mod tmp/1mdl-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5676 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mdl-align.mod
tmp/1mdl-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5676/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mdl-orig.a2m tmp/1mdl-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mdl-align.mod
Running w0.5 tmp/1mdl-orig.a2m tmp/1mdl-align.mod
Running align2model tmp/1mdl-align -i tmp/1mdl-align.mod -db tmp/1mdl-orig.a2m -db tmp/1mdl-pdb.a2m
partial PDB gets fragment 331 through 340 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1    8
GLU    2    9
LEU    3    3
LEU    4    3
GLN    5   12
LYS    6   30
TYR    7    3
SER    8    3
VAL    9    3
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mdl.47.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mdl.47.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mdl.47.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mdl.47.3.a2m \
	-target T0124 -template 1mdl \
	-out T0124-1mdl.47.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mdl-orig.a2m
Writing a2m file: tmp/1mdl-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30471


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30471/tmp -alignfile tmp/1mdl-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mdl-orig.a2m (1 sequences, 359 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30471/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30471/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30471/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30471/tmp.a2m (1 sequences, 359 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30471/tmp.mod tmp/1mdl-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30471 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mdl-align.mod
tmp/1mdl-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30471/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mdl-orig.a2m tmp/1mdl-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mdl-align.mod
Running w0.5 tmp/1mdl-orig.a2m tmp/1mdl-align.mod
Running align2model tmp/1mdl-align -i tmp/1mdl-align.mod -db tmp/1mdl-orig.a2m -db tmp/1mdl-pdb.a2m
partial PDB gets fragment 337 through 346 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
GLU    2   11
LEU    4    3
GLN    5    8
LYS    6   24
TYR    7    2
SER    8    2
VAL    9    1
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue Y 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    8     28.3097
Cluster     1 =   4   8
2 clashing residues after turn 
Residue clashes:
4-8
cluster 1 has 2 members and 0.000e+00 combinations:
 4  8 
Energy     97.3102
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
40.970406 < 97.310226: keeping 
Solved cluster 1: residual clashing 87.00
Still clashes at these sidechain pairs:
ires=    4 irot=    1 jres=    8 jrot=    2      40.9704
Residual clashes =   43.26555
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mdl.47.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mdl.48.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mdl.48.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mdl.48.1.a2m \
	-target T0124 -template 1mdl \
	-out T0124-1mdl.48.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mdl-orig.a2m
Writing a2m file: tmp/1mdl-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31755


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31755/tmp -alignfile tmp/1mdl-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mdl-orig.a2m (1 sequences, 359 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31755/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31755/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31755/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31755/tmp.a2m (1 sequences, 359 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31755/tmp.mod tmp/1mdl-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31755 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mdl-align.mod
tmp/1mdl-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31755/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mdl-orig.a2m tmp/1mdl-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mdl-align.mod
Running w0.5 tmp/1mdl-orig.a2m tmp/1mdl-align.mod
Running align2model tmp/1mdl-align -i tmp/1mdl-align.mod -db tmp/1mdl-orig.a2m -db tmp/1mdl-pdb.a2m
partial PDB gets fragment 336 through 345 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
LEU    2    2
LEU    3    3
GLN    4   15
LYS    5   30
TYR    6    2
SER    7    2
VAL    8    2
LEU    9    3
PHE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   11     12.6725
Cluster     1 =   5  11
2 clashing residues after turn 
Residue clashes:
5-11
cluster 1 has 2 members and 3.000e+01 combinations:
 11  5 
Energy     12.6725
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 3.000e+01 - Sending to search
3.914792 < 12.672470: keeping 
0.000000 < 4.023250: keeping 
Solved cluster 1: residual clashing  0.11
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mdl.48.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mdl.50.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mdl.50.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mdl.50.1.a2m \
	-target T0124 -template 1mdl \
	-out T0124-1mdl.50.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mdl-orig.a2m
Writing a2m file: tmp/1mdl-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5875


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5875/tmp -alignfile tmp/1mdl-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mdl-orig.a2m (1 sequences, 359 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5875/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5875/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5875/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5875/tmp.a2m (1 sequences, 359 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5875/tmp.mod tmp/1mdl-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5875 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mdl-align.mod
tmp/1mdl-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5875/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mdl-orig.a2m tmp/1mdl-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mdl-align.mod
Running w0.5 tmp/1mdl-orig.a2m tmp/1mdl-align.mod
Running align2model tmp/1mdl-align -i tmp/1mdl-align.mod -db tmp/1mdl-orig.a2m -db tmp/1mdl-pdb.a2m
partial PDB gets fragment 334 through 343 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLN    2   12
LYS    3   30
TYR    4    3
SER    5    3
VAL    6    3
LEU    7    3
PHE    8    2
LEU    9    2
GLU   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mdl.50.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mdl.51.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mdl.51.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mdl.51.1.a2m \
	-target T0124 -template 1mdl \
	-out T0124-1mdl.51.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mdl-orig.a2m
Writing a2m file: tmp/1mdl-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5287


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5287/tmp -alignfile tmp/1mdl-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mdl-orig.a2m (1 sequences, 359 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5287/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5287/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5287/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5287/tmp.a2m (1 sequences, 359 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5287/tmp.mod tmp/1mdl-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5287 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mdl-align.mod
tmp/1mdl-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5287/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mdl-orig.a2m tmp/1mdl-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mdl-align.mod
Running w0.5 tmp/1mdl-orig.a2m tmp/1mdl-align.mod
Running align2model tmp/1mdl-align -i tmp/1mdl-align.mod -db tmp/1mdl-orig.a2m -db tmp/1mdl-pdb.a2m
partial PDB gets fragment 333 through 342 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
LYS    2   27
TYR    3    3
SER    4    3
VAL    5    3
LEU    6    3
PHE    7    3
LEU    8    3
GLU    9    9
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    3.45414
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mdl.51.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mrj.6.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mrj.6.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mrj.6.5.a2m \
	-target T0124 -template 1mrj \
	-out T0124-1mrj.6.5 -outdir und
Skipped atom 672, because occupancy 0.5 <= existing 0.500001
Skipped atom 674, because occupancy 0.5 <= existing 0.500001
Skipped atom 676, because occupancy 0.5 <= existing 0.500001
Skipped atom 678, because occupancy 0.5 <= existing 0.500001
Skipped atom 680, because occupancy 0.5 <= existing 0.500001
Skipped atom 682, because occupancy 0.5 <= existing 0.500001
Skipped atom 684, because occupancy 0.5 <= existing 0.500001
Skipped atom 686, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 236 through 246 extending start
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
LEU    2    2
PRO    3    2
GLU    4   12
PRO    5    2
GLN    6   14
THR    7    2
SER    9    2
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mrj.6.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mrj.8.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mrj.8.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mrj.8.2.a2m \
	-target T0124 -template 1mrj \
	-out T0124-1mrj.8.2 -outdir und
Skipped atom 672, because occupancy 0.5 <= existing 0.500001
Skipped atom 674, because occupancy 0.5 <= existing 0.500001
Skipped atom 676, because occupancy 0.5 <= existing 0.500001
Skipped atom 678, because occupancy 0.5 <= existing 0.500001
Skipped atom 680, because occupancy 0.5 <= existing 0.500001
Skipped atom 682, because occupancy 0.5 <= existing 0.500001
Skipped atom 684, because occupancy 0.5 <= existing 0.500001
Skipped atom 686, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 236 through 245 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
GLU    2   11
PRO    3    2
GLN    4   13
THR    5    2
SER    7    2
LEU    8    3
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mrj.8.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.31.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.31.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.31.0.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.31.0 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18935


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18935/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18935/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18935/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18935/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18935/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18935/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18935 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18935/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 523 through 532 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLU    2   12
LYS    3   26
GLU    4   15
LYS    6   29
LEU    8    3
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    9     12.5447
Cluster     1 =   4   9
2 clashing residues after turn 
Residue clashes:
4-9
cluster 1 has 2 members and 4.200e+01 combinations:
 9  4 
Energy     12.5447
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 4.200e+01 - Sending to search
0.000000 < 12.544727: keeping 
Solved cluster 1: residual clashing  0.21
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.31.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.32.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.32.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.32.0.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.32.0 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4222


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4222/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4222/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4222/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4222/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4222/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4222/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4222 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4222/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 522 through 531 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    2   26
GLU    3   12
LEU    4    3
LYS    5   30
GLU    6   12
LEU    7    2
ARG    9   29
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.32.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.32.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.32.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.32.4.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.32.4 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-19828


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-19828/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-19828/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-19828/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-19828/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19828/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-19828/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-19828 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19828/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 520 through 532 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    2   26
GLU    3   12
LEU    4    3
GLU    6   13
LEU    7    3
GLU    8   12
LYS   10   25
SER   12    2
LYS   13   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.32.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.34.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.34.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.34.0.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.34.0 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5200


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5200/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5200/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5200/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5200/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5200/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5200/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5200 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5200/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 520 through 532 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    2    3
LYS    3   26
GLU    4   12
LEU    5    3
GLU    6   12
ARG    7   32
LYS    8   19
SER   10    2
LYS   11   25
ARG   12   26
ARG   13   28
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7   12     10.1453
Cluster     1 =   7  12
2 clashing residues after turn 
Residue clashes:
7-12
cluster 1 has 2 members and 1.040e+02 combinations:
 7  12 
Energy     10.1471
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 1.040e+02 - Sending to search
0.000000 < 10.147138: keeping 
0.000000 < 1.316993: keeping 
Solved cluster 1: residual clashing  0.40
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.34.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.35.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.35.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.35.0.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.35.0 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4144


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4144/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4144/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4144/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4144/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4144/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4144/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4144 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4144/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 519 through 532 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
16 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   26
LEU    4    3
GLU    5   12
ARG    6   27
LYS    7   26
SER    9    2
LYS   10   19
ARG   11   22
ARG   12   27
GLU   14   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   13     33.9240
Cluster     1 =   8  13
2 clashing residues after turn 
Residue clashes:
8-13
cluster 1 has 2 members and 2.940e+02 combinations:
 13  8 
Energy     34.2626
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 2.940e+02 - Sending to search
0.000000 < 34.262608: keeping 
Solved cluster 1: residual clashing  0.55
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.35.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.36.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.36.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.36.0.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.36.0 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-24447


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-24447/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-24447/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-24447/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-24447/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24447/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-24447/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-24447 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24447/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 518 through 529 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
GLU    2   15
LEU    3    3
ARG    5   28
LYS    6   26
SER    8    3
LYS    9   30
ARG   10   21
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.36.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.37.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.37.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.37.1.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.37.1 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3627


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3627/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3627/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3627/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3627/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3627/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3627/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3627 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3627/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 517 through 526 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
LEU    2    3
GLU    3   15
ARG    4   27
LYS    5   26
SER    7    3
ARG    9   28
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    5     13.3309
Cluster     1 =   2   5
2 clashing residues after turn 
Residue clashes:
2-5
cluster 1 has 2 members and 2.200e+02 combinations:
 2  5 
Energy     13.3309
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 2.200e+02 - Sending to search
1.707910 < 13.330946: keeping 
0.000000 < 1.821702: keeping 
0.000000 < 1.283534: keeping 
Solved cluster 1: residual clashing  0.71
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.37.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.40.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.40.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.40.3.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.40.3 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4918


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4918/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4918/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4918/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4918/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4918/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4918/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4918 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4918/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 522 through 531 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
LYS    2   26
SER    4    3
LYS    5   30
ARG    6   21
GLU    9   13
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   10     11.5716
Cluster     1 =   5  10
2 clashing residues after turn 
Residue clashes:
5-10
cluster 1 has 2 members and 1.600e+01 combinations:
 5  10 
Energy     11.5716
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 1.600e+01 - Sending to search
2.805975 < 11.571586: keeping 
1.702442 < 3.300251: keeping 
0.000000 < 2.234422: keeping 
0.000000 < 0.901300: keeping 
Solved cluster 1: residual clashing  0.78
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.40.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.41.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.41.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.41.2.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.41.2 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31819


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31819/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31819/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31819/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31819/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31819/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31819/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31819 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31819/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 521 through 530 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
SER    3    3
ARG    5   28
ARG    6   32
GLU    7   12
GLU    8    7
LEU    9    2
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   11     12.5548
Cluster     1 =   6  11
2 clashing residues after turn 
Residue clashes:
6-11
cluster 1 has 2 members and 2.000e+01 combinations:
 11  6 
Energy     12.8309
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 2.000e+01 - Sending to search
0.000000 < 12.830939: keeping 
Solved cluster 1: residual clashing  1.68
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.41.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.42.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.42.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.42.2.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.42.2 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1679


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1679/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1679/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1679/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1679/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1679/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1679/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1679 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1679/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 520 through 530 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
SER    2    3
LYS    3   26
ARG    4   27
ARG    5   27
GLU    6   12
GLU    7   15
LEU    9    4
GLN   10   13
LYS   11   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7   12     10.1453
Cluster     1 =   7  12
2 clashing residues after turn 
Residue clashes:
7-12
cluster 1 has 2 members and 1.040e+02 combinations:
 7  12 
Energy     10.1471
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 1.040e+02 - Sending to search
0.000000 < 10.147138: keeping 
0.000000 < 1.316993: keeping 
Solved cluster 1: residual clashing  0.40
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.42.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.43.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.43.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.43.2.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.43.2 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4123


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4123/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4123/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4123/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4123/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4123/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4123/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4123 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4123/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 519 through 529 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
LYS    2   26
ARG    3   27
ARG    4   27
GLU    5   12
GLU    6   12
LEU    7    3
LEU    8    3
GLN    9   10
LYS   10   19
TYR   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.43.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.45.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.45.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.45.4.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.45.4 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1276


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1276/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1276/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1276/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1276/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1276/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1276/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1276 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1276/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 519 through 528 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   25
GLU    4   13
LEU    5    3
LEU    6    3
GLN    7   12
LYS    8   30
TYR    9    3
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.45.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.46.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.46.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.46.0.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.46.0 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5036


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5036/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5036/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5036/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5036/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5036/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5036/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5036 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5036/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 518 through 527 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
GLU    2   15
GLU    3   12
LEU    4    3
LEU    5    3
GLN    6   12
TYR    8    4
SER    9    2
VAL   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.53467
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.46.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.47.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.47.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.47.1.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.47.1 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30876


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30876/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30876/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30876/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30876/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30876/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30876/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30876 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30876/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 517 through 526 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
GLU    2   12
LEU    3    3
LEU    4    3
GLN    5   12
LYS    6   26
TYR    7    3
SER    8    3
VAL    9    2
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    5     10.9557
Cluster     1 =   2   5
2 clashing residues after turn 
Residue clashes:
2-5
cluster 1 has 2 members and 3.000e+01 combinations:
 5  2 
Energy     10.9557
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 3.000e+01 - Sending to search
10.000000 < 10.955660: keeping 
0.000000 < 10.597076: keeping 
Solved cluster 1: residual clashing  0.76
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.47.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.48.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.48.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.48.2.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.48.2 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6371


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6371/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6371/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6371/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6371/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6371/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6371/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6371 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6371/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 516 through 525 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
LEU    2    3
LEU    3    3
GLN    4   14
LYS    5   26
TYR    6    3
SER    7    3
VAL    8    2
LEU    9    3
PHE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    8.56592
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.48.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.49.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.49.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.49.3.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.49.3 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7122


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7122/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7122/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7122/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7122/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7122/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7122/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7122 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7122/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 515 through 524 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
LEU    2    3
GLN    3   13
LYS    4   24
TYR    5    4
SER    6    3
VAL    7    2
LEU    8    3
PHE    9    3
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.49.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.50.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.50.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.50.3.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.50.3 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5549


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5549/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5549/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5549/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5549/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5549/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5549/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5549 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5549/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 514 through 523 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLN    2   14
LYS    3   27
TYR    4    3
SER    5    3
VAL    6    3
LEU    7    3
PHE    8    3
LEU    9    3
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.41367
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.50.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroA.51.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroA.51.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroA.51.3.a2m \
	-target T0124 -template 1mroA \
	-out T0124-1mroA.51.3 -outdir und
Skipped atom 1072, because occupancy 0.5 <= existing 0.500001
Skipped atom 1074, because occupancy 0.5 <= existing 0.500001
Skipped atom 1076, because occupancy 0.5 <= existing 0.500001
Skipped atom 1078, because occupancy 0.5 <= existing 0.500001
Skipped atom 1325, because occupancy 0.2 <= existing 0.800001
Skipped atom 1327, because occupancy 0.2 <= existing 0.800001
Skipped atom 1329, because occupancy 0.2 <= existing 0.800001
Skipped atom 1702, because occupancy 0.33 <= existing 0.670001
Skipped atom 1704, because occupancy 0.33 <= existing 0.670001
Skipped atom 2023, because occupancy 0.33 <= existing 0.670001
Skipped atom 2025, because occupancy 0.33 <= existing 0.670001
Skipped atom 2027, because occupancy 0.33 <= existing 0.670001
Skipped atom 2029, because occupancy 0.33 <= existing 0.670001
Skipped atom 2318, because occupancy 0.2 <= existing 0.800001
Skipped atom 2320, because occupancy 0.2 <= existing 0.800001
Skipped atom 2330, because occupancy 0.33 <= existing 0.670001
Skipped atom 2337, because occupancy 0.33 <= existing 0.670001
Skipped atom 2339, because occupancy 0.33 <= existing 0.670001
Skipped atom 2341, because occupancy 0.33 <= existing 0.670001
Skipped atom 2883, because occupancy 0.33 <= existing 0.670001
Skipped atom 3555, because occupancy 0.2 <= existing 0.800001
Skipped atom 3557, because occupancy 0.2 <= existing 0.800001
Skipped atom 3639, because occupancy 0.5 <= existing 0.500001
Skipped atom 3641, because occupancy 0.5 <= existing 0.500001
Skipped atom 3643, because occupancy 0.5 <= existing 0.500001
Skipped atom 3645, because occupancy 0.5 <= existing 0.500001
Skipped atom 3845, because occupancy 0.33 <= existing 0.670001
Skipped atom 3847, because occupancy 0.33 <= existing 0.670001
Skipped atom 4103, because occupancy 0.2 <= existing 0.800001
Skipped atom 4105, because occupancy 0.2 <= existing 0.800001
Skipped atom 4107, because occupancy 0.2 <= existing 0.800001
Skipped atom 4244, because occupancy 0.5 <= existing 0.500001
Skipped atom 4246, because occupancy 0.5 <= existing 0.500001
Skipped atom 4248, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mroA-orig.a2m
Writing a2m file: tmp/1mroA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5566


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5566/tmp -alignfile tmp/1mroA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mroA-orig.a2m (1 sequences, 548 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5566/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5566/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5566/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5566/tmp.a2m (1 sequences, 548 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5566/tmp.mod tmp/1mroA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5566 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mroA-align.mod
tmp/1mroA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5566/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mroA-orig.a2m tmp/1mroA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mroA-align.mod
Running w0.5 tmp/1mroA-orig.a2m tmp/1mroA-align.mod
Running align2model tmp/1mroA-align -i tmp/1mroA-align.mod -db tmp/1mroA-orig.a2m -db tmp/1mroA-pdb.a2m
partial PDB gets fragment 513 through 522 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
LYS    2   27
TYR    3    3
SER    4    2
VAL    5    2
LEU    6    3
PHE    7    3
LEU    8    3
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.20546
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroA.51.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.10.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.10.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.10.4.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.10.4 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 232 through 242 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
THR    3    2
SER    5    3
LEU    6    3
GLU    8   12
LEU    9    3
GLN   11   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.10.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.134.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.134.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.134.4.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.134.4 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 92 through 102 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
LYS    2   24
LYS    3   23
LEU    4    5
GLU    5   13
LYS    7   26
LEU    9    3
ASP   10    4
ARG   11   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.134.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.135.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.135.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.135.2.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.135.2 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 91 through 103 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   17
LYS    2   30
LEU    3    3
GLU    4   15
LYS    6   26
ARG    7   32
LEU    8    3
ASP    9    4
ARG   10   27
ILE   11    3
GLN   12   12
VAL   13    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.135.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.136.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.136.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.136.1.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.136.1 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 96 through 105 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LEU    2    3
GLU    3   12
LYS    5   26
LEU    7    3
ASP    8    4
ARG    9   27
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.136.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.137.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.137.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.137.0.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.137.0 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 95 through 104 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    5
GLU    2   13
LYS    4   26
LEU    6    3
ASP    7    4
ARG    8   27
ILE    9    3
GLN   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.137.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.138.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.138.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.138.2.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.138.2 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 90 through 99 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1    9
LYS    3   30
ARG    4   26
LEU    5    2
ASP    6    7
ARG    7   25
ILE    8    5
GLN    9   12
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.138.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.139.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.139.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.139.1.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.139.1 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 93 through 102 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   23
ARG    3   29
LEU    4    3
ASP    5    4
ARG    6   27
ILE    7    2
GLN    8   12
VAL    9    1
MET   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.139.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.139.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.139.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.139.2.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.139.2 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 89 through 98 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   20
ARG    3   22
LEU    4    3
ASP    5    4
ARG    6   29
ILE    7    4
GLN    8   12
VAL    9    3
MET   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.50249
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.139.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.140.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.140.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.140.2.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.140.2 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 86 through 96 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   28
ARG    2   27
LEU    3    3
ASP    4    4
ARG    5   24
ILE    6    3
GLN    7   14
VAL    8    1
MET    9   10
MET   10   12
ARG   11   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.84242
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.140.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.140.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.140.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.140.3.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.140.3 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 92 through 101 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
ARG    2   26
LEU    3    2
ASP    4    7
ARG    5   25
ILE    6    5
GLN    7   12
VAL    8    1
MET    9   10
MET   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.140.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.141.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.141.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.141.1.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.141.1 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 85 through 95 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   29
LEU    2    3
ARG    4   32
ILE    5    3
GLN    6   13
VAL    7    2
MET    8   12
MET    9   10
ARG   10   29
SER   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    7     31.8138
turnclash      5   15    9    0     27.9419
Cluster     1 =   5   7   9
3 clashing residues after turn 
Residue clashes:
5-7
5-9
cluster 1 has 3 members and 1.092e+03 combinations:
 9  7  5 
Energy     35.8069
Searching cluster 5
Combinations for 3 members in cluster 1 OK: 1.092e+03 - Sending to search
0.000000 < 35.806881: keeping 
0.000000 < 4.042426: keeping 
Solved cluster 1: residual clashing  0.83
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.141.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.142.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.142.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.142.0.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.142.0 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 84 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ASP    2    6
ARG    3   30
ILE    4    2
GLN    5   14
VAL    6    2
MET    7   10
MET    8    6
ARG    9   32
SER   10    3
THR   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue I 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.142.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.143.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.143.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.143.1.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.143.1 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 83 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    6
ARG    2   31
ILE    3    5
GLN    4   14
VAL    5    1
MET    6   12
ARG    8   23
SER    9    2
THR   10    3
SER   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue V 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.60260
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.143.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.143.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.143.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.143.4.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.143.4 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 89 through 98 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
ARG    2   24
ILE    3    3
GLN    4   14
VAL    5    1
MET    6   10
MET    7   12
ARG    8   25
SER    9    2
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.143.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.144.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.144.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.144.3.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.144.3 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 88 through 97 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   32
ILE    2    3
GLN    3   13
VAL    4    2
MET    5   12
MET    6   10
ARG    7   29
SER    8    3
THR    9    1
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    4     28.5180
turnclash      2   28    6    0     28.2180
Cluster     1 =   2   4   6
3 clashing residues after turn 
Residue clashes:
2-4
2-6
cluster 1 has 3 members and 1.131e+03 combinations:
 6  4  2 
Energy     32.5110
Searching cluster 2
Combinations for 3 members in cluster 1 OK: 1.131e+03 - Sending to search
0.000000 < 32.511024: keeping 
0.000000 < 4.003837: keeping 
Solved cluster 1: residual clashing  0.79
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.144.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.145.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.145.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.145.1.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.145.1 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 87 through 97 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
GLN    2   14
VAL    3    2
MET    4   10
MET    5    6
ARG    6   32
SER    7    3
THR    8    2
SER    9    3
ASP   10    5
LYS   11   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue I 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.145.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mroC.146.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mroC.146.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mroC.146.3.a2m \
	-target T0124 -template 1mroC \
	-out T0124-1mroC.146.3 -outdir und
Skipped atom 8056, because occupancy 0.5 <= existing 0.500001
Skipped atom 8058, because occupancy 0.5 <= existing 0.500001
Skipped atom 8064, because occupancy 0.5 <= existing 0.500001
Skipped atom 8066, because occupancy 0.5 <= existing 0.500001
Skipped atom 8068, because occupancy 0.5 <= existing 0.500001
Skipped atom 8891, because occupancy 0.33 <= existing 0.670001
Skipped atom 8893, because occupancy 0.33 <= existing 0.670001
Skipped atom 8895, because occupancy 0.33 <= existing 0.670001
Skipped atom 9575, because occupancy 0.5 <= existing 0.500001
Skipped atom 9577, because occupancy 0.5 <= existing 0.500001
Skipped atom 9579, because occupancy 0.5 <= existing 0.500001
Skipped atom 9581, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 86 through 95 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
VAL    2    1
MET    3   12
ARG    5   23
SER    6    2
THR    7    3
SER    8    3
ASP    9    5
LYS   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue V 3 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    9.60260
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mroC.146.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msc.74.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msc.74.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msc.74.4.a2m \
	-target T0124 -template 1msc \
	-out T0124-1msc.74.4 -outdir und
partial PDB gets fragment 86 through 95 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
GLU    2   13
ARG    3   27
GLU    5   13
MET    6   12
GLU    7   14
LEU    8    3
ILE    9    2
HIS   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msc.74.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msc.75.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msc.75.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msc.75.3.a2m \
	-target T0124 -template 1msc \
	-out T0124-1msc.75.3 -outdir und
partial PDB gets fragment 85 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
ARG    2   28
LEU    3    3
MET    5   10
GLU    6   12
LEU    7    3
ILE    8    4
HIS    9    4
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msc.75.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msc.75.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msc.75.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msc.75.4.a2m \
	-target T0124 -template 1msc \
	-out T0124-1msc.75.4 -outdir und
partial PDB gets fragment 83 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
ARG    2   32
GLU    4   11
ILE    8    3
HIS    9    4
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msc.75.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msc.77.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msc.77.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msc.77.2.a2m \
	-target T0124 -template 1msc \
	-out T0124-1msc.77.2 -outdir und
partial PDB gets fragment 83 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
GLU    2   15
MET    3   11
GLU    4   12
LEU    5    3
ILE    6    3
HIS    7    3
LEU    8    3
GLU   10   14
GLU   11   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msc.77.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msc.78.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msc.78.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msc.78.3.a2m \
	-target T0124 -template 1msc \
	-out T0124-1msc.78.3 -outdir und
partial PDB gets fragment 82 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
MET    2    8
GLU    3   15
ILE    5    2
HIS    6    3
LEU    7    3
GLU    9   12
GLU   10   15
TYR   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msc.78.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msc.80.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msc.80.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msc.80.3.a2m \
	-target T0124 -template 1msc \
	-out T0124-1msc.80.3 -outdir und
partial PDB gets fragment 82 through 91 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
LEU    2    2
ILE    3    4
HIS    4    3
LEU    5    3
GLU    8   12
TYR    9    3
HIS   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     9   11     56.6168
Cluster     1 =   9  11
2 clashing residues after turn 
Residue clashes:
9-11
cluster 1 has 2 members and 4.800e+01 combinations:
 11  9 
Energy     56.6168
Searching cluster 9
Combinations for 2 members in cluster 1 OK: 4.800e+01 - Sending to search
48.830044 < 56.616810: keeping 
43.485043 < 49.324318: keeping 
0.000000 < 44.017029: keeping 
Solved cluster 1: residual clashing  1.12
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msc.80.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msk.157.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msk.157.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msk.157.2.a2m \
	-target T0124 -template 1msk \
	-out T0124-1msk.157.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1msk-orig.a2m
Writing a2m file: tmp/1msk-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32603


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32603/tmp -alignfile tmp/1msk-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1msk-orig.a2m (1 sequences, 332 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32603/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32603/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32603/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32603/tmp.a2m (1 sequences, 332 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32603/tmp.mod tmp/1msk-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32603 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1msk-align.mod
tmp/1msk-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32603/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1msk-orig.a2m tmp/1msk-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1msk-align.mod
Running w0.5 tmp/1msk-orig.a2m tmp/1msk-align.mod
Running align2model tmp/1msk-align -i tmp/1msk-align.mod -db tmp/1msk-orig.a2m -db tmp/1msk-pdb.a2m
partial PDB gets fragment 68 through 77 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    2   12
GLU    3   12
ARG    4   27
LEU    5    3
LYS    6   26
LYS    7   24
GLU    8   12
ILE    9    3
ASN   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msk.157.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msk.158.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msk.158.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msk.158.1.a2m \
	-target T0124 -template 1msk \
	-out T0124-1msk.158.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1msk-orig.a2m
Writing a2m file: tmp/1msk-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12798


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12798/tmp -alignfile tmp/1msk-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1msk-orig.a2m (1 sequences, 332 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12798/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12798/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12798/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12798/tmp.a2m (1 sequences, 332 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12798/tmp.mod tmp/1msk-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12798 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1msk-align.mod
tmp/1msk-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12798/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1msk-orig.a2m tmp/1msk-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1msk-align.mod
Running w0.5 tmp/1msk-orig.a2m tmp/1msk-align.mod
Running align2model tmp/1msk-align -i tmp/1msk-align.mod -db tmp/1msk-orig.a2m -db tmp/1msk-pdb.a2m
partial PDB gets fragment 67 through 76 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLU    2   12
ARG    3   26
LEU    4    3
LYS    5   26
LYS    6   24
GLU    7   12
ILE    8    2
ASN    9    4
ASN   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msk.158.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msk.159.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msk.159.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msk.159.0.a2m \
	-target T0124 -template 1msk \
	-out T0124-1msk.159.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1msk-orig.a2m
Writing a2m file: tmp/1msk-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2311


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2311/tmp -alignfile tmp/1msk-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1msk-orig.a2m (1 sequences, 332 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2311/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2311/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2311/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2311/tmp.a2m (1 sequences, 332 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2311/tmp.mod tmp/1msk-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2311 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1msk-align.mod
tmp/1msk-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2311/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1msk-orig.a2m tmp/1msk-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1msk-align.mod
Running w0.5 tmp/1msk-orig.a2m tmp/1msk-align.mod
Running align2model tmp/1msk-align -i tmp/1msk-align.mod -db tmp/1msk-orig.a2m -db tmp/1msk-pdb.a2m
partial PDB gets fragment 66 through 75 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   29
LEU    3    2
LYS    4   25
LYS    5   26
ILE    7    2
ASN    8    4
ASN    9    4
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msk.159.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msk.160.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msk.160.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msk.160.0.a2m \
	-target T0124 -template 1msk \
	-out T0124-1msk.160.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1msk-orig.a2m
Writing a2m file: tmp/1msk-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23696


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23696/tmp -alignfile tmp/1msk-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1msk-orig.a2m (1 sequences, 332 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23696/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23696/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23696/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23696/tmp.a2m (1 sequences, 332 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23696/tmp.mod tmp/1msk-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23696 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1msk-align.mod
tmp/1msk-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23696/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1msk-orig.a2m tmp/1msk-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1msk-align.mod
Running w0.5 tmp/1msk-orig.a2m tmp/1msk-align.mod
Running align2model tmp/1msk-align -i tmp/1msk-align.mod -db tmp/1msk-orig.a2m -db tmp/1msk-pdb.a2m
partial PDB gets fragment 65 through 74 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
LEU    2    2
LYS    3   23
LYS    4   22
GLU    5   12
ILE    6    3
ASN    7    4
ASN    8    4
SER    9    3
HIS   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 12 rotamers of residue E 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msk.160.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msk.161.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msk.161.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msk.161.0.a2m \
	-target T0124 -template 1msk \
	-out T0124-1msk.161.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1msk-orig.a2m
Writing a2m file: tmp/1msk-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13308


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13308/tmp -alignfile tmp/1msk-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1msk-orig.a2m (1 sequences, 332 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13308/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13308/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13308/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13308/tmp.a2m (1 sequences, 332 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13308/tmp.mod tmp/1msk-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13308 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1msk-align.mod
tmp/1msk-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13308/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1msk-orig.a2m tmp/1msk-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1msk-align.mod
Running w0.5 tmp/1msk-orig.a2m tmp/1msk-align.mod
Running align2model tmp/1msk-align -i tmp/1msk-align.mod -db tmp/1msk-orig.a2m -db tmp/1msk-pdb.a2m
partial PDB gets fragment 64 through 73 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
LYS    2   27
LYS    3   29
GLU    4   12
ILE    5    3
ASN    6    4
ASN    7    4
SER    8    3
HIS    9    3
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 4 rotamers of residue N 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    6     13.7963
Cluster     1 =   3   6
2 clashing residues after turn 
Residue clashes:
3-6
cluster 1 has 2 members and 6.600e+01 combinations:
 6  3 
Energy     13.7963
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 6.600e+01 - Sending to search
3.062041 < 13.796349: keeping 
0.000000 < 3.459622: keeping 
Solved cluster 1: residual clashing  1.32
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msk.161.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msk.162.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msk.162.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msk.162.0.a2m \
	-target T0124 -template 1msk \
	-out T0124-1msk.162.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1msk-orig.a2m
Writing a2m file: tmp/1msk-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1610


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1610/tmp -alignfile tmp/1msk-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1msk-orig.a2m (1 sequences, 332 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1610/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1610/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1610/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1610/tmp.a2m (1 sequences, 332 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1610/tmp.mod tmp/1msk-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1610 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1msk-align.mod
tmp/1msk-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1610/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1msk-orig.a2m tmp/1msk-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1msk-align.mod
Running w0.5 tmp/1msk-orig.a2m tmp/1msk-align.mod
Running align2model tmp/1msk-align -i tmp/1msk-align.mod -db tmp/1msk-orig.a2m -db tmp/1msk-pdb.a2m
partial PDB gets fragment 63 through 72 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   29
LYS    2   21
GLU    3   13
ILE    4    3
ASN    5    6
ASN    6    5
SER    7    3
HIS    8    4
ILE    9    3
GLN   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue S 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msk.162.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msk.162.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msk.162.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msk.162.5.a2m \
	-target T0124 -template 1msk \
	-out T0124-1msk.162.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1msk-orig.a2m
Writing a2m file: tmp/1msk-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29094


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29094/tmp -alignfile tmp/1msk-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1msk-orig.a2m (1 sequences, 332 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29094/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29094/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29094/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29094/tmp.a2m (1 sequences, 332 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29094/tmp.mod tmp/1msk-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29094 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1msk-align.mod
tmp/1msk-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29094/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1msk-orig.a2m tmp/1msk-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1msk-align.mod
Running w0.5 tmp/1msk-orig.a2m tmp/1msk-align.mod
Running align2model tmp/1msk-align -i tmp/1msk-align.mod -db tmp/1msk-orig.a2m -db tmp/1msk-pdb.a2m
partial PDB gets fragment 59 through 68 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
LYS    2   24
GLU    3   16
ASN    5    4
ASN    6    4
SER    7    3
HIS    8    3
ILE    9    2
GLN   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msk.162.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msk.163.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msk.163.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msk.163.1.a2m \
	-target T0124 -template 1msk \
	-out T0124-1msk.163.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1msk-orig.a2m
Writing a2m file: tmp/1msk-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3487


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3487/tmp -alignfile tmp/1msk-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1msk-orig.a2m (1 sequences, 332 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3487/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3487/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3487/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3487/tmp.a2m (1 sequences, 332 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3487/tmp.mod tmp/1msk-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3487 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1msk-align.mod
tmp/1msk-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3487/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1msk-orig.a2m tmp/1msk-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1msk-align.mod
Running w0.5 tmp/1msk-orig.a2m tmp/1msk-align.mod
Running align2model tmp/1msk-align -i tmp/1msk-align.mod -db tmp/1msk-orig.a2m -db tmp/1msk-pdb.a2m
partial PDB gets fragment 62 through 71 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
GLU    2   15
ILE    3    2
ASN    4    5
ASN    5    5
SER    6    3
HIS    7    3
ILE    8    3
GLN    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue I 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue I 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msk.163.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msk.164.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msk.164.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msk.164.4.a2m \
	-target T0124 -template 1msk \
	-out T0124-1msk.164.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1msk-orig.a2m
Writing a2m file: tmp/1msk-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25085


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25085/tmp -alignfile tmp/1msk-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1msk-orig.a2m (1 sequences, 332 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25085/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25085/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25085/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25085/tmp.a2m (1 sequences, 332 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25085/tmp.mod tmp/1msk-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25085 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1msk-align.mod
tmp/1msk-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25085/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1msk-orig.a2m tmp/1msk-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1msk-align.mod
Running w0.5 tmp/1msk-orig.a2m tmp/1msk-align.mod
Running align2model tmp/1msk-align -i tmp/1msk-align.mod -db tmp/1msk-orig.a2m -db tmp/1msk-pdb.a2m
partial PDB gets fragment 61 through 70 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   16
ASN    3    4
ASN    4    4
SER    5    3
HIS    6    3
ILE    7    2
GLN    8   11
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 12 rotamers of residue E 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msk.164.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1msk.166.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1msk.166.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1msk.166.5.a2m \
	-target T0124 -template 1msk \
	-out T0124-1msk.166.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1msk-orig.a2m
Writing a2m file: tmp/1msk-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5251


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5251/tmp -alignfile tmp/1msk-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1msk-orig.a2m (1 sequences, 332 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5251/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5251/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5251/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5251/tmp.a2m (1 sequences, 332 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5251/tmp.mod tmp/1msk-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5251 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1msk-align.mod
tmp/1msk-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5251/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1msk-orig.a2m tmp/1msk-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1msk-align.mod
Running w0.5 tmp/1msk-orig.a2m tmp/1msk-align.mod
Running align2model tmp/1msk-align -i tmp/1msk-align.mod -db tmp/1msk-orig.a2m -db tmp/1msk-pdb.a2m
partial PDB gets fragment 59 through 68 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    5
ASN    2    5
SER    3    2
HIS    4    4
ILE    5    4
GLN    6   10
GLU    7   13
VAL    8    2
GLN   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   11     20.0000
keepclash     8   11     35.7763
Cluster     1 =   5   8  11
3 clashing residues after turn 
Residue clashes:
5-11
8-11
cluster 1 has 3 members and 1.400e+02 combinations:
 5  8  11 
Energy     56.2620
Searching cluster 5
Combinations for 3 members in cluster 1 OK: 1.400e+02 - Sending to search
55.776337 < 56.262047: keeping 
55.600204 < 56.262043: keeping 
45.510567 < 56.127392: keeping 
0.697793 < 46.053432: keeping 
0.000000 < 2.813770: keeping 
Solved cluster 1: residual clashing  2.18
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1msk.166.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.26.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.26.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.26.2.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.26.2 -outdir und
partial PDB gets fragment 482 through 491 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   29
LEU    2    5
LEU    3    2
LYS    4   27
LYS    5   20
GLN    6   14
GLU    7   14
LYS    8   24
GLU    9    8
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.26.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.27.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.27.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.27.5.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.27.5 -outdir und
partial PDB gets fragment 481 through 490 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LEU    2    3
LYS    3   32
LYS    4   17
GLN    5   13
GLU    6   11
LYS    7   24
GLU    8   14
LEU    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.27.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.28.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.28.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.28.4.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.28.4 -outdir und
partial PDB gets fragment 480 through 489 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   25
LYS    3   29
GLU    5   14
LYS    6   27
GLU    7   11
LEU    8    2
LYS    9   25
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.28.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.29.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.29.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.29.5.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.29.5 -outdir und
partial PDB gets fragment 479 through 488 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   29
LYS    2   29
GLN    3   11
GLU    4   15
LYS    5   32
GLU    6   13
LEU    7    4
LYS    8   20
GLU    9   15
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.29.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.30.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.30.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.30.5.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.30.5 -outdir und
partial PDB gets fragment 478 through 487 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    2   15
GLU    3   15
LYS    4   25
GLU    5   15
LEU    6    5
LYS    7   17
GLU    8   14
LEU    9    2
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.30.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.31.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.31.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.31.4.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.31.4 -outdir und
partial PDB gets fragment 477 through 486 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   11
GLU    2   13
LYS    3   29
GLU    4   15
LEU    5    3
LYS    6   29
GLU    7   16
LEU    8    2
GLU    9   14
ARG   10   19
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.31.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.32.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.32.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.32.2.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.32.2 -outdir und
partial PDB gets fragment 476 through 485 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
LYS    2   14
GLU    3   13
LEU    4    3
LYS    5   29
GLU    6   12
LEU    7    3
GLU    8   16
ARG    9   20
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.32.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.33.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.33.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.33.3.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.33.3 -outdir und
partial PDB gets fragment 475 through 484 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   31
GLU    2   15
LEU    3    2
GLU    5   16
GLU    7   16
ARG    8   32
LYS    9   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.33.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.33.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.33.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.33.4.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.33.4 -outdir und
partial PDB gets fragment 478 through 487 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   16
LYS    4   25
GLU    5   15
LEU    6    5
GLU    7   13
ARG    8   30
LYS    9   20
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.33.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.34.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.34.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.34.3.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.34.3 -outdir und
partial PDB gets fragment 477 through 486 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1    8
LEU    2    3
LYS    3   29
GLU    4   15
LEU    5    3
GLU    6   15
ARG    7   32
LYS    8   17
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.34.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mtyD.35.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mtyD.35.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mtyD.35.4.a2m \
	-target T0124 -template 1mtyD \
	-out T0124-1mtyD.35.4 -outdir und
partial PDB gets fragment 476 through 485 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   14
GLU    3   13
LEU    4    3
GLU    5   15
ARG    6   26
LYS    7   29
SER    9    2
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mtyD.35.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1mugA.165.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1mugA.165.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1mugA.165.3.a2m \
	-target T0124 -template 1mugA \
	-out T0124-1mugA.165.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1mugA-orig.a2m
Writing a2m file: tmp/1mugA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4337


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4337/tmp -alignfile tmp/1mugA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1mugA-orig.a2m (1 sequences, 168 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4337/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4337/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4337/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4337/tmp.a2m (1 sequences, 168 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4337/tmp.mod tmp/1mugA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4337 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1mugA-align.mod
tmp/1mugA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4337/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1mugA-orig.a2m tmp/1mugA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1mugA-align.mod
Running w0.5 tmp/1mugA-orig.a2m tmp/1mugA-align.mod
Running align2model tmp/1mugA-align -i tmp/1mugA-align.mod -db tmp/1mugA-orig.a2m -db tmp/1mugA-pdb.a2m
partial PDB gets fragment 24 through 33 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    4
ASN    2    4
ASN    3    5
SER    4    3
HIS    5    4
ILE    6    3
GLN    7   14
GLU    8   13
VAL    9    3
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.70990
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1mugA.165.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1myt.3.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1myt.3.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1myt.3.3.a2m \
	-target T0124 -template 1myt \
	-out T0124-1myt.3.3 -outdir und
partial PDB gets fragment 136 through 145 extending start
Debugging on !
Reading sequence file
Reading input structure 
Residue T11 has an incomplete backbone - it will be treated as a glycine
11 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
VAL    2    1
THR    3    2
GLN    4   11
LEU    5    3
PRO    6    2
GLU    7    9
PRO    8    2
GLN    9    9
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7    9     15.8935
Cluster     1 =   7   9
2 clashing residues after turn 
Residue clashes:
7-9
cluster 1 has 2 members and 4.000e+00 combinations:
 7  9 
Energy    128.2096
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
15.083831 < 128.209564: keeping 
0.000000 < 117.067192: keeping 
0.000000 < 92.543961: keeping 
Solved cluster 1: residual clashing 82.21
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1myt.3.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nbaA.181.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nbaA.181.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nbaA.181.4.a2m \
	-target T0124 -template 1nbaA \
	-out T0124-1nbaA.181.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nbaA-orig.a2m
Writing a2m file: tmp/1nbaA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1857


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1857/tmp -alignfile tmp/1nbaA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nbaA-orig.a2m (1 sequences, 264 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1857/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1857/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1857/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1857/tmp.a2m (1 sequences, 264 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1857/tmp.mod tmp/1nbaA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1857 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nbaA-align.mod
tmp/1nbaA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1857/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nbaA-orig.a2m tmp/1nbaA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nbaA-align.mod
Running w0.5 tmp/1nbaA-orig.a2m tmp/1nbaA-align.mod
Running align2model tmp/1nbaA-align -i tmp/1nbaA-align.mod -db tmp/1nbaA-orig.a2m -db tmp/1nbaA-pdb.a2m
partial PDB gets fragment 30 through 39 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    1
GLU    2   13
LYS    3   26
THR    4    2
ARG    6   25
TYR    7    3
GLN    8   11
GLN    9   10
LYS   10   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nbaA.181.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nbaA.182.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nbaA.182.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nbaA.182.3.a2m \
	-target T0124 -template 1nbaA \
	-out T0124-1nbaA.182.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nbaA-orig.a2m
Writing a2m file: tmp/1nbaA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15283


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15283/tmp -alignfile tmp/1nbaA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nbaA-orig.a2m (1 sequences, 264 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15283/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15283/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15283/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15283/tmp.a2m (1 sequences, 264 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15283/tmp.mod tmp/1nbaA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15283 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nbaA-align.mod
tmp/1nbaA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15283/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nbaA-orig.a2m tmp/1nbaA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nbaA-align.mod
Running w0.5 tmp/1nbaA-orig.a2m tmp/1nbaA-align.mod
Running align2model tmp/1nbaA-align -i tmp/1nbaA-align.mod -db tmp/1nbaA-orig.a2m -db tmp/1nbaA-pdb.a2m
partial PDB gets fragment 29 through 38 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1    7
LYS    2   24
THR    3    2
ARG    5   28
GLN    7   11
GLN    8   13
LYS    9   25
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nbaA.182.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nbaA.183.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nbaA.183.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nbaA.183.2.a2m \
	-target T0124 -template 1nbaA \
	-out T0124-1nbaA.183.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nbaA-orig.a2m
Writing a2m file: tmp/1nbaA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4331


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4331/tmp -alignfile tmp/1nbaA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nbaA-orig.a2m (1 sequences, 264 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4331/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4331/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4331/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4331/tmp.a2m (1 sequences, 264 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4331/tmp.mod tmp/1nbaA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4331 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nbaA-align.mod
tmp/1nbaA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4331/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nbaA-orig.a2m tmp/1nbaA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nbaA-align.mod
Running w0.5 tmp/1nbaA-orig.a2m tmp/1nbaA-align.mod
Running align2model tmp/1nbaA-align -i tmp/1nbaA-align.mod -db tmp/1nbaA-orig.a2m -db tmp/1nbaA-pdb.a2m
partial PDB gets fragment 28 through 38 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   19
THR    2    2
TYR    5    3
GLN    6   14
GLN    7   13
LYS    8   18
LEU    9    2
GLU   10   12
GLU   11   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nbaA.183.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nbaA.184.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nbaA.184.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nbaA.184.5.a2m \
	-target T0124 -template 1nbaA \
	-out T0124-1nbaA.184.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nbaA-orig.a2m
Writing a2m file: tmp/1nbaA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29884


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29884/tmp -alignfile tmp/1nbaA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nbaA-orig.a2m (1 sequences, 264 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29884/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29884/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29884/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29884/tmp.a2m (1 sequences, 264 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29884/tmp.mod tmp/1nbaA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29884 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nbaA-align.mod
tmp/1nbaA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29884/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nbaA-orig.a2m tmp/1nbaA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nbaA-align.mod
Running w0.5 tmp/1nbaA-orig.a2m tmp/1nbaA-align.mod
Running align2model tmp/1nbaA-align -i tmp/1nbaA-align.mod -db tmp/1nbaA-orig.a2m -db tmp/1nbaA-pdb.a2m
partial PDB gets fragment 27 through 36 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    1
ARG    3   19
TYR    4    3
GLN    5   12
GLN    6   12
LYS    7   25
LEU    8    3
GLU    9   12
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nbaA.184.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nbaA.84.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nbaA.84.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nbaA.84.4.a2m \
	-target T0124 -template 1nbaA \
	-out T0124-1nbaA.84.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nbaA-orig.a2m
Writing a2m file: tmp/1nbaA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31813


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31813/tmp -alignfile tmp/1nbaA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nbaA-orig.a2m (1 sequences, 264 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31813/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31813/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31813/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31813/tmp.a2m (1 sequences, 264 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31813/tmp.mod tmp/1nbaA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31813 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nbaA-align.mod
tmp/1nbaA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31813/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nbaA-orig.a2m tmp/1nbaA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nbaA-align.mod
Running w0.5 tmp/1nbaA-orig.a2m tmp/1nbaA-align.mod
Running align2model tmp/1nbaA-align -i tmp/1nbaA-align.mod -db tmp/1nbaA-orig.a2m -db tmp/1nbaA-pdb.a2m
partial PDB gets fragment 111 through 120 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    3   12
GLU    4   14
TYR    5    3
HIS    6    2
ASP    7    6
ILE    9    4
ARG   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 24 rotamers of residue R 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   10     28.8501
Cluster     1 =   8  10
2 clashing residues after turn 
Residue clashes:
8-10
cluster 1 has 2 members and 1.200e+01 combinations:
 8  10 
Energy     32.4883
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 1.200e+01 - Sending to search
0.000000 < 32.488335: keeping 
0.000000 < 4.882786: keeping 
Solved cluster 1: residual clashing  0.16
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nbaA.84.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nbaA.85.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nbaA.85.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nbaA.85.2.a2m \
	-target T0124 -template 1nbaA \
	-out T0124-1nbaA.85.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nbaA-orig.a2m
Writing a2m file: tmp/1nbaA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5280


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5280/tmp -alignfile tmp/1nbaA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nbaA-orig.a2m (1 sequences, 264 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5280/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5280/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5280/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5280/tmp.a2m (1 sequences, 264 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5280/tmp.mod tmp/1nbaA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5280 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nbaA-align.mod
tmp/1nbaA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5280/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nbaA-orig.a2m tmp/1nbaA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nbaA-align.mod
Running w0.5 tmp/1nbaA-orig.a2m tmp/1nbaA-align.mod
Running align2model tmp/1nbaA-align -i tmp/1nbaA-align.mod -db tmp/1nbaA-orig.a2m -db tmp/1nbaA-pdb.a2m
partial PDB gets fragment 110 through 119 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    3   12
TYR    4    3
HIS    5    4
ASP    6    6
ILE    8    4
ARG    9   26
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nbaA.85.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nbaA.86.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nbaA.86.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nbaA.86.1.a2m \
	-target T0124 -template 1nbaA \
	-out T0124-1nbaA.86.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nbaA-orig.a2m
Writing a2m file: tmp/1nbaA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28331


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28331/tmp -alignfile tmp/1nbaA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nbaA-orig.a2m (1 sequences, 264 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28331/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28331/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28331/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28331/tmp.a2m (1 sequences, 264 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28331/tmp.mod tmp/1nbaA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28331 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nbaA-align.mod
tmp/1nbaA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28331/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nbaA-orig.a2m tmp/1nbaA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nbaA-align.mod
Running w0.5 tmp/1nbaA-orig.a2m tmp/1nbaA-align.mod
Running align2model tmp/1nbaA-align -i tmp/1nbaA-align.mod -db tmp/1nbaA-orig.a2m -db tmp/1nbaA-pdb.a2m
partial PDB gets fragment 109 through 118 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   11
GLU    2   15
TYR    3    3
HIS    4    3
ASP    5    5
ILE    7    5
ARG    8   21
ARG    9   26
ARG   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.89730
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nbaA.86.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nbaA.87.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nbaA.87.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nbaA.87.2.a2m \
	-target T0124 -template 1nbaA \
	-out T0124-1nbaA.87.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nbaA-orig.a2m
Writing a2m file: tmp/1nbaA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22787


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22787/tmp -alignfile tmp/1nbaA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nbaA-orig.a2m (1 sequences, 264 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22787/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22787/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22787/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22787/tmp.a2m (1 sequences, 264 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22787/tmp.mod tmp/1nbaA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22787 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nbaA-align.mod
tmp/1nbaA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22787/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nbaA-orig.a2m tmp/1nbaA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nbaA-align.mod
Running w0.5 tmp/1nbaA-orig.a2m tmp/1nbaA-align.mod
Running align2model tmp/1nbaA-align -i tmp/1nbaA-align.mod -db tmp/1nbaA-orig.a2m -db tmp/1nbaA-pdb.a2m
partial PDB gets fragment 108 through 117 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
TYR    2    2
HIS    3    4
ASP    4    5
ILE    6    3
ARG    7   30
ARG    8   32
ARG    9   21
LYS   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nbaA.87.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nbaA.88.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nbaA.88.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nbaA.88.2.a2m \
	-target T0124 -template 1nbaA \
	-out T0124-1nbaA.88.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nbaA-orig.a2m
Writing a2m file: tmp/1nbaA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5460


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5460/tmp -alignfile tmp/1nbaA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nbaA-orig.a2m (1 sequences, 264 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5460/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5460/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5460/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5460/tmp.a2m (1 sequences, 264 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5460/tmp.mod tmp/1nbaA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5460 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nbaA-align.mod
tmp/1nbaA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5460/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nbaA-orig.a2m tmp/1nbaA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nbaA-align.mod
Running w0.5 tmp/1nbaA-orig.a2m tmp/1nbaA-align.mod
Running align2model tmp/1nbaA-align -i tmp/1nbaA-align.mod -db tmp/1nbaA-orig.a2m -db tmp/1nbaA-pdb.a2m
partial PDB gets fragment 107 through 116 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
HIS    2    3
ASP    3    4
ILE    5    4
ARG    6   21
ARG    7   23
ARG    8   30
LYS    9   29
GLU   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    7     21.4301
Cluster     1 =   4   7
2 clashing residues after turn 
Residue clashes:
4-7
cluster 1 has 2 members and 7.600e+01 combinations:
 4  7 
Energy     21.4301
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 7.600e+01 - Sending to search
17.987434 < 21.430080: keeping 
8.504770 < 18.421848: keeping 
0.000000 < 9.788316: keeping 
0.000000 < 1.879619: keeping 
Solved cluster 1: residual clashing  1.80
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nbaA.88.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nls.114.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nls.114.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nls.114.5.a2m \
	-target T0124 -template 1nls \
	-out T0124-1nls.114.5 -outdir und
Skipped atom 63, because occupancy 0.69 <= existing 0.690001
Skipped atom 193, because occupancy 0.33 <= existing 0.670001
Skipped atom 195, because occupancy 0.33 <= existing 0.670001
Skipped atom 198, because occupancy 0.33 <= existing 0.670001
Skipped atom 209, because occupancy 0.43 <= existing 0.570001
Skipped atom 212, because occupancy 0.43 <= existing 0.570001
Skipped atom 306, because occupancy 0.44 <= existing 0.560001
Skipped atom 308, because occupancy 0.44 <= existing 0.560001
Skipped atom 469, because occupancy 0.34 <= existing 0.660001
Skipped atom 471, because occupancy 0.34 <= existing 0.660001
Skipped atom 479, because occupancy 0.45 <= existing 0.550001
Skipped atom 481, because occupancy 0.45 <= existing 0.550001
Skipped atom 483, because occupancy 0.45 <= existing 0.550001
Skipped atom 485, because occupancy 0.45 <= existing 0.550001
Skipped atom 487, because occupancy 0.45 <= existing 0.550001
Skipped atom 519, because occupancy 0.5 <= existing 0.500001
Skipped atom 521, because occupancy 0.5 <= existing 0.500001
Skipped atom 523, because occupancy 0.5 <= existing 0.500001
Skipped atom 621, because occupancy 0.47 <= existing 0.530001
Skipped atom 623, because occupancy 0.47 <= existing 0.530001
Skipped atom 625, because occupancy 0.47 <= existing 0.530001
Skipped atom 849, because occupancy 0.23 <= existing 0.770001
Skipped atom 851, because occupancy 0.23 <= existing 0.770001
Skipped atom 878, because occupancy 0.31 <= existing 0.690001
Skipped atom 880, because occupancy 0.31 <= existing 0.690001
Skipped atom 904, because occupancy 0.45 <= existing 0.550001
Skipped atom 906, because occupancy 0.45 <= existing 0.550001
Skipped atom 1303, because occupancy 0.47 <= existing 0.530001
Skipped atom 1305, because occupancy 0.47 <= existing 0.530001
Skipped atom 1467, because occupancy 0.41 <= existing 0.590001
Skipped atom 1469, because occupancy 0.41 <= existing 0.590001
Skipped atom 1487, because occupancy 0.32 <= existing 0.680001
Skipped atom 1489, because occupancy 0.32 <= existing 0.680001
Skipped atom 1518, because occupancy 0.3 <= existing 0.700001
Skipped atom 1520, because occupancy 0.3 <= existing 0.700001
Skipped atom 1522, because occupancy 0.3 <= existing 0.700001
Skipped atom 1524, because occupancy 0.3 <= existing 0.700001
Skipped atom 1555, because occupancy 0.32 <= existing 0.680001
Skipped atom 1557, because occupancy 0.32 <= existing 0.680001
Skipped atom 1559, because occupancy 0.32 <= existing 0.680001
Skipped atom 1622, because occupancy 0.31 <= existing 0.690001
Skipped atom 1624, because occupancy 0.31 <= existing 0.690001
Skipped atom 1707, because occupancy 0.29 <= existing 0.710001
Skipped atom 1709, because occupancy 0.29 <= existing 0.710001
Skipped atom 1732, because occupancy 0.35 <= existing 0.650001
Skipped atom 1735, because occupancy 0.35 <= existing 0.650001
Skipped atom 1747, because occupancy 0.28 <= existing 0.720001
Skipped atom 1749, because occupancy 0.28 <= existing 0.720001
partial PDB gets fragment 87 through 96 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
GLN    2   14
ILE    3    4
GLU    5   12
LYS    7   25
LEU    9    2
LYS   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nls.114.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1noa.54.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1noa.54.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1noa.54.2.a2m \
	-target T0124 -template 1noa \
	-out T0124-1noa.54.2 -outdir und
partial PDB gets fragment 85 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
VAL    2    1
LEU    3    2
PHE    4    3
LEU    5    3
GLU    6   16
PRO    7    2
VAL    8    2
TYR    9    2
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    9     14.9594
Cluster     1 =   4   9
2 clashing residues after turn 
Residue clashes:
4-9
cluster 1 has 2 members and 2.000e+00 combinations:
 4  9 
Energy     17.2729
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search
Solved cluster 1: residual clashing 17.27
Still clashes at these sidechain pairs:
ires=    4 irot=    2 jres=    9 jrot=    1      14.9594
Residual clashes =   14.95941
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1noa.54.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1noa.55.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1noa.55.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1noa.55.1.a2m \
	-target T0124 -template 1noa \
	-out T0124-1noa.55.1 -outdir und
partial PDB gets fragment 84 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
LEU    2    3
PHE    3    3
LEU    4    2
GLU    5   12
PRO    6    2
VAL    7    3
TYR    8    2
PRO    9    2
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.29901
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1noa.55.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1noa.56.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1noa.56.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1noa.56.1.a2m \
	-target T0124 -template 1noa \
	-out T0124-1noa.56.1 -outdir und
partial PDB gets fragment 83 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
PHE    2    3
LEU    3    3
GLU    4   12
PRO    5    2
VAL    6    3
TYR    7    3
PRO    8    2
ARG    9   29
LEU   11    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   17.75824
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1noa.56.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1noa.57.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1noa.57.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1noa.57.0.a2m \
	-target T0124 -template 1noa \
	-out T0124-1noa.57.0 -outdir und
partial PDB gets fragment 82 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
PHE    1    3
LEU    2    3
GLU    3   13
PRO    4    2
VAL    5    1
TYR    6    3
PRO    7    2
ARG    8   21
LEU   10    3
ASP   11    6
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    8     20.0000
Cluster     1 =   6   8
2 clashing residues after turn 
Residue clashes:
6-8
cluster 1 has 2 members and 2.000e+00 combinations:
 6  8 
Energy     25.5700
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search
10.000000 < 25.569994: keeping 
Solved cluster 1: residual clashing 18.43
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1noa.57.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1noa.58.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1noa.58.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1noa.58.1.a2m \
	-target T0124 -template 1noa \
	-out T0124-1noa.58.1 -outdir und
partial PDB gets fragment 81 through 91 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   12
PRO    3    2
VAL    4    1
TYR    5    3
PRO    6    2
ARG    7   28
LEU    9    3
ASP   10    8
SER   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    6     22.0716
Cluster     1 =   3   6
2 clashing residues after turn 
Residue clashes:
3-6
cluster 1 has 2 members and 2.200e+01 combinations:
 6  3 
Energy     24.3296
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 2.200e+01 - Sending to search
20.000000 < 24.329639: keeping 
17.412666 < 22.855068: keeping 
0.000000 < 20.318258: keeping 
Solved cluster 1: residual clashing  3.02
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1noa.58.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1noa.59.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1noa.59.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1noa.59.0.a2m \
	-target T0124 -template 1noa \
	-out T0124-1noa.59.0 -outdir und
partial PDB gets fragment 80 through 89 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
PRO    2    2
VAL    3    2
TYR    4    3
PRO    5    2
ARG    6   27
LEU    8    2
ASP    9    5
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1noa.59.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1noa.60.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1noa.60.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1noa.60.3.a2m \
	-target T0124 -template 1noa \
	-out T0124-1noa.60.3 -outdir und
partial PDB gets fragment 79 through 88 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
VAL    2    3
TYR    3    2
PRO    4    2
ARG    5   32
LEU    7    3
SER    9    2
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1noa.60.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.18.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.18.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.18.4.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.18.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6327


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6327/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6327/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6327/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6327/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6327/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6327/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6327 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6327/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 183 through 192 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLN    2   14
GLN    3   14
MET    4   10
LYS    5   27
LEU    6    2
PHE    7    3
LYS    9   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.18.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.19.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.19.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.19.5.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.19.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6722


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6722/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6722/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6722/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6722/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6722/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6722/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6722 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6722/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 182 through 191 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   16
GLN    2   13
MET    3   10
LYS    4   25
LEU    5    3
PHE    6    3
LEU    7    2
LYS    8   25
LEU   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.19.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.38.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.38.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.38.4.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.38.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5952


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5952/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5952/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5952/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5952/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5952/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5952/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5952 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5952/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 173 through 182 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    5
GLU    2   15
ARG    3   26
LYS    4   26
SER    6    2
LYS    7   26
ARG    8   30
ARG    9   19
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.38.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.39.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.39.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.39.3.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.39.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7853


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7853/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7853/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7853/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7853/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7853/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7853/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7853 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7853/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 172 through 181 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
ARG    2   27
LYS    3   23
SER    5    3
LYS    6   31
ARG    7   32
ARG    8   26
GLU    9   14
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.39.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.40.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.40.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.40.0.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.40.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10638


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10638/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10638/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10638/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10638/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10638/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10638/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10638 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10638/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 171 through 180 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
LYS    2   30
SER    4    3
LYS    5   26
ARG    6   29
ARG    7   32
GLU    8    7
GLU    9   13
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.40.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.41.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.41.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.41.0.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.41.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7036


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7036/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7036/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7036/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7036/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7036/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7036/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7036 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7036/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 170 through 179 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   23
SER    3    2
LYS    4   27
ARG    5   29
ARG    6   26
GLU    7   14
GLU    8   15
LEU    9    4
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.41.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.42.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.42.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.42.0.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.42.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15397


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15397/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15397/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15397/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15397/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15397/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15397/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15397 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15397/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 169 through 178 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    2    3
LYS    3   24
ARG    4   32
ARG    5   27
GLU    6   15
GLU    7   14
LEU    8    3
GLN   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash    10   11     11.5855
Cluster     1 =  10  11
2 clashing residues after turn 
Residue clashes:
10-11
cluster 1 has 2 members and 0.000e+00 combinations:
 10  11 
Energy     11.5855
Searching cluster 10
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
0.000000 < 11.585505: keeping 
Solved cluster 1: residual clashing  1.43
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.42.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.43.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.43.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.43.0.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.43.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6141


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6141/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6141/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6141/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6141/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6141/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6141/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6141 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6141/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 168 through 177 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
LYS    2   27
ARG    3   29
ARG    4   26
GLU    5   15
GLU    6   12
LEU    8    3
GLN    9   13
LYS   10   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00016
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.43.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.44.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.44.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.44.0.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.44.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5230


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5230/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5230/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5230/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5230/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5230/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5230/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5230 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5230/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 167 through 176 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
ARG    3   30
GLU    4   15
GLU    5   11
LEU    6    3
LEU    7    5
GLN    8   13
LYS    9   26
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.44.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.45.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.45.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.45.1.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.45.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6495


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6495/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6495/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6495/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6495/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6495/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6495/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6495 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6495/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 166 through 175 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   32
ARG    2   32
GLU    3   14
GLU    4   14
LEU    5    2
LEU    6    3
GLN    7   14
LYS    8   27
TYR    9    3
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.45.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nox.46.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nox.46.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nox.46.2.a2m \
	-target T0124 -template 1nox \
	-out T0124-1nox.46.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nox-orig.a2m
Writing a2m file: tmp/1nox-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31767


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31767/tmp -alignfile tmp/1nox-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nox-orig.a2m (1 sequences, 205 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31767/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31767/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31767/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31767/tmp.a2m (1 sequences, 205 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31767/tmp.mod tmp/1nox-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31767 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nox-align.mod
tmp/1nox-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31767/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nox-orig.a2m tmp/1nox-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nox-align.mod
Running w0.5 tmp/1nox-orig.a2m tmp/1nox-align.mod
Running align2model tmp/1nox-align -i tmp/1nox-align.mod -db tmp/1nox-orig.a2m -db tmp/1nox-pdb.a2m
partial PDB gets fragment 165 through 174 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   30
GLU    2   15
GLU    3   15
LEU    4    2
LEU    5    3
GLN    6   13
LYS    7   24
TYR    8    4
SER    9    2
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nox.46.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1np1A.10.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1np1A.10.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1np1A.10.2.a2m \
	-target T0124 -template 1np1A \
	-out T0124-1np1A.10.2 -outdir und
partial PDB gets fragment 174 through 183 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
GLN    2   11
THR    3    2
SER    5    3
LEU    6    3
GLU    8   15
LEU    9    2
GLN   10    8
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1np1A.10.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1np1A.209.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1np1A.209.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1np1A.209.5.a2m \
	-target T0124 -template 1np1A \
	-out T0124-1np1A.209.5 -outdir und
partial PDB gets fragment 7 through 16 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLN    3   11
GLU    4   10
VAL    6    1
GLU    8   12
TYR    9    3
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.46746
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1np1A.209.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1np1A.210.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1np1A.210.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1np1A.210.0.a2m \
	-target T0124 -template 1np1A \
	-out T0124-1np1A.210.0 -outdir und
partial PDB gets fragment 6 through 15 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLN    2   14
GLU    3   13
VAL    5    2
GLU    7   11
TYR    8    3
GLU    9   12
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1np1A.210.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1np1A.211.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1np1A.211.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1np1A.211.0.a2m \
	-target T0124 -template 1np1A \
	-out T0124-1np1A.211.0 -outdir und
partial PDB gets fragment 5 through 14 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLU    2   12
VAL    4    3
GLU    6   10
TYR    7    2
GLU    8   11
GLU    9   13
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1np1A.211.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1np1A.212.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1np1A.212.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1np1A.212.3.a2m \
	-target T0124 -template 1np1A \
	-out T0124-1np1A.212.3 -outdir und
partial PDB gets fragment 4 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   11
VAL    3    1
GLU    5   15
TYR    6    2
GLU    7   10
GLU    8   13
LYS    9   26
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1np1A.212.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nscA.95.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nscA.95.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nscA.95.4.a2m \
	-target T0124 -template 1nscA \
	-out T0124-1nscA.95.4 -outdir und
partial PDB gets fragment 74 through 84 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   25
GLU    3   15
GLN    4   14
THR    7    2
GLU    8   15
GLN    9   14
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nscA.95.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nscA.96.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nscA.96.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nscA.96.3.a2m \
	-target T0124 -template 1nscA \
	-out T0124-1nscA.96.3 -outdir und
partial PDB gets fragment 73 through 83 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
GLU    2    8
GLN    3   10
HIS    4    3
THR    6    3
GLU    7   13
GLN    8   12
THR    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nscA.96.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nscA.97.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nscA.97.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nscA.97.3.a2m \
	-target T0124 -template 1nscA \
	-out T0124-1nscA.97.3 -outdir und
partial PDB gets fragment 72 through 82 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
GLN    2   14
HIS    3    2
THR    5    2
GLU    6   15
GLN    7   15
THR    8    2
LYS   10   31
ILE   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue H 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    6     20.0000
Cluster     1 =   4   6
2 clashing residues after turn 
Residue clashes:
4-6
cluster 1 has 2 members and 4.000e+00 combinations:
 4  6 
Energy     27.0543
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
0.000000 < 27.054329: keeping 
Solved cluster 1: residual clashing  9.37
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nscA.97.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nscA.98.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nscA.98.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nscA.98.3.a2m \
	-target T0124 -template 1nscA \
	-out T0124-1nscA.98.3 -outdir und
partial PDB gets fragment 69 through 79 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
HIS    2    3
THR    4    2
GLU    5   15
GLN    6    8
THR    7    1
LYS    9   30
ILE   10    5
THR   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nscA.98.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nulA.133.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nulA.133.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nulA.133.4.a2m \
	-target T0124 -template 1nulA \
	-out T0124-1nulA.133.4 -outdir und
Skipped atom 155, because occupancy 0.5 <= existing 0.500001
Skipped atom 157, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1000, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nulA-orig.a2m
Writing a2m file: tmp/1nulA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7352


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7352/tmp -alignfile tmp/1nulA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nulA-orig.a2m (1 sequences, 152 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7352/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7352/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7352/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7352/tmp.a2m (1 sequences, 152 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7352/tmp.mod tmp/1nulA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7352 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nulA-align.mod
tmp/1nulA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7352/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nulA-orig.a2m tmp/1nulA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nulA-align.mod
Running w0.5 tmp/1nulA-orig.a2m tmp/1nulA-align.mod
Running align2model tmp/1nulA-align -i tmp/1nulA-align.mod -db tmp/1nulA-orig.a2m -db tmp/1nulA-pdb.a2m
partial PDB gets fragment 60 through 65 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
8 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   12
LYS    4   25
ARG    5   32
LEU    6    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nulA.133.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1nulA.134.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1nulA.134.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1nulA.134.5.a2m \
	-target T0124 -template 1nulA \
	-out T0124-1nulA.134.5 -outdir und
Skipped atom 155, because occupancy 0.5 <= existing 0.500001
Skipped atom 157, because occupancy 0.5 <= existing 0.500001
Skipped atom 994, because occupancy 0.5 <= existing 0.500001
Skipped atom 996, because occupancy 0.5 <= existing 0.500001
Skipped atom 998, because occupancy 0.5 <= existing 0.500001
Skipped atom 1000, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nulA-orig.a2m
Writing a2m file: tmp/1nulA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9439


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9439/tmp -alignfile tmp/1nulA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nulA-orig.a2m (1 sequences, 152 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9439/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9439/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9439/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9439/tmp.a2m (1 sequences, 152 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9439/tmp.mod tmp/1nulA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9439 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nulA-align.mod
tmp/1nulA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9439/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nulA-orig.a2m tmp/1nulA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nulA-align.mod
Running w0.5 tmp/1nulA-orig.a2m tmp/1nulA-align.mod
Running align2model tmp/1nulA-align -i tmp/1nulA-align.mod -db tmp/1nulA-orig.a2m -db tmp/1nulA-pdb.a2m
partial PDB gets fragment 60 through 64 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
7 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   25
ARG    3   27
ASP    5    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1nulA.134.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pbwA.116.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pbwA.116.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pbwA.116.4.a2m \
	-target T0124 -template 1pbwA \
	-out T0124-1pbwA.116.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pbwA-orig.a2m
Writing a2m file: tmp/1pbwA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8719


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8719/tmp -alignfile tmp/1pbwA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pbwA-orig.a2m (1 sequences, 216 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8719/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8719/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8719/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8719/tmp.a2m (1 sequences, 216 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8719/tmp.mod tmp/1pbwA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8719 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pbwA-align.mod
tmp/1pbwA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8719/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pbwA-orig.a2m tmp/1pbwA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pbwA-align.mod
Running w0.5 tmp/1pbwA-orig.a2m tmp/1pbwA-align.mod
Running align2model tmp/1pbwA-align -i tmp/1pbwA-align.mod -db tmp/1pbwA-orig.a2m -db tmp/1pbwA-pdb.a2m
partial PDB gets fragment 66 through 78 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    4
GLU    3   12
LEU    4    3
LYS    5   26
LEU    7    3
LYS    8   26
GLU    9   12
SER   10    3
SER   11    2
GLU   12   13
SER   13    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pbwA.116.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pbwA.117.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pbwA.117.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pbwA.117.3.a2m \
	-target T0124 -template 1pbwA \
	-out T0124-1pbwA.117.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pbwA-orig.a2m
Writing a2m file: tmp/1pbwA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32067


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32067/tmp -alignfile tmp/1pbwA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pbwA-orig.a2m (1 sequences, 216 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32067/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32067/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32067/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32067/tmp.a2m (1 sequences, 216 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32067/tmp.mod tmp/1pbwA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32067 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pbwA-align.mod
tmp/1pbwA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32067/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pbwA-orig.a2m tmp/1pbwA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pbwA-align.mod
Running w0.5 tmp/1pbwA-orig.a2m tmp/1pbwA-align.mod
Running align2model tmp/1pbwA-align -i tmp/1pbwA-align.mod -db tmp/1pbwA-orig.a2m -db tmp/1pbwA-pdb.a2m
partial PDB gets fragment 69 through 78 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   12
LEU    3    3
LEU    6    3
LYS    7   26
GLU    8   15
SER    9    2
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pbwA.117.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pbwA.117.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pbwA.117.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pbwA.117.5.a2m \
	-target T0124 -template 1pbwA \
	-out T0124-1pbwA.117.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pbwA-orig.a2m
Writing a2m file: tmp/1pbwA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17590


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17590/tmp -alignfile tmp/1pbwA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pbwA-orig.a2m (1 sequences, 216 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17590/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17590/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17590/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17590/tmp.a2m (1 sequences, 216 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17590/tmp.mod tmp/1pbwA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17590 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pbwA-align.mod
tmp/1pbwA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17590/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pbwA-orig.a2m tmp/1pbwA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pbwA-align.mod
Running w0.5 tmp/1pbwA-orig.a2m tmp/1pbwA-align.mod
Running align2model tmp/1pbwA-align -i tmp/1pbwA-align.mod -db tmp/1pbwA-orig.a2m -db tmp/1pbwA-pdb.a2m
partial PDB gets fragment 65 through 77 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   13
LYS    4   29
LEU    6    3
LYS    7   24
GLU    8   15
SER    9    3
SER   10    3
GLU   11   12
SER   12    2
ASN   13    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pbwA.117.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pbwA.118.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pbwA.118.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pbwA.118.5.a2m \
	-target T0124 -template 1pbwA \
	-out T0124-1pbwA.118.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pbwA-orig.a2m
Writing a2m file: tmp/1pbwA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7170


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7170/tmp -alignfile tmp/1pbwA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pbwA-orig.a2m (1 sequences, 216 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7170/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7170/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7170/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7170/tmp.a2m (1 sequences, 216 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7170/tmp.mod tmp/1pbwA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7170 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pbwA-align.mod
tmp/1pbwA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7170/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pbwA-orig.a2m tmp/1pbwA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pbwA-align.mod
Running w0.5 tmp/1pbwA-orig.a2m tmp/1pbwA-align.mod
Running align2model tmp/1pbwA-align -i tmp/1pbwA-align.mod -db tmp/1pbwA-orig.a2m -db tmp/1pbwA-pdb.a2m
partial PDB gets fragment 64 through 76 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    2    3
LYS    3   28
LEU    5    3
LYS    6   26
GLU    7   12
SER    8    3
SER    9    2
GLU   10   12
SER   11    3
ASN   12    4
ILE   13    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pbwA.118.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pbwA.120.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pbwA.120.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pbwA.120.4.a2m \
	-target T0124 -template 1pbwA \
	-out T0124-1pbwA.120.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pbwA-orig.a2m
Writing a2m file: tmp/1pbwA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7281


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7281/tmp -alignfile tmp/1pbwA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pbwA-orig.a2m (1 sequences, 216 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7281/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7281/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7281/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7281/tmp.a2m (1 sequences, 216 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7281/tmp.mod tmp/1pbwA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7281 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pbwA-align.mod
tmp/1pbwA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7281/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pbwA-orig.a2m tmp/1pbwA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pbwA-align.mod
Running w0.5 tmp/1pbwA-orig.a2m tmp/1pbwA-align.mod
Running align2model tmp/1pbwA-align -i tmp/1pbwA-align.mod -db tmp/1pbwA-orig.a2m -db tmp/1pbwA-pdb.a2m
partial PDB gets fragment 64 through 75 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
LEU    3    3
LYS    4   26
GLU    5   12
SER    6    3
SER    7    3
GLU    8   12
SER    9    2
ASN   10    4
ILE   11    3
LYS   12   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pbwA.120.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pbwA.122.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pbwA.122.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pbwA.122.2.a2m \
	-target T0124 -template 1pbwA \
	-out T0124-1pbwA.122.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pbwA-orig.a2m
Writing a2m file: tmp/1pbwA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7183


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7183/tmp -alignfile tmp/1pbwA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pbwA-orig.a2m (1 sequences, 216 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7183/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7183/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7183/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7183/tmp.a2m (1 sequences, 216 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7183/tmp.mod tmp/1pbwA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7183 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pbwA-align.mod
tmp/1pbwA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7183/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pbwA-orig.a2m tmp/1pbwA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pbwA-align.mod
Running w0.5 tmp/1pbwA-orig.a2m tmp/1pbwA-align.mod
Running align2model tmp/1pbwA-align -i tmp/1pbwA-align.mod -db tmp/1pbwA-orig.a2m -db tmp/1pbwA-pdb.a2m
partial PDB gets fragment 64 through 73 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   30
GLU    3   13
SER    4    3
SER    5    3
GLU    6   12
SER    7    3
ASN    8    4
ILE    9    5
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pbwA.122.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.165.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.165.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.165.1.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.165.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6800


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6800/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6800/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6800/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6800/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6800/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6800/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6800 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6800/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 45 through 45 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
3 residues read 
Measuring phi and psi 
Getting chi values
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.165.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.166.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.166.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.166.2.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.166.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7794


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7794/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7794/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7794/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7794/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7794/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7794/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7794 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7794/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 44 through 45 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
4 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    5
ASN    2    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.166.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.167.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.167.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.167.4.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.167.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22248


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22248/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22248/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22248/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22248/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22248/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22248/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22248 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22248/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 43 through 45 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
5 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
SER    2    3
HIS    3    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.167.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.182.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.182.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.182.2.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.182.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6401


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6401/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6401/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6401/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6401/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6401/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6401/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6401 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6401/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 30 through 39 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    2   25
THR    3    2
ARG    5   28
TYR    6    3
GLN    7   12
GLN    8   13
LYS    9   32
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.182.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.183.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.183.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.183.4.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.183.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7295


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7295/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7295/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7295/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7295/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7295/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7295/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7295 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7295/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 29 through 38 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
THR    2    1
ARG    4   26
TYR    5    3
GLN    6   13
GLN    7   12
LYS    8   25
LEU    9    3
GLU   10   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.183.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.185.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.185.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.185.5.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.185.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7343


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7343/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7343/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7343/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7343/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7343/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7343/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7343 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7343/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 27 through 36 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   29
TYR    3    3
GLN    4    8
GLN    5   14
LYS    6   27
LEU    7    3
GLU    9   12
LYS   10   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    6     15.4188
Cluster     1 =   3   6
2 clashing residues after turn 
Residue clashes:
3-6
cluster 1 has 2 members and 3.240e+02 combinations:
 6  3 
Energy     17.0987
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 3.240e+02 - Sending to search
0.000000 < 17.098679: keeping 
0.000000 < 2.963397: keeping 
0.000000 < 1.792587: keeping 
Solved cluster 1: residual clashing  0.11
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.185.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.197.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.197.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.197.3.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.197.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2885


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2885/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2885/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2885/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2885/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2885/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2885/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2885 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2885/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 22 through 31 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
ASN    2    4
ARG    4   28
ILE    6    4
GLN    7   13
GLU    8   15
LYS    9   18
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   11     35.1224
turnclash      8   10    7    0     40.0000
Cluster     1 =   7   8  11
3 clashing residues after turn 
Residue clashes:
8-11
8-7
cluster 1 has 3 members and 6.240e+02 combinations:
 7  11  8 
Energy     37.5379
Searching cluster 7
Combinations for 3 members in cluster 1 OK: 6.240e+02 - Sending to search
25.134661 < 37.537926: keeping 
18.671734 < 27.604881: keeping 
0.000000 < 21.195692: keeping 
0.000000 < 2.529971: keeping 
0.000000 < 1.135664: keeping 
Solved cluster 1: residual clashing  0.76
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.197.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.198.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.198.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.198.3.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.198.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5988


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5988/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5988/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5988/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5988/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5988/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5988/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5988 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5988/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 21 through 30 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
LEU    2    3
ARG    3   27
ILE    5    3
GLN    6   12
GLU    7   15
LYS    8   25
GLU    9   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.198.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.199.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.199.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.199.4.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.199.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8478


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8478/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8478/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8478/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8478/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8478/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8478/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8478 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8478/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 20 through 29 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ARG    2   26
ILE    4    3
GLN    5   12
GLU    6   12
LYS    7   26
GLU    8   15
GLN   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.199.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.200.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.200.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.200.5.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.200.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9117


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9117/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9117/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9117/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9117/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9117/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9117/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9117 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9117/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 19 through 28 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
ILE    3    2
GLN    4   12
GLU    5   12
LYS    6   26
GLU    7   12
GLN    9   13
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.200.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pda.202.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pda.202.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pda.202.4.a2m \
	-target T0124 -template 1pda \
	-out T0124-1pda.202.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pda-orig.a2m
Writing a2m file: tmp/1pda-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8387


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8387/tmp -alignfile tmp/1pda-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pda-orig.a2m (1 sequences, 313 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8387/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8387/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8387/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8387/tmp.a2m (1 sequences, 313 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8387/tmp.mod tmp/1pda-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8387 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pda-align.mod
tmp/1pda-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8387/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pda-orig.a2m tmp/1pda-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pda-align.mod
Running w0.5 tmp/1pda-orig.a2m tmp/1pda-align.mod
Running align2model tmp/1pda-align -i tmp/1pda-align.mod -db tmp/1pda-orig.a2m -db tmp/1pda-pdb.a2m
partial PDB gets fragment 17 through 26 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
GLN    2   12
GLU    3   12
LYS    4   24
GLU    5   12
GLN    7   12
GLN    9   13
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pda.202.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pdo.184.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pdo.184.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pdo.184.3.a2m \
	-target T0124 -template 1pdo \
	-out T0124-1pdo.184.3 -outdir und
Skipped atom 473, because occupancy 0.59 <= existing 0.670001
Skipped atom 475, because occupancy 0.59 <= existing 0.670001
Skipped atom 477, because occupancy 0.59 <= existing 0.670001
Skipped atom 479, because occupancy 0.59 <= existing 0.670001
Skipped atom 940, because occupancy 0.36 <= existing 0.600001
Skipped atom 942, because occupancy 0.36 <= existing 0.600001
Skipped atom 944, because occupancy 0.36 <= existing 0.600001
Skipped atom 946, because occupancy 0.36 <= existing 0.600001
Skipped atom 948, because occupancy 0.36 <= existing 0.600001
Skipped atom 950, because occupancy 0.36 <= existing 0.600001
Skipped atom 952, because occupancy 0.36 <= existing 0.600001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pdo-orig.a2m
Writing a2m file: tmp/1pdo-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9263


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9263/tmp -alignfile tmp/1pdo-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pdo-orig.a2m (1 sequences, 135 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9263/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9263/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9263/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9263/tmp.a2m (1 sequences, 135 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9263/tmp.mod tmp/1pdo-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9263 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pdo-align.mod
tmp/1pdo-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9263/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pdo-orig.a2m tmp/1pdo-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pdo-align.mod
Running w0.5 tmp/1pdo-orig.a2m tmp/1pdo-align.mod
Running align2model tmp/1pdo-align -i tmp/1pdo-align.mod -db tmp/1pdo-orig.a2m -db tmp/1pdo-pdb.a2m
partial PDB gets fragment 27 through 36 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
ARG    3   29
TYR    4    2
GLN    5   15
GLN    6   15
LYS    7   23
LEU    8    3
GLU    9   15
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pdo.184.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pdo.185.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pdo.185.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pdo.185.3.a2m \
	-target T0124 -template 1pdo \
	-out T0124-1pdo.185.3 -outdir und
Skipped atom 473, because occupancy 0.59 <= existing 0.670001
Skipped atom 475, because occupancy 0.59 <= existing 0.670001
Skipped atom 477, because occupancy 0.59 <= existing 0.670001
Skipped atom 479, because occupancy 0.59 <= existing 0.670001
Skipped atom 940, because occupancy 0.36 <= existing 0.600001
Skipped atom 942, because occupancy 0.36 <= existing 0.600001
Skipped atom 944, because occupancy 0.36 <= existing 0.600001
Skipped atom 946, because occupancy 0.36 <= existing 0.600001
Skipped atom 948, because occupancy 0.36 <= existing 0.600001
Skipped atom 950, because occupancy 0.36 <= existing 0.600001
Skipped atom 952, because occupancy 0.36 <= existing 0.600001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pdo-orig.a2m
Writing a2m file: tmp/1pdo-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22973


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22973/tmp -alignfile tmp/1pdo-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pdo-orig.a2m (1 sequences, 135 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22973/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22973/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22973/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22973/tmp.a2m (1 sequences, 135 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22973/tmp.mod tmp/1pdo-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22973 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pdo-align.mod
tmp/1pdo-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22973/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pdo-orig.a2m tmp/1pdo-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pdo-align.mod
Running w0.5 tmp/1pdo-orig.a2m tmp/1pdo-align.mod
Running align2model tmp/1pdo-align -i tmp/1pdo-align.mod -db tmp/1pdo-orig.a2m -db tmp/1pdo-pdb.a2m
partial PDB gets fragment 26 through 36 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   26
TYR    3    2
GLN    4   13
GLN    5   12
LYS    6   28
LEU    7    5
GLU    8   14
GLU    9   13
LYS   10   24
GLN   11   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pdo.185.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pdo.187.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pdo.187.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pdo.187.4.a2m \
	-target T0124 -template 1pdo \
	-out T0124-1pdo.187.4 -outdir und
Skipped atom 473, because occupancy 0.59 <= existing 0.670001
Skipped atom 475, because occupancy 0.59 <= existing 0.670001
Skipped atom 477, because occupancy 0.59 <= existing 0.670001
Skipped atom 479, because occupancy 0.59 <= existing 0.670001
Skipped atom 940, because occupancy 0.36 <= existing 0.600001
Skipped atom 942, because occupancy 0.36 <= existing 0.600001
Skipped atom 944, because occupancy 0.36 <= existing 0.600001
Skipped atom 946, because occupancy 0.36 <= existing 0.600001
Skipped atom 948, because occupancy 0.36 <= existing 0.600001
Skipped atom 950, because occupancy 0.36 <= existing 0.600001
Skipped atom 952, because occupancy 0.36 <= existing 0.600001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pdo-orig.a2m
Writing a2m file: tmp/1pdo-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7046


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7046/tmp -alignfile tmp/1pdo-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pdo-orig.a2m (1 sequences, 135 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7046/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7046/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7046/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7046/tmp.a2m (1 sequences, 135 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7046/tmp.mod tmp/1pdo-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7046 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pdo-align.mod
tmp/1pdo-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7046/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pdo-orig.a2m tmp/1pdo-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pdo-align.mod
Running w0.5 tmp/1pdo-orig.a2m tmp/1pdo-align.mod
Running align2model tmp/1pdo-align -i tmp/1pdo-align.mod -db tmp/1pdo-orig.a2m -db tmp/1pdo-pdb.a2m
partial PDB gets fragment 26 through 35 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
GLN    2   11
GLN    3    7
LYS    4   29
LEU    5    3
GLU    6   14
GLU    7   15
LYS    8   23
GLN    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pdo.187.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pmi.137.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pmi.137.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pmi.137.4.a2m \
	-target T0124 -template 1pmi \
	-out T0124-1pmi.137.4 -outdir und
partial PDB gets fragment 53 through 62 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   15
LYS    4   25
ARG    5   27
LEU    6    3
ASP    7    4
ARG    8   27
ILE    9    5
GLN   10    7
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pmi.137.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pmi.138.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pmi.138.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pmi.138.3.a2m \
	-target T0124 -template 1pmi \
	-out T0124-1pmi.138.3 -outdir und
partial PDB gets fragment 52 through 61 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
LYS    3   30
ARG    4   30
LEU    5    3
ASP    6    5
ARG    7   27
ILE    8    4
GLN    9   12
VAL   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pmi.138.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pmi.139.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pmi.139.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pmi.139.3.a2m \
	-target T0124 -template 1pmi \
	-out T0124-1pmi.139.3 -outdir und
partial PDB gets fragment 51 through 60 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   27
ARG    3   32
LEU    4    3
ASP    5    2
ARG    6   30
ILE    7    2
GLN    8   13
VAL    9    1
MET   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pmi.139.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.203.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.203.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.203.4.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.203.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13623


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13623/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13623/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13623/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13623/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13623/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13623/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13623 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13623/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 10 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   15
GLU    2   12
LYS    3   23
GLU    4   12
GLN    6   13
LEU    7    3
GLN    8   13
GLN    9   15
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.203.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.203.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.203.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.203.5.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.203.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8748


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8748/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8748/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8748/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8748/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8748/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8748/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8748 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8748/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 12 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   11
GLU    2   12
LYS    3   27
GLU    4   13
GLN    6   13
LEU    7    4
GLN    8   11
GLN    9   14
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.203.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.204.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.204.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.204.2.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.204.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8075


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8075/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8075/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8075/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8075/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8075/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8075/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8075 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8075/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 9 through 18 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
LYS    2   30
GLU    3   12
GLN    5   12
LEU    6    3
GLN    7   13
GLN    8   13
GLU    9   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.204.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.204.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.204.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.204.4.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.204.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3897


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3897/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3897/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3897/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3897/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3897/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3897/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3897 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3897/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 7 through 17 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
LYS    2   26
GLU    3   14
GLN    5   12
LEU    6    3
GLN    7   12
GLN    8   13
GLU    9   13
VAL   11    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.204.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.205.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.205.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.205.2.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.205.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2353


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2353/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2353/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2353/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2353/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2353/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2353/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2353 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2353/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 6 through 16 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
GLU    2   13
GLN    4   10
LEU    5    3
GLN    6   12
GLN    7   11
GLU    8   12
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.205.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.206.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.206.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.206.1.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.206.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6808


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6808/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6808/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6808/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6808/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6808/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6808/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6808 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6808/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 5 through 15 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
GLN    3   12
LEU    4    3
GLN    5   10
GLN    6   15
GLU    7   12
VAL    9    1
GLU   11   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.206.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.207.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.207.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.207.0.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.207.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8539


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8539/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8539/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8539/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8539/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8539/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8539/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8539 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8539/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 4 through 14 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    2   12
LEU    3    3
GLN    4   12
GLN    5   13
GLU    6   14
VAL    8    2
GLU   10   12
TYR   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4   12     16.9277
keepclash     6   12     57.3572
Cluster     1 =   4   6  12
3 clashing residues after turn 
Residue clashes:
4-6
4-12
6-12
cluster 1 has 3 members and 4.200e+01 combinations:
 12  4  6 
Energy     74.2850
Searching cluster 4
Combinations for 3 members in cluster 1 OK: 4.200e+01 - Sending to search
45.337418 < 74.284950: keeping 
28.409681 < 45.392143: keeping 
Solved cluster 1: residual clashing 28.69
Still clashes at these sidechain pairs:
ires=    6 irot=    2 jres=   12 jrot=    1      28.4097
Residual clashes =   28.40968
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.207.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.208.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.208.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.208.1.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.208.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1552


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1552/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1552/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1552/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1552/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1552/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1552/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1552 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1552/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 3 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
LEU    2    3
GLN    3   12
GLN    4   12
GLU    5   13
VAL    7    2
GLU    9   12
TYR   10    3
GLU   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.208.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.209.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.209.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.209.2.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.209.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30738


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30738/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30738/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30738/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30738/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30738/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30738/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30738 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30738/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 2 through 12 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
GLN    2   12
GLN    3   12
GLU    4   13
GLU    8   14
TYR    9    3
GLU   10   12
GLU   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.209.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.210.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.210.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.210.2.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.210.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-24820


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-24820/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-24820/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-24820/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-24820/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24820/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-24820/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-24820 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24820/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 1 through 11 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
GLN    2   13
VAL    5    1
GLU    7   13
TYR    8    3
GLU    9   14
LYS   11   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.210.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.211.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.211.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.211.3.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.211.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27343


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27343/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27343/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27343/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27343/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27343/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27343/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27343 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27343/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 0 through 10 extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    0   15
GLU    1   15
VAL    3    1
GLU    5   13
TYR    6    3
GLU    7   13
GLU    8   14
LYS    9   20
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.211.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.213.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.213.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.213.3.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.213.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14522


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14522/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14522/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14522/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14522/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14522/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14522/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14522 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14522/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 0 through 9 extending end
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
TYR    4    2
GLU    5   13
GLU    6   12
LYS    7   26
LEU    8    3
LYS    9   20
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.213.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pnkA.213.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pnkA.213.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pnkA.213.4.a2m \
	-target T0124 -template 1pnkA \
	-out T0124-1pnkA.213.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pnkA-orig.a2m
Writing a2m file: tmp/1pnkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9048


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9048/tmp -alignfile tmp/1pnkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pnkA-orig.a2m (1 sequences, 209 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9048/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9048/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9048/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9048/tmp.a2m (1 sequences, 209 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9048/tmp.mod tmp/1pnkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9048 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pnkA-align.mod
tmp/1pnkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9048/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pnkA-orig.a2m tmp/1pnkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pnkA-align.mod
Running w0.5 tmp/1pnkA-orig.a2m tmp/1pnkA-align.mod
Running align2model tmp/1pnkA-align -i tmp/1pnkA-align.mod -db tmp/1pnkA-orig.a2m -db tmp/1pnkA-pdb.a2m
partial PDB gets fragment 0 through 7 extending end
Debugging on !
Reading sequence file
Reading input structure 
9 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
TYR    2    3
GLU    4   11
LEU    6    3
LYS    7   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pnkA.213.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ppfE.49.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ppfE.49.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ppfE.49.5.a2m \
	-target T0124 -template 1ppfE \
	-out T0124-1ppfE.49.5 -outdir und
partial PDB gets fragment 201 through 210 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LEU    2    2
GLN    3   12
LYS    4   24
TYR    5    3
SER    6    2
VAL    7    3
LEU    8    2
PHE    9    3
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ppfE.49.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ppfE.50.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ppfE.50.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ppfE.50.4.a2m \
	-target T0124 -template 1ppfE \
	-out T0124-1ppfE.50.4 -outdir und
partial PDB gets fragment 200 through 209 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLN    2   13
LYS    3   24
TYR    4    3
SER    5    3
LEU    7    3
PHE    8    3
LEU    9    2
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   10     60.7268
Cluster     1 =   5  10
2 clashing residues after turn 
Residue clashes:
5-10
cluster 1 has 2 members and 6.000e+00 combinations:
 10  5 
Energy     60.7268
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 6.000e+00 - Sending to search
0.000000 < 60.726814: keeping 
Solved cluster 1: residual clashing  0.27
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ppfE.50.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ppfE.51.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ppfE.51.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ppfE.51.5.a2m \
	-target T0124 -template 1ppfE \
	-out T0124-1ppfE.51.5 -outdir und
partial PDB gets fragment 199 through 208 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
LYS    2   25
TYR    3    3
SER    4    3
VAL    5    1
LEU    6    3
PHE    7    3
LEU    8    3
GLU    9   14
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ppfE.51.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.203.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.203.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.203.3.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.203.3 -outdir und
partial PDB gets fragment 14 through 23 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
GLU    2   12
LYS    3   26
GLU    4   12
GLN    6   13
LEU    7    3
GLN    8   11
GLN    9   15
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.203.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.204.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.204.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.204.3.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.204.3 -outdir und
partial PDB gets fragment 13 through 22 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   11
LYS    2   30
GLU    3   12
GLN    5   12
LEU    6    3
GLN    7   13
GLN    8   13
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.204.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.205.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.205.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.205.1.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.205.1 -outdir und
partial PDB gets fragment 12 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
GLU    2   11
GLN    4   11
LEU    5    3
GLN    6   12
GLN    7   15
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.205.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.206.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.206.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.206.2.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.206.2 -outdir und
partial PDB gets fragment 11 through 22 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
GLN    3   13
LEU    4    3
GLN    5   11
GLN    6   12
GLU    7   12
VAL    9    2
GLU   11   12
TYR   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.206.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.206.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.206.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.206.5.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.206.5 -outdir und
partial PDB gets fragment 15 through 24 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
GLN    3   12
LEU    4    3
GLN    5   13
GLN    6   13
GLU    7   12
VAL    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.206.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.207.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.207.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.207.3.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.207.3 -outdir und
partial PDB gets fragment 10 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    2   12
LEU    3    3
GLN    4   13
GLN    5   14
GLU    6   12
VAL    8    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.207.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.208.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.208.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.208.4.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.208.4 -outdir und
partial PDB gets fragment 9 through 18 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
LEU    2    3
GLN    3   12
GLN    4   14
GLU    5   11
VAL    7    1
GLU    9   12
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.208.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.209.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.209.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.209.3.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.209.3 -outdir und
partial PDB gets fragment 12 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLN    2   13
GLN    3   14
GLU    4   12
VAL    6    1
TYR    9    3
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.209.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.210.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.210.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.210.4.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.210.4 -outdir und
partial PDB gets fragment 11 through 20 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLN    2   14
GLU    3   11
VAL    5    1
GLU    7   12
TYR    8    3
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.210.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.211.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.211.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.211.4.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.211.4 -outdir und
partial PDB gets fragment 10 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLU    2   12
VAL    4    3
GLU    6   12
TYR    7    3
GLU    8   12
GLU    9   15
LYS   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.211.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pprM.212.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pprM.212.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pprM.212.5.a2m \
	-target T0124 -template 1pprM \
	-out T0124-1pprM.212.5 -outdir und
partial PDB gets fragment 9 through 18 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
VAL    3    1
GLU    5   15
GLU    7   12
GLU    8   12
LYS    9   26
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pprM.212.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pszA.142.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pszA.142.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pszA.142.5.a2m \
	-target T0124 -template 1pszA \
	-out T0124-1pszA.142.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pszA-orig.a2m
Writing a2m file: tmp/1pszA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17202


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17202/tmp -alignfile tmp/1pszA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pszA-orig.a2m (1 sequences, 303 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17202/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17202/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17202/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17202/tmp.a2m (1 sequences, 303 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17202/tmp.mod tmp/1pszA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17202 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pszA-align.mod
tmp/1pszA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17202/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pszA-orig.a2m tmp/1pszA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pszA-align.mod
Running w0.5 tmp/1pszA-orig.a2m tmp/1pszA-align.mod
Running align2model tmp/1pszA-align -i tmp/1pszA-align.mod -db tmp/1pszA-orig.a2m -db tmp/1pszA-pdb.a2m
partial PDB gets fragment 59 through 68 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ASP    2    4
ARG    3   27
ILE    4    3
GLN    5   14
VAL    6    2
MET    7    6
MET    8   10
ARG    9   22
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pszA.142.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pszA.33.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pszA.33.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pszA.33.2.a2m \
	-target T0124 -template 1pszA \
	-out T0124-1pszA.33.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pszA-orig.a2m
Writing a2m file: tmp/1pszA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5496


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5496/tmp -alignfile tmp/1pszA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pszA-orig.a2m (1 sequences, 303 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5496/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5496/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5496/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5496/tmp.a2m (1 sequences, 303 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5496/tmp.mod tmp/1pszA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5496 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pszA-align.mod
tmp/1pszA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5496/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pszA-orig.a2m tmp/1pszA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pszA-align.mod
Running w0.5 tmp/1pszA-orig.a2m tmp/1pszA-align.mod
Running align2model tmp/1pszA-align -i tmp/1pszA-align.mod -db tmp/1pszA-orig.a2m -db tmp/1pszA-pdb.a2m
partial PDB gets fragment 274 through 283 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
GLU    2   12
LYS    4   28
GLU    5   12
LEU    6    3
GLU    7   12
ARG    8   27
LYS    9   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pszA.33.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pszA.34.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pszA.34.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pszA.34.4.a2m \
	-target T0124 -template 1pszA \
	-out T0124-1pszA.34.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pszA-orig.a2m
Writing a2m file: tmp/1pszA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8527


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8527/tmp -alignfile tmp/1pszA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pszA-orig.a2m (1 sequences, 303 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8527/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8527/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8527/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8527/tmp.a2m (1 sequences, 303 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8527/tmp.mod tmp/1pszA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8527 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pszA-align.mod
tmp/1pszA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8527/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pszA-orig.a2m tmp/1pszA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pszA-align.mod
Running w0.5 tmp/1pszA-orig.a2m tmp/1pszA-align.mod
Running align2model tmp/1pszA-align -i tmp/1pszA-align.mod -db tmp/1pszA-orig.a2m -db tmp/1pszA-pdb.a2m
partial PDB gets fragment 273 through 282 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    2    3
LYS    3   25
GLU    4   12
LEU    5    3
GLU    6   12
ARG    7   27
LYS    8   24
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.17848
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pszA.34.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pszA.35.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pszA.35.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pszA.35.3.a2m \
	-target T0124 -template 1pszA \
	-out T0124-1pszA.35.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pszA-orig.a2m
Writing a2m file: tmp/1pszA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-192


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-192/tmp -alignfile tmp/1pszA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pszA-orig.a2m (1 sequences, 303 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-192/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-192/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-192/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-192/tmp.a2m (1 sequences, 303 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-192/tmp.mod tmp/1pszA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-192 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pszA-align.mod
tmp/1pszA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-192/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pszA-orig.a2m tmp/1pszA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pszA-align.mod
Running w0.5 tmp/1pszA-orig.a2m tmp/1pszA-align.mod
Running align2model tmp/1pszA-align -i tmp/1pszA-align.mod -db tmp/1pszA-orig.a2m -db tmp/1pszA-pdb.a2m
partial PDB gets fragment 272 through 281 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    3   12
LEU    4    3
GLU    5   12
ARG    6   26
SER    9    3
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pszA.35.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pszA.36.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pszA.36.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pszA.36.3.a2m \
	-target T0124 -template 1pszA \
	-out T0124-1pszA.36.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pszA-orig.a2m
Writing a2m file: tmp/1pszA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7921


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7921/tmp -alignfile tmp/1pszA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pszA-orig.a2m (1 sequences, 303 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7921/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7921/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7921/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7921/tmp.a2m (1 sequences, 303 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7921/tmp.mod tmp/1pszA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7921 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pszA-align.mod
tmp/1pszA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7921/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pszA-orig.a2m tmp/1pszA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pszA-align.mod
Running w0.5 tmp/1pszA-orig.a2m tmp/1pszA-align.mod
Running align2model tmp/1pszA-align -i tmp/1pszA-align.mod -db tmp/1pszA-orig.a2m -db tmp/1pszA-pdb.a2m
partial PDB gets fragment 271 through 280 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
GLU    2   12
LEU    3    3
GLU    4   12
ARG    5   26
LYS    6   25
SER    8    3
LYS    9   26
ARG   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pszA.36.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1pszA.37.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1pszA.37.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1pszA.37.3.a2m \
	-target T0124 -template 1pszA \
	-out T0124-1pszA.37.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pszA-orig.a2m
Writing a2m file: tmp/1pszA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30459


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30459/tmp -alignfile tmp/1pszA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pszA-orig.a2m (1 sequences, 303 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30459/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30459/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30459/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30459/tmp.a2m (1 sequences, 303 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30459/tmp.mod tmp/1pszA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30459 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pszA-align.mod
tmp/1pszA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30459/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pszA-orig.a2m tmp/1pszA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pszA-align.mod
Running w0.5 tmp/1pszA-orig.a2m tmp/1pszA-align.mod
Running align2model tmp/1pszA-align -i tmp/1pszA-align.mod -db tmp/1pszA-orig.a2m -db tmp/1pszA-pdb.a2m
partial PDB gets fragment 270 through 279 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
LEU    2    3
GLU    3   12
ARG    4   26
LYS    5   24
SER    7    3
LYS    8   25
ARG    9   27
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1pszA.37.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qb7A.91.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qb7A.91.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qb7A.91.5.a2m \
	-target T0124 -template 1qb7A \
	-out T0124-1qb7A.91.5 -outdir und
Skipped atom 1087, because occupancy 0.5 <= existing 0.500001
Skipped atom 1089, because occupancy 0.5 <= existing 0.500001
Skipped atom 1091, because occupancy 0.5 <= existing 0.500001
Skipped atom 1146, because occupancy 0.5 <= existing 0.500001
Skipped atom 1148, because occupancy 0.5 <= existing 0.500001
Skipped atom 1150, because occupancy 0.5 <= existing 0.500001
Skipped atom 1278, because occupancy 0.5 <= existing 0.500001
Skipped atom 1280, because occupancy 0.5 <= existing 0.500001
Skipped atom 1282, because occupancy 0.5 <= existing 0.500001
Skipped atom 1284, because occupancy 0.5 <= existing 0.500001
Skipped atom 1441, because occupancy 0.5 <= existing 0.500001
Skipped atom 1443, because occupancy 0.5 <= existing 0.500001
Skipped atom 1445, because occupancy 0.5 <= existing 0.500001
Skipped atom 1447, because occupancy 0.5 <= existing 0.500001
Skipped atom 1589, because occupancy 0.5 <= existing 0.500001
Skipped atom 1626, because occupancy 0.5 <= existing 0.500001
Skipped atom 1628, because occupancy 0.5 <= existing 0.500001
Skipped atom 1630, because occupancy 0.5 <= existing 0.500001
Skipped atom 1786, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 94 through 104 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ILE    2    5
ARG    3   26
ARG    4   29
ARG    5   28
LYS    6   26
GLU    7   13
GLN    8   14
HIS    9    4
THR   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qb7A.91.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qd9A.60.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qd9A.60.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qd9A.60.0.a2m \
	-target T0124 -template 1qd9A \
	-out T0124-1qd9A.60.0 -outdir und
Skipped atom 598, because occupancy 0.23 <= existing 0.770001
Skipped atom 600, because occupancy 0.23 <= existing 0.770001
Skipped atom 602, because occupancy 0.23 <= existing 0.770001
partial PDB gets fragment 87 through 96 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
PRO    4    2
ARG    5   32
LEU    7    3
SER    9    2
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.96702
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qd9A.60.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qd9A.62.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qd9A.62.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qd9A.62.5.a2m \
	-target T0124 -template 1qd9A \
	-out T0124-1qd9A.62.5 -outdir und
Skipped atom 598, because occupancy 0.23 <= existing 0.770001
Skipped atom 600, because occupancy 0.23 <= existing 0.770001
Skipped atom 602, because occupancy 0.23 <= existing 0.770001
partial PDB gets fragment 83 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
PRO    2    2
ARG    3   27
LEU    5    3
ASP    6    4
SER    7    3
GLN    8   15
VAL    9    3
VAL   10    2
GLU   11   11
LEU   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    6.01170
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qd9A.62.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qd9A.63.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qd9A.63.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qd9A.63.4.a2m \
	-target T0124 -template 1qd9A \
	-out T0124-1qd9A.63.4 -outdir und
Skipped atom 598, because occupancy 0.23 <= existing 0.770001
Skipped atom 600, because occupancy 0.23 <= existing 0.770001
Skipped atom 602, because occupancy 0.23 <= existing 0.770001
partial PDB gets fragment 82 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
ARG    2   27
LEU    4    3
ASP    5    4
SER    6    3
GLN    7   12
VAL    8    2
VAL    9    3
GLU   10   15
LEU   11    2
LYS   12   22
GLU   13   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qd9A.63.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qd9A.66.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qd9A.66.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qd9A.66.3.a2m \
	-target T0124 -template 1qd9A \
	-out T0124-1qd9A.66.3 -outdir und
Skipped atom 598, because occupancy 0.23 <= existing 0.770001
Skipped atom 600, because occupancy 0.23 <= existing 0.770001
Skipped atom 602, because occupancy 0.23 <= existing 0.770001
partial PDB gets fragment 83 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ASP    2    4
SER    3    3
GLN    4   12
VAL    5    1
GLU    7   13
LEU    8    3
LYS    9   30
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qd9A.66.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qd9A.68.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qd9A.68.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qd9A.68.4.a2m \
	-target T0124 -template 1qd9A \
	-out T0124-1qd9A.68.4 -outdir und
Skipped atom 598, because occupancy 0.23 <= existing 0.770001
Skipped atom 600, because occupancy 0.23 <= existing 0.770001
Skipped atom 602, because occupancy 0.23 <= existing 0.770001
partial PDB gets fragment 81 through 90 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
GLN    2   11
VAL    3    1
VAL    4    2
GLU    5   12
LEU    6    3
LYS    7   26
GLU    8   12
ARG    9   29
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qd9A.68.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qg8A.3.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qg8A.3.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qg8A.3.4.a2m \
	-target T0124 -template 1qg8A \
	-out T0124-1qg8A.3.4 -outdir und
Skipped atom 162, because occupancy 0.5 <= existing 0.500001
Skipped atom 317, because occupancy 0.5 <= existing 0.500001
Skipped atom 585, because occupancy 0.5 <= existing 0.500001
Skipped atom 587, because occupancy 0.5 <= existing 0.500001
Skipped atom 589, because occupancy 0.5 <= existing 0.500001
Skipped atom 591, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 673, because occupancy 0.5 <= existing 0.500001
Skipped atom 675, because occupancy 0.5 <= existing 0.500001
Skipped atom 677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1037, because occupancy 0.5 <= existing 0.500001
Skipped atom 1039, because occupancy 0.5 <= existing 0.500001
Skipped atom 1041, because occupancy 0.5 <= existing 0.500001
Skipped atom 1043, because occupancy 0.5 <= existing 0.500001
Skipped atom 1932, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qg8A-orig.a2m
Writing a2m file: tmp/1qg8A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4822


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4822/tmp -alignfile tmp/1qg8A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qg8A-orig.a2m (1 sequences, 255 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4822/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4822/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4822/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4822/tmp.a2m (1 sequences, 255 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4822/tmp.mod tmp/1qg8A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4822 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qg8A-align.mod
tmp/1qg8A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4822/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qg8A-orig.a2m tmp/1qg8A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qg8A-align.mod
Running w0.5 tmp/1qg8A-orig.a2m tmp/1qg8A-align.mod
Running align2model tmp/1qg8A-align -i tmp/1qg8A-align.mod -db tmp/1qg8A-orig.a2m -db tmp/1qg8A-pdb.a2m
partial PDB gets fragment 228 through 237 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
VAL    2    2
THR    3    2
GLN    4   12
LEU    5    3
PRO    6    2
GLU    7   12
PRO    8    2
GLN    9   13
THR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qg8A.3.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qg8A.5.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qg8A.5.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qg8A.5.0.a2m \
	-target T0124 -template 1qg8A \
	-out T0124-1qg8A.5.0 -outdir und
Skipped atom 162, because occupancy 0.5 <= existing 0.500001
Skipped atom 317, because occupancy 0.5 <= existing 0.500001
Skipped atom 585, because occupancy 0.5 <= existing 0.500001
Skipped atom 587, because occupancy 0.5 <= existing 0.500001
Skipped atom 589, because occupancy 0.5 <= existing 0.500001
Skipped atom 591, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 673, because occupancy 0.5 <= existing 0.500001
Skipped atom 675, because occupancy 0.5 <= existing 0.500001
Skipped atom 677, because occupancy 0.5 <= existing 0.500001
Skipped atom 1037, because occupancy 0.5 <= existing 0.500001
Skipped atom 1039, because occupancy 0.5 <= existing 0.500001
Skipped atom 1041, because occupancy 0.5 <= existing 0.500001
Skipped atom 1043, because occupancy 0.5 <= existing 0.500001
Skipped atom 1932, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qg8A-orig.a2m
Writing a2m file: tmp/1qg8A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4090


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4090/tmp -alignfile tmp/1qg8A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qg8A-orig.a2m (1 sequences, 255 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4090/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4090/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4090/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4090/tmp.a2m (1 sequences, 255 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4090/tmp.mod tmp/1qg8A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4090 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qg8A-align.mod
tmp/1qg8A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4090/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qg8A-orig.a2m tmp/1qg8A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qg8A-align.mod
Running w0.5 tmp/1qg8A-orig.a2m tmp/1qg8A-align.mod
Running align2model tmp/1qg8A-align -i tmp/1qg8A-align.mod -db tmp/1qg8A-orig.a2m -db tmp/1qg8A-pdb.a2m
partial PDB gets fragment 228 through 237 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
GLN    2   12
LEU    3    3
PRO    4    2
GLU    5   12
PRO    6    2
GLN    7   12
THR    8    2
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qg8A.5.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.104.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.104.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.104.1.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.104.1 -outdir und
partial PDB gets fragment 88 through 100 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
THR    1    1
LYS    3   27
ILE    4    5
THR    5    2
GLU    6   15
LEU    7    4
ARG    9   28
GLU   10   12
LYS   11   24
GLN   12   12
ILE   13    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.104.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.104.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.104.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.104.3.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.104.3 -outdir und
partial PDB gets fragment 86 through 98 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
ILE    4    2
THR    5    2
GLU    6   15
LEU    7    3
ARG    9   30
GLU   10   12
LYS   11   26
GLN   12   12
ILE   13    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    5     15.2316
Cluster     1 =   4   5
2 clashing residues after turn 
Residue clashes:
4-5
cluster 1 has 2 members and 0.000e+00 combinations:
 4  5 
Energy     15.2316
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
Solved cluster 1: residual clashing 15.23
Still clashes at these sidechain pairs:
ires=    4 irot=    1 jres=    5 jrot=    1      15.2316
Residual clashes =   24.44932
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.104.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.105.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.105.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.105.1.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.105.1 -outdir und
partial PDB gets fragment 85 through 98 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
16 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   25
ILE    3    5
THR    4    1
GLU    5   13
LEU    6    3
ARG    8   22
GLU    9   15
LYS   10   28
GLN   11   12
ILE   12    3
GLU   14   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue L 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 15 rotamers of residue E 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.105.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.105.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.105.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.105.4.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.105.4 -outdir und
partial PDB gets fragment 91 through 100 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   23
ILE    3    5
THR    4    2
GLU    5   12
LEU    6    3
ARG    8   26
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.105.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.106.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.106.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.106.0.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.106.0 -outdir und
partial PDB gets fragment 84 through 97 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
16 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
ILE    2    3
THR    3    2
GLU    4   15
LEU    5    2
ARG    7   27
GLU    8   15
LYS    9   23
GLN   10   14
ILE   11    3
GLU   13   13
LEU   14    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue I 3 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 14 rotamers of residue Q 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue L 15 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4   11     24.8583
Cluster     1 =   4  11
2 clashing residues after turn 
Residue clashes:
4-11
cluster 1 has 2 members and 1.400e+01 combinations:
 4  11 
Energy     70.7204
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 1.400e+01 - Sending to search
4.862169 < 70.720421: keeping 
Solved cluster 1: residual clashing 15.32
Still clashes at these sidechain pairs:
Residual clashes =   17.12841
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.106.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.107.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.107.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.107.1.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.107.1 -outdir und
partial PDB gets fragment 83 through 95 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
THR    2    2
GLU    3   12
LEU    4    3
ARG    6   30
GLU    7   13
LYS    8   27
GLN    9   13
ILE   10    3
GLU   12   14
LEU   13    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    9     98.4767
Cluster     1 =   4   9
2 clashing residues after turn 
Residue clashes:
4-9
cluster 1 has 2 members and 2.200e+01 combinations:
 4  9 
Energy    101.8616
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 2.200e+01 - Sending to search
98.476685 < 101.861557: keeping 
0.000000 < 101.861549: keeping 
Solved cluster 1: residual clashing  2.66
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.107.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.108.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.108.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.108.1.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.108.1 -outdir und
partial PDB gets fragment 82 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
GLU    2   12
LEU    3    3
ARG    5   26
GLU    6   15
GLN    8   11
ILE    9    3
GLU   11   14
LEU   12    3
LYS   13   28
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue L 13 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   13     10.0700
Cluster     1 =   6  13
2 clashing residues after turn 
Residue clashes:
6-13
cluster 1 has 2 members and 3.900e+01 combinations:
 13  6 
Energy    115.4225
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 3.900e+01 - Sending to search
0.000000 < 115.422485: keeping 
11.928091 < 113.341759: keeping 
11.101041 < 81.737518: keeping 
Solved cluster 1: residual clashing 81.14
Still clashes at these sidechain pairs:
ires=    6 irot=    4 jres=   13 jrot=    3      11.1010
Residual clashes =   14.05493
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.108.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.109.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.109.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.109.3.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.109.3 -outdir und
partial PDB gets fragment 81 through 93 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    2    3
ARG    4   28
GLU    5   12
LYS    6   25
GLN    7   14
ILE    8    3
GLU   10   13
LEU   11    3
LYS   12   23
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue I 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   11    102.6418
Cluster     1 =   6  11
2 clashing residues after turn 
Residue clashes:
6-11
cluster 1 has 2 members and 1.000e+01 combinations:
 6  11 
Energy    107.6971
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 1.000e+01 - Sending to search
102.641754 < 107.697105: keeping 
0.000000 < 107.697098: keeping 
Solved cluster 1: residual clashing  2.49
Still clashes at these sidechain pairs:
Residual clashes =    1.01734
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.109.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.110.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.110.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.110.3.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.110.3 -outdir und
partial PDB gets fragment 80 through 90 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    3   27
GLU    4   12
LYS    5   26
GLN    6   12
ILE    7    2
GLU    9   13
LEU   10    2
LYS   11   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.110.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.111.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.111.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.111.3.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.111.3 -outdir und
partial PDB gets fragment 79 through 89 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   26
GLU    3   12
GLN    5   13
ILE    6    3
GLU    8   12
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.111.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.112.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.112.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.112.5.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.112.5 -outdir und
partial PDB gets fragment 78 through 88 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
GLU    2   12
LYS    3   24
GLN    4   12
ILE    5    3
GLU    7   13
LEU    8    3
LYS    9   25
LEU   11    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.112.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.113.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.113.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.113.3.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.113.3 -outdir und
partial PDB gets fragment 83 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    2   26
GLN    3   12
ILE    4    2
GLU    6   13
LEU    7    2
LYS    8   27
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.113.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.114.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.114.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.114.2.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.114.2 -outdir und
partial PDB gets fragment 78 through 87 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
GLN    2   12
ILE    3    2
GLU    5   12
LEU    6    3
LYS    7   26
LEU    9    3
LYS   10   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.114.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.115.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.115.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.115.2.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.115.2 -outdir und
partial PDB gets fragment 77 through 86 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
ILE    2    3
GLU    4   12
LEU    5    3
LEU    8    3
LYS    9   26
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.115.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.116.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.116.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.116.3.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.116.3 -outdir und
partial PDB gets fragment 76 through 85 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
GLU    3   12
LEU    4    3
LYS    5   24
LEU    7    3
LYS    8   26
GLU    9   12
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.116.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.116.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.116.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.116.5.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.116.5 -outdir und
partial PDB gets fragment 80 through 89 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
GLU    3   12
LEU    4    3
LYS    5   26
LEU    7    3
LYS    8   30
GLU    9   13
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.116.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qgiA.164.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qgiA.164.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qgiA.164.1.a2m \
	-target T0124 -template 1qgiA \
	-out T0124-1qgiA.164.1 -outdir und
partial PDB gets fragment 37 through 46 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
ILE    2    3
ASN    3    4
ASN    4    5
SER    5    3
HIS    6    4
GLN    8   11
GLU    9   12
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2   10     76.6037
Cluster     1 =   2  10
2 clashing residues after turn 
Residue clashes:
2-10
cluster 1 has 2 members and 8.400e+01 combinations:
 10  2 
Energy     76.6037
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 8.400e+01 - Sending to search
71.719498 < 76.603729: keeping 
9.567717 < 72.316574: keeping 
4.590190 < 10.326617: keeping 
4.106361 < 6.409097: keeping 
0.000000 < 6.234734: keeping 
0.000000 < 2.415974: keeping 
Solved cluster 1: residual clashing  1.52
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qgiA.164.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qh3A.176.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qh3A.176.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qh3A.176.5.a2m \
	-target T0124 -template 1qh3A \
	-out T0124-1qh3A.176.5 -outdir und
partial PDB gets fragment 33 through 42 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
ILE    2    3
LYS    3   24
LEU    4    3
LEU    5    3
THR    6    1
GLU    7   12
LYS    8   26
THR    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qh3A.176.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qh3A.177.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qh3A.177.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qh3A.177.4.a2m \
	-target T0124 -template 1qh3A \
	-out T0124-1qh3A.177.4 -outdir und
partial PDB gets fragment 32 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
LYS    2   26
LEU    3    3
LEU    4    3
THR    5    1
GLU    6   12
LYS    7   24
THR    8    2
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qh3A.177.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qh3A.178.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qh3A.178.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qh3A.178.4.a2m \
	-target T0124 -template 1qh3A \
	-out T0124-1qh3A.178.4 -outdir und
partial PDB gets fragment 31 through 40 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
LEU    2    3
LEU    3    3
THR    4    2
GLU    5   12
LYS    6   24
THR    7    2
ARG    9   28
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qh3A.178.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qh8A.1.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qh8A.1.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qh8A.1.4.a2m \
	-target T0124 -template 1qh8A \
	-out T0124-1qh8A.1.4 -outdir und
Skipped atom 369, because occupancy 0.5 <= existing 0.500001
Skipped atom 371, because occupancy 0.5 <= existing 0.500001
Skipped atom 776, because occupancy 0.5 <= existing 0.500001
Skipped atom 778, because occupancy 0.5 <= existing 0.500001
Skipped atom 974, because occupancy 0.5 <= existing 0.500001
Skipped atom 976, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 468 through 477 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
MET    1   11
LYS    2   28
GLU    3   13
VAL    4    1
THR    5    2
GLN    6   12
LEU    7    3
GLU    9   12
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue V 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.93660
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qh8A.1.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qh8A.2.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qh8A.2.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qh8A.2.3.a2m \
	-target T0124 -template 1qh8A \
	-out T0124-1qh8A.2.3 -outdir und
Skipped atom 369, because occupancy 0.5 <= existing 0.500001
Skipped atom 371, because occupancy 0.5 <= existing 0.500001
Skipped atom 776, because occupancy 0.5 <= existing 0.500001
Skipped atom 778, because occupancy 0.5 <= existing 0.500001
Skipped atom 974, because occupancy 0.5 <= existing 0.500001
Skipped atom 976, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 467 through 476 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   29
GLU    2   15
VAL    3    3
THR    4    1
GLN    5   11
PRO    7    2
GLU    8   15
GLN   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.36513
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qh8A.2.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qh8A.5.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qh8A.5.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qh8A.5.5.a2m \
	-target T0124 -template 1qh8A \
	-out T0124-1qh8A.5.5 -outdir und
Skipped atom 369, because occupancy 0.5 <= existing 0.500001
Skipped atom 371, because occupancy 0.5 <= existing 0.500001
Skipped atom 776, because occupancy 0.5 <= existing 0.500001
Skipped atom 778, because occupancy 0.5 <= existing 0.500001
Skipped atom 974, because occupancy 0.5 <= existing 0.500001
Skipped atom 976, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 468 through 477 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
GLN    2   15
LEU    3    2
PRO    4    2
GLU    5   12
PRO    6    2
GLN    7   15
THR    8    2
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qh8A.5.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qh8A.7.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qh8A.7.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qh8A.7.4.a2m \
	-target T0124 -template 1qh8A \
	-out T0124-1qh8A.7.4 -outdir und
Skipped atom 369, because occupancy 0.5 <= existing 0.500001
Skipped atom 371, because occupancy 0.5 <= existing 0.500001
Skipped atom 776, because occupancy 0.5 <= existing 0.500001
Skipped atom 778, because occupancy 0.5 <= existing 0.500001
Skipped atom 974, because occupancy 0.5 <= existing 0.500001
Skipped atom 976, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 466 through 475 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    3   13
PRO    4    2
GLN    5    9
THR    6    1
SER    8    3
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qh8A.7.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qhvA.114.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qhvA.114.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qhvA.114.4.a2m \
	-target T0124 -template 1qhvA \
	-out T0124-1qhvA.114.4 -outdir und
Skipped atom 434, because occupancy 0.4 <= existing 0.600001
Skipped atom 436, because occupancy 0.4 <= existing 0.600001
Skipped atom 499, because occupancy 0.5 <= existing 0.500001
Skipped atom 501, because occupancy 0.5 <= existing 0.500001
Skipped atom 1079, because occupancy 0.5 <= existing 0.500001
Skipped atom 1081, because occupancy 0.5 <= existing 0.500001
Skipped atom 1083, because occupancy 0.5 <= existing 0.500001
Skipped atom 1085, because occupancy 0.5 <= existing 0.500001
Skipped atom 1087, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1219, because occupancy 0.5 <= existing 0.500001
Skipped atom 1221, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 42 through 51 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   22
ILE    3    4
GLU    5   15
LEU    6    3
LYS    7   30
LEU    9    3
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qhvA.114.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qhvA.129.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qhvA.129.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qhvA.129.3.a2m \
	-target T0124 -template 1qhvA \
	-out T0124-1qhvA.129.3 -outdir und
Skipped atom 434, because occupancy 0.4 <= existing 0.600001
Skipped atom 436, because occupancy 0.4 <= existing 0.600001
Skipped atom 499, because occupancy 0.5 <= existing 0.500001
Skipped atom 501, because occupancy 0.5 <= existing 0.500001
Skipped atom 1079, because occupancy 0.5 <= existing 0.500001
Skipped atom 1081, because occupancy 0.5 <= existing 0.500001
Skipped atom 1083, because occupancy 0.5 <= existing 0.500001
Skipped atom 1085, because occupancy 0.5 <= existing 0.500001
Skipped atom 1087, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1219, because occupancy 0.5 <= existing 0.500001
Skipped atom 1221, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 38 through 47 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
ILE    2    2
LYS    3   23
ASP    4    4
ILE    5    3
LYS    6   26
LYS    7   27
LYS    8   27
LEU    9    3
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    9     50.2673
Cluster     1 =   4   9
2 clashing residues after turn 
Residue clashes:
4-9
cluster 1 has 2 members and 5.200e+02 combinations:
 4  9 
Energy     50.2673
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 5.200e+02 - Sending to search
10.000000 < 50.267250: keeping 
0.000000 < 10.217809: keeping 
0.357077 < 1.532945: keeping 
0.000000 < 1.337774: keeping 
Solved cluster 1: residual clashing  1.20
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qhvA.129.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qhvA.130.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qhvA.130.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qhvA.130.3.a2m \
	-target T0124 -template 1qhvA \
	-out T0124-1qhvA.130.3 -outdir und
Skipped atom 434, because occupancy 0.4 <= existing 0.600001
Skipped atom 436, because occupancy 0.4 <= existing 0.600001
Skipped atom 499, because occupancy 0.5 <= existing 0.500001
Skipped atom 501, because occupancy 0.5 <= existing 0.500001
Skipped atom 1079, because occupancy 0.5 <= existing 0.500001
Skipped atom 1081, because occupancy 0.5 <= existing 0.500001
Skipped atom 1083, because occupancy 0.5 <= existing 0.500001
Skipped atom 1085, because occupancy 0.5 <= existing 0.500001
Skipped atom 1087, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1219, because occupancy 0.5 <= existing 0.500001
Skipped atom 1221, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 37 through 46 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
LYS    2   26
ASP    3    5
ILE    4    3
LYS    5   19
LYS    6   22
LYS    7   26
LEU    8    3
GLU    9   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qhvA.130.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qhvA.131.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qhvA.131.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qhvA.131.1.a2m \
	-target T0124 -template 1qhvA \
	-out T0124-1qhvA.131.1 -outdir und
Skipped atom 434, because occupancy 0.4 <= existing 0.600001
Skipped atom 436, because occupancy 0.4 <= existing 0.600001
Skipped atom 499, because occupancy 0.5 <= existing 0.500001
Skipped atom 501, because occupancy 0.5 <= existing 0.500001
Skipped atom 1079, because occupancy 0.5 <= existing 0.500001
Skipped atom 1081, because occupancy 0.5 <= existing 0.500001
Skipped atom 1083, because occupancy 0.5 <= existing 0.500001
Skipped atom 1085, because occupancy 0.5 <= existing 0.500001
Skipped atom 1087, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1219, because occupancy 0.5 <= existing 0.500001
Skipped atom 1221, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 36 through 45 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
ASP    2    4
ILE    3    2
LYS    5   28
LYS    6   19
LEU    7    2
GLU    8   14
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   11     50.1749
Cluster     1 =   6  11
2 clashing residues after turn 
Residue clashes:
6-11
cluster 1 has 2 members and 5.980e+02 combinations:
 6  11 
Energy     50.1749
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 5.980e+02 - Sending to search
10.000000 < 50.174896: keeping 
0.000000 < 10.217809: keeping 
0.390101 < 1.532945: keeping 
0.000000 < 1.370801: keeping 
Solved cluster 1: residual clashing  1.20
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qhvA.131.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qhvA.132.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qhvA.132.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qhvA.132.0.a2m \
	-target T0124 -template 1qhvA \
	-out T0124-1qhvA.132.0 -outdir und
Skipped atom 434, because occupancy 0.4 <= existing 0.600001
Skipped atom 436, because occupancy 0.4 <= existing 0.600001
Skipped atom 499, because occupancy 0.5 <= existing 0.500001
Skipped atom 501, because occupancy 0.5 <= existing 0.500001
Skipped atom 1079, because occupancy 0.5 <= existing 0.500001
Skipped atom 1081, because occupancy 0.5 <= existing 0.500001
Skipped atom 1083, because occupancy 0.5 <= existing 0.500001
Skipped atom 1085, because occupancy 0.5 <= existing 0.500001
Skipped atom 1087, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1219, because occupancy 0.5 <= existing 0.500001
Skipped atom 1221, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 35 through 44 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    3
ILE    2    2
LYS    3   27
LYS    4   26
LEU    6    3
GLU    7    8
LYS    9   26
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qhvA.132.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qhvA.133.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qhvA.133.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qhvA.133.0.a2m \
	-target T0124 -template 1qhvA \
	-out T0124-1qhvA.133.0 -outdir und
Skipped atom 434, because occupancy 0.4 <= existing 0.600001
Skipped atom 436, because occupancy 0.4 <= existing 0.600001
Skipped atom 499, because occupancy 0.5 <= existing 0.500001
Skipped atom 501, because occupancy 0.5 <= existing 0.500001
Skipped atom 1079, because occupancy 0.5 <= existing 0.500001
Skipped atom 1081, because occupancy 0.5 <= existing 0.500001
Skipped atom 1083, because occupancy 0.5 <= existing 0.500001
Skipped atom 1085, because occupancy 0.5 <= existing 0.500001
Skipped atom 1087, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1219, because occupancy 0.5 <= existing 0.500001
Skipped atom 1221, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 34 through 43 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
LYS    2   27
LYS    3   26
LYS    4   27
LEU    5    3
GLU    6   12
LYS    8   19
ARG    9   24
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qhvA.133.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qhvA.134.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qhvA.134.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qhvA.134.0.a2m \
	-target T0124 -template 1qhvA \
	-out T0124-1qhvA.134.0 -outdir und
Skipped atom 434, because occupancy 0.4 <= existing 0.600001
Skipped atom 436, because occupancy 0.4 <= existing 0.600001
Skipped atom 499, because occupancy 0.5 <= existing 0.500001
Skipped atom 501, because occupancy 0.5 <= existing 0.500001
Skipped atom 1079, because occupancy 0.5 <= existing 0.500001
Skipped atom 1081, because occupancy 0.5 <= existing 0.500001
Skipped atom 1083, because occupancy 0.5 <= existing 0.500001
Skipped atom 1085, because occupancy 0.5 <= existing 0.500001
Skipped atom 1087, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1219, because occupancy 0.5 <= existing 0.500001
Skipped atom 1221, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 33 through 42 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LYS    2   27
LYS    3   27
LEU    4    3
GLU    5   13
ARG    8   27
LEU    9    3
ASP   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qhvA.134.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qhvA.135.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qhvA.135.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qhvA.135.1.a2m \
	-target T0124 -template 1qhvA \
	-out T0124-1qhvA.135.1 -outdir und
Skipped atom 434, because occupancy 0.4 <= existing 0.600001
Skipped atom 436, because occupancy 0.4 <= existing 0.600001
Skipped atom 499, because occupancy 0.5 <= existing 0.500001
Skipped atom 501, because occupancy 0.5 <= existing 0.500001
Skipped atom 1079, because occupancy 0.5 <= existing 0.500001
Skipped atom 1081, because occupancy 0.5 <= existing 0.500001
Skipped atom 1083, because occupancy 0.5 <= existing 0.500001
Skipped atom 1085, because occupancy 0.5 <= existing 0.500001
Skipped atom 1087, because occupancy 0.5 <= existing 0.500001
Skipped atom 1188, because occupancy 0.5 <= existing 0.500001
Skipped atom 1190, because occupancy 0.5 <= existing 0.500001
Skipped atom 1219, because occupancy 0.5 <= existing 0.500001
Skipped atom 1221, because occupancy 0.5 <= existing 0.500001
partial PDB gets fragment 32 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   24
LEU    3    3
GLU    4   13
LYS    6   27
ARG    7   27
LEU    8    3
ASP    9    5
ARG   10   22
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qhvA.135.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qnf.38.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qnf.38.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qnf.38.5.a2m \
	-target T0124 -template 1qnf \
	-out T0124-1qnf.38.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qnf-orig.a2m
Writing a2m file: tmp/1qnf-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1047


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1047/tmp -alignfile tmp/1qnf-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qnf-orig.a2m (1 sequences, 484 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1047/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1047/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1047/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1047/tmp.a2m (1 sequences, 484 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1047/tmp.mod tmp/1qnf-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1047 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qnf-align.mod
tmp/1qnf-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1047/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qnf-orig.a2m tmp/1qnf-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qnf-align.mod
Running w0.5 tmp/1qnf-orig.a2m tmp/1qnf-align.mod
Running align2model tmp/1qnf-align -i tmp/1qnf-align.mod -db tmp/1qnf-orig.a2m -db tmp/1qnf-pdb.a2m
partial PDB gets fragment 462 through 471 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   12
ARG    3   27
LYS    4   24
SER    6    3
LYS    7   26
ARG    8   26
ARG    9   25
GLU   10   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qnf.38.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qq7A.123.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qq7A.123.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qq7A.123.2.a2m \
	-target T0124 -template 1qq7A \
	-out T0124-1qq7A.123.2 -outdir und
Skipped atom 192, because occupancy 0.5 <= existing 0.500001
Skipped atom 194, because occupancy 0.5 <= existing 0.500001
Skipped atom 196, because occupancy 0.5 <= existing 0.500001
Skipped atom 198, because occupancy 0.5 <= existing 0.500001
Skipped atom 200, because occupancy 0.5 <= existing 0.500001
Skipped atom 202, because occupancy 0.5 <= existing 0.500001
Skipped atom 204, because occupancy 0.5 <= existing 0.500001
Skipped atom 764, because occupancy 0.5 <= existing 0.500001
Skipped atom 766, because occupancy 0.5 <= existing 0.500001
Skipped atom 768, because occupancy 0.5 <= existing 0.500001
Skipped atom 883, because occupancy 0.5 <= existing 0.500001
Skipped atom 885, because occupancy 0.5 <= existing 0.500001
Skipped atom 887, because occupancy 0.5 <= existing 0.500001
Skipped atom 889, because occupancy 0.5 <= existing 0.500001
Skipped atom 891, because occupancy 0.5 <= existing 0.500001
Skipped atom 1207, because occupancy 0.5 <= existing 0.500001
Skipped atom 1209, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1360, because occupancy 0.5 <= existing 0.500001
Skipped atom 1460, because occupancy 0.5 <= existing 0.500001
Skipped atom 1462, because occupancy 0.5 <= existing 0.500001
Skipped atom 1620, because occupancy 0.5 <= existing 0.500001
Skipped atom 1622, because occupancy 0.5 <= existing 0.500001
Skipped atom 1624, because occupancy 0.5 <= existing 0.500001
Skipped atom 1626, because occupancy 0.5 <= existing 0.500001
Skipped atom 1628, because occupancy 0.5 <= existing 0.500001
Skipped atom 1630, because occupancy 0.5 <= existing 0.500001
Skipped atom 1632, because occupancy 0.5 <= existing 0.500001
Skipped atom 1634, because occupancy 0.5 <= existing 0.500001
Skipped atom 1636, because occupancy 0.5 <= existing 0.500001
Skipped atom 1638, because occupancy 0.5 <= existing 0.500001
Skipped atom 1640, because occupancy 0.5 <= existing 0.500001
Skipped atom 1642, because occupancy 0.5 <= existing 0.500001
Skipped atom 1644, because occupancy 0.5 <= existing 0.500001
Skipped atom 1646, because occupancy 0.5 <= existing 0.500001
Skipped atom 1648, because occupancy 0.5 <= existing 0.500001
Skipped atom 1650, because occupancy 0.5 <= existing 0.500001
Skipped atom 1652, because occupancy 0.5 <= existing 0.500001
Skipped atom 1654, because occupancy 0.5 <= existing 0.500001
Skipped atom 1656, because occupancy 0.5 <= existing 0.500001
Skipped atom 1658, because occupancy 0.5 <= existing 0.500001
Skipped atom 1660, because occupancy 0.5 <= existing 0.500001
Skipped atom 1662, because occupancy 0.5 <= existing 0.500001
Skipped atom 1664, because occupancy 0.5 <= existing 0.500001
Skipped atom 1666, because occupancy 0.5 <= existing 0.500001
Skipped atom 1668, because occupancy 0.5 <= existing 0.500001
Skipped atom 1670, because occupancy 0.5 <= existing 0.500001
Skipped atom 1672, because occupancy 0.5 <= existing 0.500001
Skipped atom 1674, because occupancy 0.5 <= existing 0.500001
Skipped atom 1676, because occupancy 0.5 <= existing 0.500001
Skipped atom 1678, because occupancy 0.5 <= existing 0.500001
Skipped atom 1680, because occupancy 0.5 <= existing 0.500001
Skipped atom 1682, because occupancy 0.5 <= existing 0.500001
Skipped atom 1684, because occupancy 0.5 <= existing 0.500001
Skipped atom 1686, because occupancy 0.5 <= existing 0.500001
Skipped atom 1688, because occupancy 0.5 <= existing 0.500001
Skipped atom 1690, because occupancy 0.5 <= existing 0.500001
Skipped atom 1692, because occupancy 0.5 <= existing 0.500001
Skipped atom 1694, because occupancy 0.5 <= existing 0.500001
Skipped atom 1696, because occupancy 0.5 <= existing 0.500001
Skipped atom 1698, because occupancy 0.5 <= existing 0.500001
Skipped atom 1700, because occupancy 0.5 <= existing 0.500001
Skipped atom 1702, because occupancy 0.5 <= existing 0.500001
Skipped atom 1704, because occupancy 0.5 <= existing 0.500001
Skipped atom 1706, because occupancy 0.5 <= existing 0.500001
Skipped atom 1708, because occupancy 0.5 <= existing 0.500001
Skipped atom 1710, because occupancy 0.5 <= existing 0.500001
Skipped atom 1749, because occupancy 0.5 <= existing 0.500001
Skipped atom 1751, because occupancy 0.5 <= existing 0.500001
Skipped atom 1753, because occupancy 0.5 <= existing 0.500001
Skipped atom 1755, because occupancy 0.5 <= existing 0.500001
Skipped atom 1790, because occupancy 0.5 <= existing 0.500001
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1817, because occupancy 0.5 <= existing 0.500001
Skipped atom 1819, because occupancy 0.5 <= existing 0.500001
Skipped atom 1821, because occupancy 0.5 <= existing 0.500001
Skipped atom 1823, because occupancy 0.5 <= existing 0.500001
Skipped atom 1825, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qq7A-orig.a2m
Writing a2m file: tmp/1qq7A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6914


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6914/tmp -alignfile tmp/1qq7A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qq7A-orig.a2m (1 sequences, 253 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6914/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6914/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6914/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6914/tmp.a2m (1 sequences, 253 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6914/tmp.mod tmp/1qq7A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6914 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qq7A-align.mod
tmp/1qq7A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6914/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qq7A-orig.a2m tmp/1qq7A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qq7A-align.mod
Running w0.5 tmp/1qq7A-orig.a2m tmp/1qq7A-align.mod
Running align2model tmp/1qq7A-align -i tmp/1qq7A-align.mod -db tmp/1qq7A-orig.a2m -db tmp/1qq7A-pdb.a2m
partial PDB gets fragment 76 through 85 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
SER    4    3
GLU    5   12
SER    6    3
ASN    7    5
ILE    8    3
LYS    9   31
ASP   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.34051
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qq7A.123.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qq7A.124.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qq7A.124.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qq7A.124.3.a2m \
	-target T0124 -template 1qq7A \
	-out T0124-1qq7A.124.3 -outdir und
Skipped atom 192, because occupancy 0.5 <= existing 0.500001
Skipped atom 194, because occupancy 0.5 <= existing 0.500001
Skipped atom 196, because occupancy 0.5 <= existing 0.500001
Skipped atom 198, because occupancy 0.5 <= existing 0.500001
Skipped atom 200, because occupancy 0.5 <= existing 0.500001
Skipped atom 202, because occupancy 0.5 <= existing 0.500001
Skipped atom 204, because occupancy 0.5 <= existing 0.500001
Skipped atom 764, because occupancy 0.5 <= existing 0.500001
Skipped atom 766, because occupancy 0.5 <= existing 0.500001
Skipped atom 768, because occupancy 0.5 <= existing 0.500001
Skipped atom 883, because occupancy 0.5 <= existing 0.500001
Skipped atom 885, because occupancy 0.5 <= existing 0.500001
Skipped atom 887, because occupancy 0.5 <= existing 0.500001
Skipped atom 889, because occupancy 0.5 <= existing 0.500001
Skipped atom 891, because occupancy 0.5 <= existing 0.500001
Skipped atom 1207, because occupancy 0.5 <= existing 0.500001
Skipped atom 1209, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1360, because occupancy 0.5 <= existing 0.500001
Skipped atom 1460, because occupancy 0.5 <= existing 0.500001
Skipped atom 1462, because occupancy 0.5 <= existing 0.500001
Skipped atom 1620, because occupancy 0.5 <= existing 0.500001
Skipped atom 1622, because occupancy 0.5 <= existing 0.500001
Skipped atom 1624, because occupancy 0.5 <= existing 0.500001
Skipped atom 1626, because occupancy 0.5 <= existing 0.500001
Skipped atom 1628, because occupancy 0.5 <= existing 0.500001
Skipped atom 1630, because occupancy 0.5 <= existing 0.500001
Skipped atom 1632, because occupancy 0.5 <= existing 0.500001
Skipped atom 1634, because occupancy 0.5 <= existing 0.500001
Skipped atom 1636, because occupancy 0.5 <= existing 0.500001
Skipped atom 1638, because occupancy 0.5 <= existing 0.500001
Skipped atom 1640, because occupancy 0.5 <= existing 0.500001
Skipped atom 1642, because occupancy 0.5 <= existing 0.500001
Skipped atom 1644, because occupancy 0.5 <= existing 0.500001
Skipped atom 1646, because occupancy 0.5 <= existing 0.500001
Skipped atom 1648, because occupancy 0.5 <= existing 0.500001
Skipped atom 1650, because occupancy 0.5 <= existing 0.500001
Skipped atom 1652, because occupancy 0.5 <= existing 0.500001
Skipped atom 1654, because occupancy 0.5 <= existing 0.500001
Skipped atom 1656, because occupancy 0.5 <= existing 0.500001
Skipped atom 1658, because occupancy 0.5 <= existing 0.500001
Skipped atom 1660, because occupancy 0.5 <= existing 0.500001
Skipped atom 1662, because occupancy 0.5 <= existing 0.500001
Skipped atom 1664, because occupancy 0.5 <= existing 0.500001
Skipped atom 1666, because occupancy 0.5 <= existing 0.500001
Skipped atom 1668, because occupancy 0.5 <= existing 0.500001
Skipped atom 1670, because occupancy 0.5 <= existing 0.500001
Skipped atom 1672, because occupancy 0.5 <= existing 0.500001
Skipped atom 1674, because occupancy 0.5 <= existing 0.500001
Skipped atom 1676, because occupancy 0.5 <= existing 0.500001
Skipped atom 1678, because occupancy 0.5 <= existing 0.500001
Skipped atom 1680, because occupancy 0.5 <= existing 0.500001
Skipped atom 1682, because occupancy 0.5 <= existing 0.500001
Skipped atom 1684, because occupancy 0.5 <= existing 0.500001
Skipped atom 1686, because occupancy 0.5 <= existing 0.500001
Skipped atom 1688, because occupancy 0.5 <= existing 0.500001
Skipped atom 1690, because occupancy 0.5 <= existing 0.500001
Skipped atom 1692, because occupancy 0.5 <= existing 0.500001
Skipped atom 1694, because occupancy 0.5 <= existing 0.500001
Skipped atom 1696, because occupancy 0.5 <= existing 0.500001
Skipped atom 1698, because occupancy 0.5 <= existing 0.500001
Skipped atom 1700, because occupancy 0.5 <= existing 0.500001
Skipped atom 1702, because occupancy 0.5 <= existing 0.500001
Skipped atom 1704, because occupancy 0.5 <= existing 0.500001
Skipped atom 1706, because occupancy 0.5 <= existing 0.500001
Skipped atom 1708, because occupancy 0.5 <= existing 0.500001
Skipped atom 1710, because occupancy 0.5 <= existing 0.500001
Skipped atom 1749, because occupancy 0.5 <= existing 0.500001
Skipped atom 1751, because occupancy 0.5 <= existing 0.500001
Skipped atom 1753, because occupancy 0.5 <= existing 0.500001
Skipped atom 1755, because occupancy 0.5 <= existing 0.500001
Skipped atom 1790, because occupancy 0.5 <= existing 0.500001
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1817, because occupancy 0.5 <= existing 0.500001
Skipped atom 1819, because occupancy 0.5 <= existing 0.500001
Skipped atom 1821, because occupancy 0.5 <= existing 0.500001
Skipped atom 1823, because occupancy 0.5 <= existing 0.500001
Skipped atom 1825, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qq7A-orig.a2m
Writing a2m file: tmp/1qq7A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6849


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6849/tmp -alignfile tmp/1qq7A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qq7A-orig.a2m (1 sequences, 253 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6849/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6849/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6849/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6849/tmp.a2m (1 sequences, 253 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6849/tmp.mod tmp/1qq7A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6849 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qq7A-align.mod
tmp/1qq7A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6849/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qq7A-orig.a2m tmp/1qq7A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qq7A-align.mod
Running w0.5 tmp/1qq7A-orig.a2m tmp/1qq7A-align.mod
Running align2model tmp/1qq7A-align -i tmp/1qq7A-align.mod -db tmp/1qq7A-orig.a2m -db tmp/1qq7A-pdb.a2m
partial PDB gets fragment 75 through 84 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
SER    2    2
SER    3    3
GLU    4   12
SER    5    3
ASN    6    4
ILE    7    3
LYS    8   25
ASP    9    4
ILE   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qq7A.124.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qq7A.125.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qq7A.125.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qq7A.125.4.a2m \
	-target T0124 -template 1qq7A \
	-out T0124-1qq7A.125.4 -outdir und
Skipped atom 192, because occupancy 0.5 <= existing 0.500001
Skipped atom 194, because occupancy 0.5 <= existing 0.500001
Skipped atom 196, because occupancy 0.5 <= existing 0.500001
Skipped atom 198, because occupancy 0.5 <= existing 0.500001
Skipped atom 200, because occupancy 0.5 <= existing 0.500001
Skipped atom 202, because occupancy 0.5 <= existing 0.500001
Skipped atom 204, because occupancy 0.5 <= existing 0.500001
Skipped atom 764, because occupancy 0.5 <= existing 0.500001
Skipped atom 766, because occupancy 0.5 <= existing 0.500001
Skipped atom 768, because occupancy 0.5 <= existing 0.500001
Skipped atom 883, because occupancy 0.5 <= existing 0.500001
Skipped atom 885, because occupancy 0.5 <= existing 0.500001
Skipped atom 887, because occupancy 0.5 <= existing 0.500001
Skipped atom 889, because occupancy 0.5 <= existing 0.500001
Skipped atom 891, because occupancy 0.5 <= existing 0.500001
Skipped atom 1207, because occupancy 0.5 <= existing 0.500001
Skipped atom 1209, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1360, because occupancy 0.5 <= existing 0.500001
Skipped atom 1460, because occupancy 0.5 <= existing 0.500001
Skipped atom 1462, because occupancy 0.5 <= existing 0.500001
Skipped atom 1620, because occupancy 0.5 <= existing 0.500001
Skipped atom 1622, because occupancy 0.5 <= existing 0.500001
Skipped atom 1624, because occupancy 0.5 <= existing 0.500001
Skipped atom 1626, because occupancy 0.5 <= existing 0.500001
Skipped atom 1628, because occupancy 0.5 <= existing 0.500001
Skipped atom 1630, because occupancy 0.5 <= existing 0.500001
Skipped atom 1632, because occupancy 0.5 <= existing 0.500001
Skipped atom 1634, because occupancy 0.5 <= existing 0.500001
Skipped atom 1636, because occupancy 0.5 <= existing 0.500001
Skipped atom 1638, because occupancy 0.5 <= existing 0.500001
Skipped atom 1640, because occupancy 0.5 <= existing 0.500001
Skipped atom 1642, because occupancy 0.5 <= existing 0.500001
Skipped atom 1644, because occupancy 0.5 <= existing 0.500001
Skipped atom 1646, because occupancy 0.5 <= existing 0.500001
Skipped atom 1648, because occupancy 0.5 <= existing 0.500001
Skipped atom 1650, because occupancy 0.5 <= existing 0.500001
Skipped atom 1652, because occupancy 0.5 <= existing 0.500001
Skipped atom 1654, because occupancy 0.5 <= existing 0.500001
Skipped atom 1656, because occupancy 0.5 <= existing 0.500001
Skipped atom 1658, because occupancy 0.5 <= existing 0.500001
Skipped atom 1660, because occupancy 0.5 <= existing 0.500001
Skipped atom 1662, because occupancy 0.5 <= existing 0.500001
Skipped atom 1664, because occupancy 0.5 <= existing 0.500001
Skipped atom 1666, because occupancy 0.5 <= existing 0.500001
Skipped atom 1668, because occupancy 0.5 <= existing 0.500001
Skipped atom 1670, because occupancy 0.5 <= existing 0.500001
Skipped atom 1672, because occupancy 0.5 <= existing 0.500001
Skipped atom 1674, because occupancy 0.5 <= existing 0.500001
Skipped atom 1676, because occupancy 0.5 <= existing 0.500001
Skipped atom 1678, because occupancy 0.5 <= existing 0.500001
Skipped atom 1680, because occupancy 0.5 <= existing 0.500001
Skipped atom 1682, because occupancy 0.5 <= existing 0.500001
Skipped atom 1684, because occupancy 0.5 <= existing 0.500001
Skipped atom 1686, because occupancy 0.5 <= existing 0.500001
Skipped atom 1688, because occupancy 0.5 <= existing 0.500001
Skipped atom 1690, because occupancy 0.5 <= existing 0.500001
Skipped atom 1692, because occupancy 0.5 <= existing 0.500001
Skipped atom 1694, because occupancy 0.5 <= existing 0.500001
Skipped atom 1696, because occupancy 0.5 <= existing 0.500001
Skipped atom 1698, because occupancy 0.5 <= existing 0.500001
Skipped atom 1700, because occupancy 0.5 <= existing 0.500001
Skipped atom 1702, because occupancy 0.5 <= existing 0.500001
Skipped atom 1704, because occupancy 0.5 <= existing 0.500001
Skipped atom 1706, because occupancy 0.5 <= existing 0.500001
Skipped atom 1708, because occupancy 0.5 <= existing 0.500001
Skipped atom 1710, because occupancy 0.5 <= existing 0.500001
Skipped atom 1749, because occupancy 0.5 <= existing 0.500001
Skipped atom 1751, because occupancy 0.5 <= existing 0.500001
Skipped atom 1753, because occupancy 0.5 <= existing 0.500001
Skipped atom 1755, because occupancy 0.5 <= existing 0.500001
Skipped atom 1790, because occupancy 0.5 <= existing 0.500001
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1817, because occupancy 0.5 <= existing 0.500001
Skipped atom 1819, because occupancy 0.5 <= existing 0.500001
Skipped atom 1821, because occupancy 0.5 <= existing 0.500001
Skipped atom 1823, because occupancy 0.5 <= existing 0.500001
Skipped atom 1825, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qq7A-orig.a2m
Writing a2m file: tmp/1qq7A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10158


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10158/tmp -alignfile tmp/1qq7A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qq7A-orig.a2m (1 sequences, 253 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10158/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10158/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10158/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10158/tmp.a2m (1 sequences, 253 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10158/tmp.mod tmp/1qq7A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10158 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qq7A-align.mod
tmp/1qq7A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10158/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qq7A-orig.a2m tmp/1qq7A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qq7A-align.mod
Running w0.5 tmp/1qq7A-orig.a2m tmp/1qq7A-align.mod
Running align2model tmp/1qq7A-align -i tmp/1qq7A-align.mod -db tmp/1qq7A-orig.a2m -db tmp/1qq7A-pdb.a2m
partial PDB gets fragment 74 through 83 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
SER    2    3
GLU    3   15
SER    4    3
ASN    5    4
ILE    6    3
LYS    7   25
ASP    8    4
ILE    9    2
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qq7A.125.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qq7A.126.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qq7A.126.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qq7A.126.4.a2m \
	-target T0124 -template 1qq7A \
	-out T0124-1qq7A.126.4 -outdir und
Skipped atom 192, because occupancy 0.5 <= existing 0.500001
Skipped atom 194, because occupancy 0.5 <= existing 0.500001
Skipped atom 196, because occupancy 0.5 <= existing 0.500001
Skipped atom 198, because occupancy 0.5 <= existing 0.500001
Skipped atom 200, because occupancy 0.5 <= existing 0.500001
Skipped atom 202, because occupancy 0.5 <= existing 0.500001
Skipped atom 204, because occupancy 0.5 <= existing 0.500001
Skipped atom 764, because occupancy 0.5 <= existing 0.500001
Skipped atom 766, because occupancy 0.5 <= existing 0.500001
Skipped atom 768, because occupancy 0.5 <= existing 0.500001
Skipped atom 883, because occupancy 0.5 <= existing 0.500001
Skipped atom 885, because occupancy 0.5 <= existing 0.500001
Skipped atom 887, because occupancy 0.5 <= existing 0.500001
Skipped atom 889, because occupancy 0.5 <= existing 0.500001
Skipped atom 891, because occupancy 0.5 <= existing 0.500001
Skipped atom 1207, because occupancy 0.5 <= existing 0.500001
Skipped atom 1209, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1360, because occupancy 0.5 <= existing 0.500001
Skipped atom 1460, because occupancy 0.5 <= existing 0.500001
Skipped atom 1462, because occupancy 0.5 <= existing 0.500001
Skipped atom 1620, because occupancy 0.5 <= existing 0.500001
Skipped atom 1622, because occupancy 0.5 <= existing 0.500001
Skipped atom 1624, because occupancy 0.5 <= existing 0.500001
Skipped atom 1626, because occupancy 0.5 <= existing 0.500001
Skipped atom 1628, because occupancy 0.5 <= existing 0.500001
Skipped atom 1630, because occupancy 0.5 <= existing 0.500001
Skipped atom 1632, because occupancy 0.5 <= existing 0.500001
Skipped atom 1634, because occupancy 0.5 <= existing 0.500001
Skipped atom 1636, because occupancy 0.5 <= existing 0.500001
Skipped atom 1638, because occupancy 0.5 <= existing 0.500001
Skipped atom 1640, because occupancy 0.5 <= existing 0.500001
Skipped atom 1642, because occupancy 0.5 <= existing 0.500001
Skipped atom 1644, because occupancy 0.5 <= existing 0.500001
Skipped atom 1646, because occupancy 0.5 <= existing 0.500001
Skipped atom 1648, because occupancy 0.5 <= existing 0.500001
Skipped atom 1650, because occupancy 0.5 <= existing 0.500001
Skipped atom 1652, because occupancy 0.5 <= existing 0.500001
Skipped atom 1654, because occupancy 0.5 <= existing 0.500001
Skipped atom 1656, because occupancy 0.5 <= existing 0.500001
Skipped atom 1658, because occupancy 0.5 <= existing 0.500001
Skipped atom 1660, because occupancy 0.5 <= existing 0.500001
Skipped atom 1662, because occupancy 0.5 <= existing 0.500001
Skipped atom 1664, because occupancy 0.5 <= existing 0.500001
Skipped atom 1666, because occupancy 0.5 <= existing 0.500001
Skipped atom 1668, because occupancy 0.5 <= existing 0.500001
Skipped atom 1670, because occupancy 0.5 <= existing 0.500001
Skipped atom 1672, because occupancy 0.5 <= existing 0.500001
Skipped atom 1674, because occupancy 0.5 <= existing 0.500001
Skipped atom 1676, because occupancy 0.5 <= existing 0.500001
Skipped atom 1678, because occupancy 0.5 <= existing 0.500001
Skipped atom 1680, because occupancy 0.5 <= existing 0.500001
Skipped atom 1682, because occupancy 0.5 <= existing 0.500001
Skipped atom 1684, because occupancy 0.5 <= existing 0.500001
Skipped atom 1686, because occupancy 0.5 <= existing 0.500001
Skipped atom 1688, because occupancy 0.5 <= existing 0.500001
Skipped atom 1690, because occupancy 0.5 <= existing 0.500001
Skipped atom 1692, because occupancy 0.5 <= existing 0.500001
Skipped atom 1694, because occupancy 0.5 <= existing 0.500001
Skipped atom 1696, because occupancy 0.5 <= existing 0.500001
Skipped atom 1698, because occupancy 0.5 <= existing 0.500001
Skipped atom 1700, because occupancy 0.5 <= existing 0.500001
Skipped atom 1702, because occupancy 0.5 <= existing 0.500001
Skipped atom 1704, because occupancy 0.5 <= existing 0.500001
Skipped atom 1706, because occupancy 0.5 <= existing 0.500001
Skipped atom 1708, because occupancy 0.5 <= existing 0.500001
Skipped atom 1710, because occupancy 0.5 <= existing 0.500001
Skipped atom 1749, because occupancy 0.5 <= existing 0.500001
Skipped atom 1751, because occupancy 0.5 <= existing 0.500001
Skipped atom 1753, because occupancy 0.5 <= existing 0.500001
Skipped atom 1755, because occupancy 0.5 <= existing 0.500001
Skipped atom 1790, because occupancy 0.5 <= existing 0.500001
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1817, because occupancy 0.5 <= existing 0.500001
Skipped atom 1819, because occupancy 0.5 <= existing 0.500001
Skipped atom 1821, because occupancy 0.5 <= existing 0.500001
Skipped atom 1823, because occupancy 0.5 <= existing 0.500001
Skipped atom 1825, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qq7A-orig.a2m
Writing a2m file: tmp/1qq7A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10051


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10051/tmp -alignfile tmp/1qq7A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qq7A-orig.a2m (1 sequences, 253 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10051/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10051/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10051/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10051/tmp.a2m (1 sequences, 253 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10051/tmp.mod tmp/1qq7A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10051 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qq7A-align.mod
tmp/1qq7A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10051/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qq7A-orig.a2m tmp/1qq7A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qq7A-align.mod
Running w0.5 tmp/1qq7A-orig.a2m tmp/1qq7A-align.mod
Running align2model tmp/1qq7A-align -i tmp/1qq7A-align.mod -db tmp/1qq7A-orig.a2m -db tmp/1qq7A-pdb.a2m
partial PDB gets fragment 77 through 86 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
GLU    2   12
SER    3    3
ASN    4    4
ILE    5    3
LYS    6   25
ASP    7    4
ILE    8    4
LYS    9   31
LYS   10   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qq7A.126.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qq7A.127.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qq7A.127.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qq7A.127.2.a2m \
	-target T0124 -template 1qq7A \
	-out T0124-1qq7A.127.2 -outdir und
Skipped atom 192, because occupancy 0.5 <= existing 0.500001
Skipped atom 194, because occupancy 0.5 <= existing 0.500001
Skipped atom 196, because occupancy 0.5 <= existing 0.500001
Skipped atom 198, because occupancy 0.5 <= existing 0.500001
Skipped atom 200, because occupancy 0.5 <= existing 0.500001
Skipped atom 202, because occupancy 0.5 <= existing 0.500001
Skipped atom 204, because occupancy 0.5 <= existing 0.500001
Skipped atom 764, because occupancy 0.5 <= existing 0.500001
Skipped atom 766, because occupancy 0.5 <= existing 0.500001
Skipped atom 768, because occupancy 0.5 <= existing 0.500001
Skipped atom 883, because occupancy 0.5 <= existing 0.500001
Skipped atom 885, because occupancy 0.5 <= existing 0.500001
Skipped atom 887, because occupancy 0.5 <= existing 0.500001
Skipped atom 889, because occupancy 0.5 <= existing 0.500001
Skipped atom 891, because occupancy 0.5 <= existing 0.500001
Skipped atom 1207, because occupancy 0.5 <= existing 0.500001
Skipped atom 1209, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1360, because occupancy 0.5 <= existing 0.500001
Skipped atom 1460, because occupancy 0.5 <= existing 0.500001
Skipped atom 1462, because occupancy 0.5 <= existing 0.500001
Skipped atom 1620, because occupancy 0.5 <= existing 0.500001
Skipped atom 1622, because occupancy 0.5 <= existing 0.500001
Skipped atom 1624, because occupancy 0.5 <= existing 0.500001
Skipped atom 1626, because occupancy 0.5 <= existing 0.500001
Skipped atom 1628, because occupancy 0.5 <= existing 0.500001
Skipped atom 1630, because occupancy 0.5 <= existing 0.500001
Skipped atom 1632, because occupancy 0.5 <= existing 0.500001
Skipped atom 1634, because occupancy 0.5 <= existing 0.500001
Skipped atom 1636, because occupancy 0.5 <= existing 0.500001
Skipped atom 1638, because occupancy 0.5 <= existing 0.500001
Skipped atom 1640, because occupancy 0.5 <= existing 0.500001
Skipped atom 1642, because occupancy 0.5 <= existing 0.500001
Skipped atom 1644, because occupancy 0.5 <= existing 0.500001
Skipped atom 1646, because occupancy 0.5 <= existing 0.500001
Skipped atom 1648, because occupancy 0.5 <= existing 0.500001
Skipped atom 1650, because occupancy 0.5 <= existing 0.500001
Skipped atom 1652, because occupancy 0.5 <= existing 0.500001
Skipped atom 1654, because occupancy 0.5 <= existing 0.500001
Skipped atom 1656, because occupancy 0.5 <= existing 0.500001
Skipped atom 1658, because occupancy 0.5 <= existing 0.500001
Skipped atom 1660, because occupancy 0.5 <= existing 0.500001
Skipped atom 1662, because occupancy 0.5 <= existing 0.500001
Skipped atom 1664, because occupancy 0.5 <= existing 0.500001
Skipped atom 1666, because occupancy 0.5 <= existing 0.500001
Skipped atom 1668, because occupancy 0.5 <= existing 0.500001
Skipped atom 1670, because occupancy 0.5 <= existing 0.500001
Skipped atom 1672, because occupancy 0.5 <= existing 0.500001
Skipped atom 1674, because occupancy 0.5 <= existing 0.500001
Skipped atom 1676, because occupancy 0.5 <= existing 0.500001
Skipped atom 1678, because occupancy 0.5 <= existing 0.500001
Skipped atom 1680, because occupancy 0.5 <= existing 0.500001
Skipped atom 1682, because occupancy 0.5 <= existing 0.500001
Skipped atom 1684, because occupancy 0.5 <= existing 0.500001
Skipped atom 1686, because occupancy 0.5 <= existing 0.500001
Skipped atom 1688, because occupancy 0.5 <= existing 0.500001
Skipped atom 1690, because occupancy 0.5 <= existing 0.500001
Skipped atom 1692, because occupancy 0.5 <= existing 0.500001
Skipped atom 1694, because occupancy 0.5 <= existing 0.500001
Skipped atom 1696, because occupancy 0.5 <= existing 0.500001
Skipped atom 1698, because occupancy 0.5 <= existing 0.500001
Skipped atom 1700, because occupancy 0.5 <= existing 0.500001
Skipped atom 1702, because occupancy 0.5 <= existing 0.500001
Skipped atom 1704, because occupancy 0.5 <= existing 0.500001
Skipped atom 1706, because occupancy 0.5 <= existing 0.500001
Skipped atom 1708, because occupancy 0.5 <= existing 0.500001
Skipped atom 1710, because occupancy 0.5 <= existing 0.500001
Skipped atom 1749, because occupancy 0.5 <= existing 0.500001
Skipped atom 1751, because occupancy 0.5 <= existing 0.500001
Skipped atom 1753, because occupancy 0.5 <= existing 0.500001
Skipped atom 1755, because occupancy 0.5 <= existing 0.500001
Skipped atom 1790, because occupancy 0.5 <= existing 0.500001
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1817, because occupancy 0.5 <= existing 0.500001
Skipped atom 1819, because occupancy 0.5 <= existing 0.500001
Skipped atom 1821, because occupancy 0.5 <= existing 0.500001
Skipped atom 1823, because occupancy 0.5 <= existing 0.500001
Skipped atom 1825, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qq7A-orig.a2m
Writing a2m file: tmp/1qq7A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-19812


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-19812/tmp -alignfile tmp/1qq7A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qq7A-orig.a2m (1 sequences, 253 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-19812/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-19812/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-19812/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19812/tmp.a2m (1 sequences, 253 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-19812/tmp.mod tmp/1qq7A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-19812 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qq7A-align.mod
tmp/1qq7A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19812/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qq7A-orig.a2m tmp/1qq7A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qq7A-align.mod
Running w0.5 tmp/1qq7A-orig.a2m tmp/1qq7A-align.mod
Running align2model tmp/1qq7A-align -i tmp/1qq7A-align.mod -db tmp/1qq7A-orig.a2m -db tmp/1qq7A-pdb.a2m
partial PDB gets fragment 76 through 85 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
SER    2    3
ASN    3    4
ILE    4    3
LYS    5   25
ASP    6    4
ILE    7    2
LYS    8   26
LYS    9   31
LYS   10   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.60379
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qq7A.127.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qq7A.128.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qq7A.128.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qq7A.128.2.a2m \
	-target T0124 -template 1qq7A \
	-out T0124-1qq7A.128.2 -outdir und
Skipped atom 192, because occupancy 0.5 <= existing 0.500001
Skipped atom 194, because occupancy 0.5 <= existing 0.500001
Skipped atom 196, because occupancy 0.5 <= existing 0.500001
Skipped atom 198, because occupancy 0.5 <= existing 0.500001
Skipped atom 200, because occupancy 0.5 <= existing 0.500001
Skipped atom 202, because occupancy 0.5 <= existing 0.500001
Skipped atom 204, because occupancy 0.5 <= existing 0.500001
Skipped atom 764, because occupancy 0.5 <= existing 0.500001
Skipped atom 766, because occupancy 0.5 <= existing 0.500001
Skipped atom 768, because occupancy 0.5 <= existing 0.500001
Skipped atom 883, because occupancy 0.5 <= existing 0.500001
Skipped atom 885, because occupancy 0.5 <= existing 0.500001
Skipped atom 887, because occupancy 0.5 <= existing 0.500001
Skipped atom 889, because occupancy 0.5 <= existing 0.500001
Skipped atom 891, because occupancy 0.5 <= existing 0.500001
Skipped atom 1207, because occupancy 0.5 <= existing 0.500001
Skipped atom 1209, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1360, because occupancy 0.5 <= existing 0.500001
Skipped atom 1460, because occupancy 0.5 <= existing 0.500001
Skipped atom 1462, because occupancy 0.5 <= existing 0.500001
Skipped atom 1620, because occupancy 0.5 <= existing 0.500001
Skipped atom 1622, because occupancy 0.5 <= existing 0.500001
Skipped atom 1624, because occupancy 0.5 <= existing 0.500001
Skipped atom 1626, because occupancy 0.5 <= existing 0.500001
Skipped atom 1628, because occupancy 0.5 <= existing 0.500001
Skipped atom 1630, because occupancy 0.5 <= existing 0.500001
Skipped atom 1632, because occupancy 0.5 <= existing 0.500001
Skipped atom 1634, because occupancy 0.5 <= existing 0.500001
Skipped atom 1636, because occupancy 0.5 <= existing 0.500001
Skipped atom 1638, because occupancy 0.5 <= existing 0.500001
Skipped atom 1640, because occupancy 0.5 <= existing 0.500001
Skipped atom 1642, because occupancy 0.5 <= existing 0.500001
Skipped atom 1644, because occupancy 0.5 <= existing 0.500001
Skipped atom 1646, because occupancy 0.5 <= existing 0.500001
Skipped atom 1648, because occupancy 0.5 <= existing 0.500001
Skipped atom 1650, because occupancy 0.5 <= existing 0.500001
Skipped atom 1652, because occupancy 0.5 <= existing 0.500001
Skipped atom 1654, because occupancy 0.5 <= existing 0.500001
Skipped atom 1656, because occupancy 0.5 <= existing 0.500001
Skipped atom 1658, because occupancy 0.5 <= existing 0.500001
Skipped atom 1660, because occupancy 0.5 <= existing 0.500001
Skipped atom 1662, because occupancy 0.5 <= existing 0.500001
Skipped atom 1664, because occupancy 0.5 <= existing 0.500001
Skipped atom 1666, because occupancy 0.5 <= existing 0.500001
Skipped atom 1668, because occupancy 0.5 <= existing 0.500001
Skipped atom 1670, because occupancy 0.5 <= existing 0.500001
Skipped atom 1672, because occupancy 0.5 <= existing 0.500001
Skipped atom 1674, because occupancy 0.5 <= existing 0.500001
Skipped atom 1676, because occupancy 0.5 <= existing 0.500001
Skipped atom 1678, because occupancy 0.5 <= existing 0.500001
Skipped atom 1680, because occupancy 0.5 <= existing 0.500001
Skipped atom 1682, because occupancy 0.5 <= existing 0.500001
Skipped atom 1684, because occupancy 0.5 <= existing 0.500001
Skipped atom 1686, because occupancy 0.5 <= existing 0.500001
Skipped atom 1688, because occupancy 0.5 <= existing 0.500001
Skipped atom 1690, because occupancy 0.5 <= existing 0.500001
Skipped atom 1692, because occupancy 0.5 <= existing 0.500001
Skipped atom 1694, because occupancy 0.5 <= existing 0.500001
Skipped atom 1696, because occupancy 0.5 <= existing 0.500001
Skipped atom 1698, because occupancy 0.5 <= existing 0.500001
Skipped atom 1700, because occupancy 0.5 <= existing 0.500001
Skipped atom 1702, because occupancy 0.5 <= existing 0.500001
Skipped atom 1704, because occupancy 0.5 <= existing 0.500001
Skipped atom 1706, because occupancy 0.5 <= existing 0.500001
Skipped atom 1708, because occupancy 0.5 <= existing 0.500001
Skipped atom 1710, because occupancy 0.5 <= existing 0.500001
Skipped atom 1749, because occupancy 0.5 <= existing 0.500001
Skipped atom 1751, because occupancy 0.5 <= existing 0.500001
Skipped atom 1753, because occupancy 0.5 <= existing 0.500001
Skipped atom 1755, because occupancy 0.5 <= existing 0.500001
Skipped atom 1790, because occupancy 0.5 <= existing 0.500001
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1817, because occupancy 0.5 <= existing 0.500001
Skipped atom 1819, because occupancy 0.5 <= existing 0.500001
Skipped atom 1821, because occupancy 0.5 <= existing 0.500001
Skipped atom 1823, because occupancy 0.5 <= existing 0.500001
Skipped atom 1825, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qq7A-orig.a2m
Writing a2m file: tmp/1qq7A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4334


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4334/tmp -alignfile tmp/1qq7A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qq7A-orig.a2m (1 sequences, 253 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4334/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4334/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4334/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4334/tmp.a2m (1 sequences, 253 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4334/tmp.mod tmp/1qq7A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4334 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qq7A-align.mod
tmp/1qq7A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4334/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qq7A-orig.a2m tmp/1qq7A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qq7A-align.mod
Running w0.5 tmp/1qq7A-orig.a2m tmp/1qq7A-align.mod
Running align2model tmp/1qq7A-align -i tmp/1qq7A-align.mod -db tmp/1qq7A-orig.a2m -db tmp/1qq7A-pdb.a2m
partial PDB gets fragment 75 through 84 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
ASN    2    5
ILE    3    4
LYS    4   24
ASP    5    4
ILE    6    2
LYS    7   26
LYS    8   25
LYS    9   26
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.65247
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qq7A.128.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qq7A.36.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qq7A.36.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qq7A.36.5.a2m \
	-target T0124 -template 1qq7A \
	-out T0124-1qq7A.36.5 -outdir und
Skipped atom 192, because occupancy 0.5 <= existing 0.500001
Skipped atom 194, because occupancy 0.5 <= existing 0.500001
Skipped atom 196, because occupancy 0.5 <= existing 0.500001
Skipped atom 198, because occupancy 0.5 <= existing 0.500001
Skipped atom 200, because occupancy 0.5 <= existing 0.500001
Skipped atom 202, because occupancy 0.5 <= existing 0.500001
Skipped atom 204, because occupancy 0.5 <= existing 0.500001
Skipped atom 764, because occupancy 0.5 <= existing 0.500001
Skipped atom 766, because occupancy 0.5 <= existing 0.500001
Skipped atom 768, because occupancy 0.5 <= existing 0.500001
Skipped atom 883, because occupancy 0.5 <= existing 0.500001
Skipped atom 885, because occupancy 0.5 <= existing 0.500001
Skipped atom 887, because occupancy 0.5 <= existing 0.500001
Skipped atom 889, because occupancy 0.5 <= existing 0.500001
Skipped atom 891, because occupancy 0.5 <= existing 0.500001
Skipped atom 1207, because occupancy 0.5 <= existing 0.500001
Skipped atom 1209, because occupancy 0.5 <= existing 0.500001
Skipped atom 1358, because occupancy 0.5 <= existing 0.500001
Skipped atom 1360, because occupancy 0.5 <= existing 0.500001
Skipped atom 1460, because occupancy 0.5 <= existing 0.500001
Skipped atom 1462, because occupancy 0.5 <= existing 0.500001
Skipped atom 1620, because occupancy 0.5 <= existing 0.500001
Skipped atom 1622, because occupancy 0.5 <= existing 0.500001
Skipped atom 1624, because occupancy 0.5 <= existing 0.500001
Skipped atom 1626, because occupancy 0.5 <= existing 0.500001
Skipped atom 1628, because occupancy 0.5 <= existing 0.500001
Skipped atom 1630, because occupancy 0.5 <= existing 0.500001
Skipped atom 1632, because occupancy 0.5 <= existing 0.500001
Skipped atom 1634, because occupancy 0.5 <= existing 0.500001
Skipped atom 1636, because occupancy 0.5 <= existing 0.500001
Skipped atom 1638, because occupancy 0.5 <= existing 0.500001
Skipped atom 1640, because occupancy 0.5 <= existing 0.500001
Skipped atom 1642, because occupancy 0.5 <= existing 0.500001
Skipped atom 1644, because occupancy 0.5 <= existing 0.500001
Skipped atom 1646, because occupancy 0.5 <= existing 0.500001
Skipped atom 1648, because occupancy 0.5 <= existing 0.500001
Skipped atom 1650, because occupancy 0.5 <= existing 0.500001
Skipped atom 1652, because occupancy 0.5 <= existing 0.500001
Skipped atom 1654, because occupancy 0.5 <= existing 0.500001
Skipped atom 1656, because occupancy 0.5 <= existing 0.500001
Skipped atom 1658, because occupancy 0.5 <= existing 0.500001
Skipped atom 1660, because occupancy 0.5 <= existing 0.500001
Skipped atom 1662, because occupancy 0.5 <= existing 0.500001
Skipped atom 1664, because occupancy 0.5 <= existing 0.500001
Skipped atom 1666, because occupancy 0.5 <= existing 0.500001
Skipped atom 1668, because occupancy 0.5 <= existing 0.500001
Skipped atom 1670, because occupancy 0.5 <= existing 0.500001
Skipped atom 1672, because occupancy 0.5 <= existing 0.500001
Skipped atom 1674, because occupancy 0.5 <= existing 0.500001
Skipped atom 1676, because occupancy 0.5 <= existing 0.500001
Skipped atom 1678, because occupancy 0.5 <= existing 0.500001
Skipped atom 1680, because occupancy 0.5 <= existing 0.500001
Skipped atom 1682, because occupancy 0.5 <= existing 0.500001
Skipped atom 1684, because occupancy 0.5 <= existing 0.500001
Skipped atom 1686, because occupancy 0.5 <= existing 0.500001
Skipped atom 1688, because occupancy 0.5 <= existing 0.500001
Skipped atom 1690, because occupancy 0.5 <= existing 0.500001
Skipped atom 1692, because occupancy 0.5 <= existing 0.500001
Skipped atom 1694, because occupancy 0.5 <= existing 0.500001
Skipped atom 1696, because occupancy 0.5 <= existing 0.500001
Skipped atom 1698, because occupancy 0.5 <= existing 0.500001
Skipped atom 1700, because occupancy 0.5 <= existing 0.500001
Skipped atom 1702, because occupancy 0.5 <= existing 0.500001
Skipped atom 1704, because occupancy 0.5 <= existing 0.500001
Skipped atom 1706, because occupancy 0.5 <= existing 0.500001
Skipped atom 1708, because occupancy 0.5 <= existing 0.500001
Skipped atom 1710, because occupancy 0.5 <= existing 0.500001
Skipped atom 1749, because occupancy 0.5 <= existing 0.500001
Skipped atom 1751, because occupancy 0.5 <= existing 0.500001
Skipped atom 1753, because occupancy 0.5 <= existing 0.500001
Skipped atom 1755, because occupancy 0.5 <= existing 0.500001
Skipped atom 1790, because occupancy 0.5 <= existing 0.500001
Skipped atom 1792, because occupancy 0.5 <= existing 0.500001
Skipped atom 1794, because occupancy 0.5 <= existing 0.500001
Skipped atom 1817, because occupancy 0.5 <= existing 0.500001
Skipped atom 1819, because occupancy 0.5 <= existing 0.500001
Skipped atom 1821, because occupancy 0.5 <= existing 0.500001
Skipped atom 1823, because occupancy 0.5 <= existing 0.500001
Skipped atom 1825, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qq7A-orig.a2m
Writing a2m file: tmp/1qq7A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12778


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12778/tmp -alignfile tmp/1qq7A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qq7A-orig.a2m (1 sequences, 253 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12778/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12778/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12778/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12778/tmp.a2m (1 sequences, 253 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12778/tmp.mod tmp/1qq7A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12778 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qq7A-align.mod
tmp/1qq7A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12778/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qq7A-orig.a2m tmp/1qq7A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qq7A-align.mod
Running w0.5 tmp/1qq7A-orig.a2m tmp/1qq7A-align.mod
Running align2model tmp/1qq7A-align -i tmp/1qq7A-align.mod -db tmp/1qq7A-orig.a2m -db tmp/1qq7A-pdb.a2m
partial PDB gets fragment 217 through 226 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   22
LEU    3    4
GLU    4   15
ARG    5   27
LYS    6   21
SER    8    3
LYS    9   29
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qq7A.36.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qqp1.71.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qqp1.71.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qqp1.71.5.a2m \
	-target T0124 -template 1qqp1 \
	-out T0124-1qqp1.71.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qqp1-orig.a2m
Writing a2m file: tmp/1qqp1-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7909


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp -alignfile tmp/1qqp1-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qqp1-orig.a2m (1 sequences, 213 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp.a2m (1 sequences, 213 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp.mod tmp/1qqp1-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7909 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qqp1-align.mod
tmp/1qqp1-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qqp1-orig.a2m tmp/1qqp1-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qqp1-align.mod
Running w0.5 tmp/1qqp1-orig.a2m tmp/1qqp1-align.mod
Running align2model tmp/1qqp1-align -i tmp/1qqp1-align.mod -db tmp/1qqp1-orig.a2m -db tmp/1qqp1-pdb.a2m
partial PDB gets fragment 111 through 120 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
GLU    2   12
LEU    3    3
LYS    4   27
GLU    5   13
ARG    6   29
LEU    7    2
GLU    8   15
MET    9    9
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qqp1.71.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qqp1.72.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qqp1.72.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qqp1.72.5.a2m \
	-target T0124 -template 1qqp1 \
	-out T0124-1qqp1.72.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qqp1-orig.a2m
Writing a2m file: tmp/1qqp1-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10658


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10658/tmp -alignfile tmp/1qqp1-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qqp1-orig.a2m (1 sequences, 213 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10658/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10658/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10658/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10658/tmp.a2m (1 sequences, 213 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10658/tmp.mod tmp/1qqp1-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10658 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qqp1-align.mod
tmp/1qqp1-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10658/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qqp1-orig.a2m tmp/1qqp1-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qqp1-align.mod
Running w0.5 tmp/1qqp1-orig.a2m tmp/1qqp1-align.mod
Running align2model tmp/1qqp1-align -i tmp/1qqp1-align.mod -db tmp/1qqp1-orig.a2m -db tmp/1qqp1-pdb.a2m
partial PDB gets fragment 110 through 119 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    3   29
GLU    4   12
ARG    5   29
LEU    6    3
GLU    7   15
MET    8    9
GLU    9   15
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qqp1.72.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qqp1.73.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qqp1.73.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qqp1.73.5.a2m \
	-target T0124 -template 1qqp1 \
	-out T0124-1qqp1.73.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1qqp1-orig.a2m
Writing a2m file: tmp/1qqp1-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1433


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1433/tmp -alignfile tmp/1qqp1-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1qqp1-orig.a2m (1 sequences, 213 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1433/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1433/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1433/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1433/tmp.a2m (1 sequences, 213 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1433/tmp.mod tmp/1qqp1-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1433 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qqp1-align.mod
tmp/1qqp1-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1433/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1qqp1-orig.a2m tmp/1qqp1-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1qqp1-align.mod
Running w0.5 tmp/1qqp1-orig.a2m tmp/1qqp1-align.mod
Running align2model tmp/1qqp1-align -i tmp/1qqp1-align.mod -db tmp/1qqp1-orig.a2m -db tmp/1qqp1-pdb.a2m
partial PDB gets fragment 109 through 118 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   22
GLU    3    9
ARG    4   27
LEU    5    3
GLU    6   15
MET    7   10
GLU    8   15
LEU    9    2
ILE   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qqp1.73.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qtwA.20.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qtwA.20.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qtwA.20.5.a2m \
	-target T0124 -template 1qtwA \
	-out T0124-1qtwA.20.5 -outdir und
Skipped atom 954, because occupancy 0.35 <= existing 0.650001
Skipped atom 1724, because occupancy 0.48 <= existing 0.520001
Skipped atom 3265, because occupancy 0.15 <= existing 0.850001
Skipped atom 3267, because occupancy 0.15 <= existing 0.850001
Skipped atom 4035, because occupancy 0.44 <= existing 0.560001
partial PDB gets fragment 256 through 267 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
MET    2   10
LYS    3   26
PHE    5    3
LEU    6    2
LYS    7   21
LEU    8    3
LEU    9    3
LYS   10   31
LYS   11   20
GLN   12   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    4     37.6054
keepclash    10   13     19.3170
turnclash      4    8    6    0     34.9433
Cluster     1 =   2   4   6
Cluster     2 =  10  13
5 clashing residues after turn 
Residue clashes:
2-4
4-6
10-13
cluster 1 has 3 members and 8.250e+02 combinations:
 6  2  4 
Energy     37.6054
Searching cluster 2
Combinations for 3 members in cluster 1 OK: 8.250e+02 - Sending to search
8.739542 < 37.605434: keeping 
0.000000 < 8.740631: keeping 
0.000000 < 1.316226: keeping 
Solved cluster 1: residual clashing  0.47
cluster 2 has 2 members and 2.700e+01 combinations:
 10  13 
Energy     19.3170
Searching cluster 10
Combinations for 2 members in cluster 2 OK: 2.700e+01 - Sending to search
8.671207 < 19.316998: keeping 
0.000000 < 8.779663: keeping 
Solved cluster 2: residual clashing  0.11
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qtwA.20.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qtwA.22.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qtwA.22.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qtwA.22.3.a2m \
	-target T0124 -template 1qtwA \
	-out T0124-1qtwA.22.3 -outdir und
Skipped atom 954, because occupancy 0.35 <= existing 0.650001
Skipped atom 1724, because occupancy 0.48 <= existing 0.520001
Skipped atom 3265, because occupancy 0.15 <= existing 0.850001
Skipped atom 3267, because occupancy 0.15 <= existing 0.850001
Skipped atom 4035, because occupancy 0.44 <= existing 0.560001
partial PDB gets fragment 256 through 266 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
PHE    3    3
LYS    5   31
LEU    6    2
LEU    7    2
LYS    8   24
LYS    9   31
GLN   10   15
GLU   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.55021
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qtwA.22.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1qtwA.23.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1qtwA.23.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1qtwA.23.2.a2m \
	-target T0124 -template 1qtwA \
	-out T0124-1qtwA.23.2 -outdir und
Skipped atom 954, because occupancy 0.35 <= existing 0.650001
Skipped atom 1724, because occupancy 0.48 <= existing 0.520001
Skipped atom 3265, because occupancy 0.15 <= existing 0.850001
Skipped atom 3267, because occupancy 0.15 <= existing 0.850001
Skipped atom 4035, because occupancy 0.44 <= existing 0.560001
partial PDB gets fragment 255 through 265 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
PHE    2    3
LYS    4   26
LEU    6    3
LYS    7   28
LYS    8   21
GLN    9   12
GLU   10   15
LYS   11   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1qtwA.23.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1rie.36.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1rie.36.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1rie.36.4.a2m \
	-target T0124 -template 1rie \
	-out T0124-1rie.36.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1rie-orig.a2m
Writing a2m file: tmp/1rie-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9231


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9231/tmp -alignfile tmp/1rie-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1rie-orig.a2m (1 sequences, 129 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9231/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9231/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9231/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9231/tmp.a2m (1 sequences, 129 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9231/tmp.mod tmp/1rie-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9231 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1rie-align.mod
tmp/1rie-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9231/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1rie-orig.a2m tmp/1rie-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1rie-align.mod
Running w0.5 tmp/1rie-orig.a2m tmp/1rie-align.mod
Running align2model tmp/1rie-align -i tmp/1rie-align.mod -db tmp/1rie-orig.a2m -db tmp/1rie-pdb.a2m
partial PDB gets fragment 95 through 104 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
GLU    2   14
LEU    3    2
GLU    4   12
ARG    5   27
LYS    6   27
SER    8    3
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.41079
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1rie.36.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1rie.37.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1rie.37.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1rie.37.4.a2m \
	-target T0124 -template 1rie \
	-out T0124-1rie.37.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1rie-orig.a2m
Writing a2m file: tmp/1rie-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10536


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10536/tmp -alignfile tmp/1rie-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1rie-orig.a2m (1 sequences, 129 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10536/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10536/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10536/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10536/tmp.a2m (1 sequences, 129 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10536/tmp.mod tmp/1rie-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10536 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1rie-align.mod
tmp/1rie-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10536/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1rie-orig.a2m tmp/1rie-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1rie-align.mod
Running w0.5 tmp/1rie-orig.a2m tmp/1rie-align.mod
Running align2model tmp/1rie-align -i tmp/1rie-align.mod -db tmp/1rie-orig.a2m -db tmp/1rie-pdb.a2m
partial PDB gets fragment 94 through 103 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    2    3
GLU    3   14
ARG    4   28
LYS    5   22
SER    7    3
LYS    8   27
ARG   10   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4   10     48.4432
Cluster     1 =   4  10
2 clashing residues after turn 
Residue clashes:
4-10
cluster 1 has 2 members and 0.000e+00 combinations:
 10  4 
Energy     50.6479
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
46.777592 < 50.647854: keeping 
8.804356 < 49.668110: keeping 
0.000000 < 11.827197: keeping 
Solved cluster 1: residual clashing  1.48
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1rie.37.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1rie.38.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1rie.38.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1rie.38.1.a2m \
	-target T0124 -template 1rie \
	-out T0124-1rie.38.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1rie-orig.a2m
Writing a2m file: tmp/1rie-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12539


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12539/tmp -alignfile tmp/1rie-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1rie-orig.a2m (1 sequences, 129 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12539/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12539/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12539/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12539/tmp.a2m (1 sequences, 129 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12539/tmp.mod tmp/1rie-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12539 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1rie-align.mod
tmp/1rie-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12539/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1rie-orig.a2m tmp/1rie-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1rie-align.mod
Running w0.5 tmp/1rie-orig.a2m tmp/1rie-align.mod
Running align2model tmp/1rie-align -i tmp/1rie-align.mod -db tmp/1rie-orig.a2m -db tmp/1rie-pdb.a2m
partial PDB gets fragment 93 through 103 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   12
ARG    3   29
LYS    4   19
LYS    7   23
ARG    9   32
GLU   10   13
GLU   11   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   11     62.2489
turnclash      5   12    9    0     43.5785
Cluster     1 =   5   9  11
3 clashing residues after turn 
Residue clashes:
5-11
5-9
cluster 1 has 3 members and 0.000e+00 combinations:
 9  11  5 
Energy     62.8460
Searching cluster 5
Combinations for 3 members in cluster 1 OK: 0.000e+00 - Sending to search
50.864738 < 62.846001: keeping 
50.817894 < 52.940895: keeping 
43.578506 < 52.922585: keeping 
0.000000 < 47.020145: keeping 
0.000000 < 3.650927: keeping 
Solved cluster 1: residual clashing  1.86
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1rie.38.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1rie.39.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1rie.39.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1rie.39.2.a2m \
	-target T0124 -template 1rie \
	-out T0124-1rie.39.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1rie-orig.a2m
Writing a2m file: tmp/1rie-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30040


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30040/tmp -alignfile tmp/1rie-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1rie-orig.a2m (1 sequences, 129 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30040/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30040/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30040/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30040/tmp.a2m (1 sequences, 129 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30040/tmp.mod tmp/1rie-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30040 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1rie-align.mod
tmp/1rie-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30040/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1rie-orig.a2m tmp/1rie-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1rie-align.mod
Running w0.5 tmp/1rie-orig.a2m tmp/1rie-align.mod
Running align2model tmp/1rie-align -i tmp/1rie-align.mod -db tmp/1rie-orig.a2m -db tmp/1rie-pdb.a2m
partial PDB gets fragment 92 through 101 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1    9
ARG    2   27
LYS    3   27
SER    5    2
LYS    6   29
ARG    7   24
ARG    8   27
GLU    9   14
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1rie.39.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1rie.40.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1rie.40.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1rie.40.4.a2m \
	-target T0124 -template 1rie \
	-out T0124-1rie.40.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1rie-orig.a2m
Writing a2m file: tmp/1rie-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10688


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10688/tmp -alignfile tmp/1rie-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1rie-orig.a2m (1 sequences, 129 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10688/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10688/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10688/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10688/tmp.a2m (1 sequences, 129 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10688/tmp.mod tmp/1rie-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10688 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1rie-align.mod
tmp/1rie-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10688/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1rie-orig.a2m tmp/1rie-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1rie-align.mod
Running w0.5 tmp/1rie-orig.a2m tmp/1rie-align.mod
Running align2model tmp/1rie-align -i tmp/1rie-align.mod -db tmp/1rie-orig.a2m -db tmp/1rie-pdb.a2m
partial PDB gets fragment 91 through 100 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
LYS    2   21
SER    4    2
LYS    5   26
ARG    6   23
ARG    7   28
GLU    8   12
GLU    9    9
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1rie.40.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ryc.145.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ryc.145.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ryc.145.2.a2m \
	-target T0124 -template 1ryc \
	-out T0124-1ryc.145.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ryc-orig.a2m
Writing a2m file: tmp/1ryc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10534


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10534/tmp -alignfile tmp/1ryc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ryc-orig.a2m (1 sequences, 294 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10534/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10534/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10534/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10534/tmp.a2m (1 sequences, 294 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10534/tmp.mod tmp/1ryc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10534 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ryc-align.mod
tmp/1ryc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10534/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ryc-orig.a2m tmp/1ryc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ryc-align.mod
Running w0.5 tmp/1ryc-orig.a2m tmp/1ryc-align.mod
Running align2model tmp/1ryc-align -i tmp/1ryc-align.mod -db tmp/1ryc-orig.a2m -db tmp/1ryc-pdb.a2m
partial PDB gets fragment 52 through 61 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    4
GLN    2   14
VAL    3    1
MET    4   12
MET    5   10
ARG    6   21
SER    7    2
SER    9    3
ASP   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 4 rotamers of residue I 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue S 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ryc.145.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ryc.146.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ryc.146.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ryc.146.2.a2m \
	-target T0124 -template 1ryc \
	-out T0124-1ryc.146.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ryc-orig.a2m
Writing a2m file: tmp/1ryc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10362


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10362/tmp -alignfile tmp/1ryc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ryc-orig.a2m (1 sequences, 294 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10362/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10362/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10362/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10362/tmp.a2m (1 sequences, 294 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10362/tmp.mod tmp/1ryc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10362 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ryc-align.mod
tmp/1ryc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10362/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ryc-orig.a2m tmp/1ryc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ryc-align.mod
Running w0.5 tmp/1ryc-orig.a2m tmp/1ryc-align.mod
Running align2model tmp/1ryc-align -i tmp/1ryc-align.mod -db tmp/1ryc-orig.a2m -db tmp/1ryc-pdb.a2m
partial PDB gets fragment 51 through 60 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   15
VAL    2    3
MET    3   12
MET    4   10
ARG    5   32
SER    6    3
THR    7    1
SER    8    2
ASP    9    5
LYS   10   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue V 3 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 16 rotamers of residue K 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ryc.146.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ryc.148.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ryc.148.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ryc.148.1.a2m \
	-target T0124 -template 1ryc \
	-out T0124-1ryc.148.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ryc-orig.a2m
Writing a2m file: tmp/1ryc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9516


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9516/tmp -alignfile tmp/1ryc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ryc-orig.a2m (1 sequences, 294 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9516/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9516/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9516/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9516/tmp.a2m (1 sequences, 294 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9516/tmp.mod tmp/1ryc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9516 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ryc-align.mod
tmp/1ryc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9516/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ryc-orig.a2m tmp/1ryc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ryc-align.mod
Running w0.5 tmp/1ryc-orig.a2m tmp/1ryc-align.mod
Running align2model tmp/1ryc-align -i tmp/1ryc-align.mod -db tmp/1ryc-orig.a2m -db tmp/1ryc-pdb.a2m
partial PDB gets fragment 49 through 59 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
MET    1   11
MET    2   11
ARG    3   30
SER    4    2
THR    5    3
SER    6    2
ASP    7    5
LYS    8   28
GLN   11   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ryc.148.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ryc.148.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ryc.148.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ryc.148.4.a2m \
	-target T0124 -template 1ryc \
	-out T0124-1ryc.148.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ryc-orig.a2m
Writing a2m file: tmp/1ryc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14738


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14738/tmp -alignfile tmp/1ryc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ryc-orig.a2m (1 sequences, 294 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14738/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14738/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14738/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14738/tmp.a2m (1 sequences, 294 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14738/tmp.mod tmp/1ryc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14738 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ryc-align.mod
tmp/1ryc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14738/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ryc-orig.a2m tmp/1ryc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ryc-align.mod
Running w0.5 tmp/1ryc-orig.a2m tmp/1ryc-align.mod
Running align2model tmp/1ryc-align -i tmp/1ryc-align.mod -db tmp/1ryc-orig.a2m -db tmp/1ryc-pdb.a2m
partial PDB gets fragment 53 through 62 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   12
MET    2   10
ARG    3   32
SER    4    3
THR    5    1
SER    6    2
ASP    7    5
LYS    8   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 16 rotamers of residue K 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ryc.148.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ryc.149.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ryc.149.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ryc.149.4.a2m \
	-target T0124 -template 1ryc \
	-out T0124-1ryc.149.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ryc-orig.a2m
Writing a2m file: tmp/1ryc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9224


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9224/tmp -alignfile tmp/1ryc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ryc-orig.a2m (1 sequences, 294 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9224/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9224/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9224/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9224/tmp.a2m (1 sequences, 294 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9224/tmp.mod tmp/1ryc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9224 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ryc-align.mod
tmp/1ryc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9224/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ryc-orig.a2m tmp/1ryc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ryc-align.mod
Running w0.5 tmp/1ryc-orig.a2m tmp/1ryc-align.mod
Running align2model tmp/1ryc-align -i tmp/1ryc-align.mod -db tmp/1ryc-orig.a2m -db tmp/1ryc-pdb.a2m
partial PDB gets fragment 48 through 58 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
ARG    2   32
THR    4    2
SER    5    2
ASP    6    5
LYS    7   27
GLN   10   14
GLU   11    7
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ryc.149.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ryc.150.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ryc.150.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ryc.150.4.a2m \
	-target T0124 -template 1ryc \
	-out T0124-1ryc.150.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ryc-orig.a2m
Writing a2m file: tmp/1ryc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7953


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7953/tmp -alignfile tmp/1ryc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ryc-orig.a2m (1 sequences, 294 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7953/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7953/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7953/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7953/tmp.a2m (1 sequences, 294 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7953/tmp.mod tmp/1ryc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7953 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ryc-align.mod
tmp/1ryc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7953/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ryc-orig.a2m tmp/1ryc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ryc-align.mod
Running w0.5 tmp/1ryc-orig.a2m tmp/1ryc-align.mod
Running align2model tmp/1ryc-align -i tmp/1ryc-align.mod -db tmp/1ryc-orig.a2m -db tmp/1ryc-pdb.a2m
partial PDB gets fragment 47 through 57 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
SER    2    2
THR    3    2
ASP    5    4
LYS    6   28
GLN    9   15
GLU   10   13
ARG   11   21
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 4 rotamers of residue D 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ryc.150.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ryc.151.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ryc.151.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ryc.151.5.a2m \
	-target T0124 -template 1ryc \
	-out T0124-1ryc.151.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ryc-orig.a2m
Writing a2m file: tmp/1ryc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10901


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10901/tmp -alignfile tmp/1ryc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ryc-orig.a2m (1 sequences, 294 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10901/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10901/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10901/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10901/tmp.a2m (1 sequences, 294 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10901/tmp.mod tmp/1ryc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10901 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ryc-align.mod
tmp/1ryc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10901/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ryc-orig.a2m tmp/1ryc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ryc-align.mod
Running w0.5 tmp/1ryc-orig.a2m tmp/1ryc-align.mod
Running align2model tmp/1ryc-align -i tmp/1ryc-align.mod -db tmp/1ryc-orig.a2m -db tmp/1ryc-pdb.a2m
partial PDB gets fragment 46 through 56 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
THR    2    2
SER    3    2
ASP    4    5
LYS    5   25
GLN    8   14
GLU    9   12
ARG   10   32
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ryc.151.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ryc.153.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ryc.153.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ryc.153.2.a2m \
	-target T0124 -template 1ryc \
	-out T0124-1ryc.153.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ryc-orig.a2m
Writing a2m file: tmp/1ryc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20076


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20076/tmp -alignfile tmp/1ryc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ryc-orig.a2m (1 sequences, 294 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20076/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20076/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20076/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20076/tmp.a2m (1 sequences, 294 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20076/tmp.mod tmp/1ryc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20076 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ryc-align.mod
tmp/1ryc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20076/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ryc-orig.a2m tmp/1ryc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ryc-align.mod
Running w0.5 tmp/1ryc-orig.a2m tmp/1ryc-align.mod
Running align2model tmp/1ryc-align -i tmp/1ryc-align.mod -db tmp/1ryc-orig.a2m -db tmp/1ryc-pdb.a2m
partial PDB gets fragment 46 through 55 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
ASP    2    4
LYS    3   30
GLN    6   15
GLU    7   15
ARG    8   32
LEU    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ryc.153.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ryc.153.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ryc.153.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ryc.153.5.a2m \
	-target T0124 -template 1ryc \
	-out T0124-1ryc.153.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ryc-orig.a2m
Writing a2m file: tmp/1ryc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9345


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9345/tmp -alignfile tmp/1ryc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ryc-orig.a2m (1 sequences, 294 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9345/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9345/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9345/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9345/tmp.a2m (1 sequences, 294 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9345/tmp.mod tmp/1ryc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9345 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ryc-align.mod
tmp/1ryc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9345/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ryc-orig.a2m tmp/1ryc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ryc-align.mod
Running w0.5 tmp/1ryc-orig.a2m tmp/1ryc-align.mod
Running align2model tmp/1ryc-align -i tmp/1ryc-align.mod -db tmp/1ryc-orig.a2m -db tmp/1ryc-pdb.a2m
partial PDB gets fragment 50 through 59 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    2    4
LYS    3   28
GLN    6   15
GLU    7   13
ARG    8   21
LEU    9    2
LYS   10   21
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ryc.153.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1ryc.154.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1ryc.154.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1ryc.154.5.a2m \
	-target T0124 -template 1ryc \
	-out T0124-1ryc.154.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1ryc-orig.a2m
Writing a2m file: tmp/1ryc-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9858


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9858/tmp -alignfile tmp/1ryc-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1ryc-orig.a2m (1 sequences, 294 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9858/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9858/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9858/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9858/tmp.a2m (1 sequences, 294 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9858/tmp.mod tmp/1ryc-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9858 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ryc-align.mod
tmp/1ryc-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9858/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1ryc-orig.a2m tmp/1ryc-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1ryc-align.mod
Running w0.5 tmp/1ryc-orig.a2m tmp/1ryc-align.mod
Running align2model tmp/1ryc-align -i tmp/1ryc-align.mod -db tmp/1ryc-orig.a2m -db tmp/1ryc-pdb.a2m
partial PDB gets fragment 49 through 58 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    5
LYS    2   25
GLN    5   14
GLU    6   12
ARG    7   32
LEU    8    3
LYS    9   24
LYS   10   18
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1ryc.154.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1shkA.130.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1shkA.130.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1shkA.130.2.a2m \
	-target T0124 -template 1shkA \
	-out T0124-1shkA.130.2 -outdir und
Skipped atom 151, because occupancy 0.5 <= existing 0.500001
Skipped atom 153, because occupancy 0.5 <= existing 0.500001
Skipped atom 155, because occupancy 0.5 <= existing 0.500001
Skipped atom 157, because occupancy 0.5 <= existing 0.500001
Skipped atom 177, because occupancy 0.5 <= existing 0.500001
Skipped atom 179, because occupancy 0.5 <= existing 0.500001
Skipped atom 181, because occupancy 0.5 <= existing 0.500001
Skipped atom 183, because occupancy 0.5 <= existing 0.500001
Skipped atom 185, because occupancy 0.5 <= existing 0.500001
Skipped atom 187, because occupancy 0.5 <= existing 0.500001
Skipped atom 455, because occupancy 0.5 <= existing 0.500001
Skipped atom 457, because occupancy 0.5 <= existing 0.500001
Skipped atom 459, because occupancy 0.5 <= existing 0.500001
Skipped atom 461, because occupancy 0.5 <= existing 0.500001
Skipped atom 463, because occupancy 0.5 <= existing 0.500001
Skipped atom 465, because occupancy 0.5 <= existing 0.500001
Skipped atom 498, because occupancy 0.5 <= existing 0.500001
Skipped atom 500, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 524, because occupancy 0.5 <= existing 0.500001
Skipped atom 526, because occupancy 0.5 <= existing 0.500001
Skipped atom 528, because occupancy 0.5 <= existing 0.500001
Skipped atom 530, because occupancy 0.5 <= existing 0.500001
Skipped atom 829, because occupancy 0.5 <= existing 0.500001
Skipped atom 831, because occupancy 0.5 <= existing 0.500001
Skipped atom 833, because occupancy 0.5 <= existing 0.500001
Skipped atom 835, because occupancy 0.5 <= existing 0.500001
Skipped atom 951, because occupancy 0.5 <= existing 0.500001
Skipped atom 953, because occupancy 0.5 <= existing 0.500001
Skipped atom 955, because occupancy 0.5 <= existing 0.500001
Skipped atom 957, because occupancy 0.5 <= existing 0.500001
Skipped atom 959, because occupancy 0.5 <= existing 0.500001
Skipped atom 961, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1shkA-orig.a2m
Writing a2m file: tmp/1shkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4434


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4434/tmp -alignfile tmp/1shkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1shkA-orig.a2m (1 sequences, 173 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4434/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4434/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4434/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4434/tmp.a2m (1 sequences, 173 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4434/tmp.mod tmp/1shkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4434 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1shkA-align.mod
tmp/1shkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4434/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1shkA-orig.a2m tmp/1shkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1shkA-align.mod
Running w0.5 tmp/1shkA-orig.a2m tmp/1shkA-align.mod
Running align2model tmp/1shkA-align -i tmp/1shkA-align.mod -db tmp/1shkA-orig.a2m -db tmp/1shkA-pdb.a2m
partial PDB gets fragment 51 through 60 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
LYS    2   17
ASP    3    4
ILE    4    3
LYS    5   26
LYS    6   26
LYS    7   30
LEU    8    3
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue I 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 26 rotamers of residue K 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    6     28.2349
Cluster     1 =   2   6
2 clashing residues after turn 
Residue clashes:
2-6
cluster 1 has 2 members and 5.200e+01 combinations:
 2  6 
Energy    124.3368
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 5.200e+01 - Sending to search
8.234940 < 124.336807: keeping 
Solved cluster 1: residual clashing 67.70
Still clashes at these sidechain pairs:
Residual clashes =    8.23494
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1shkA.130.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1shkA.131.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1shkA.131.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1shkA.131.0.a2m \
	-target T0124 -template 1shkA \
	-out T0124-1shkA.131.0 -outdir und
Skipped atom 151, because occupancy 0.5 <= existing 0.500001
Skipped atom 153, because occupancy 0.5 <= existing 0.500001
Skipped atom 155, because occupancy 0.5 <= existing 0.500001
Skipped atom 157, because occupancy 0.5 <= existing 0.500001
Skipped atom 177, because occupancy 0.5 <= existing 0.500001
Skipped atom 179, because occupancy 0.5 <= existing 0.500001
Skipped atom 181, because occupancy 0.5 <= existing 0.500001
Skipped atom 183, because occupancy 0.5 <= existing 0.500001
Skipped atom 185, because occupancy 0.5 <= existing 0.500001
Skipped atom 187, because occupancy 0.5 <= existing 0.500001
Skipped atom 455, because occupancy 0.5 <= existing 0.500001
Skipped atom 457, because occupancy 0.5 <= existing 0.500001
Skipped atom 459, because occupancy 0.5 <= existing 0.500001
Skipped atom 461, because occupancy 0.5 <= existing 0.500001
Skipped atom 463, because occupancy 0.5 <= existing 0.500001
Skipped atom 465, because occupancy 0.5 <= existing 0.500001
Skipped atom 498, because occupancy 0.5 <= existing 0.500001
Skipped atom 500, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 524, because occupancy 0.5 <= existing 0.500001
Skipped atom 526, because occupancy 0.5 <= existing 0.500001
Skipped atom 528, because occupancy 0.5 <= existing 0.500001
Skipped atom 530, because occupancy 0.5 <= existing 0.500001
Skipped atom 829, because occupancy 0.5 <= existing 0.500001
Skipped atom 831, because occupancy 0.5 <= existing 0.500001
Skipped atom 833, because occupancy 0.5 <= existing 0.500001
Skipped atom 835, because occupancy 0.5 <= existing 0.500001
Skipped atom 951, because occupancy 0.5 <= existing 0.500001
Skipped atom 953, because occupancy 0.5 <= existing 0.500001
Skipped atom 955, because occupancy 0.5 <= existing 0.500001
Skipped atom 957, because occupancy 0.5 <= existing 0.500001
Skipped atom 959, because occupancy 0.5 <= existing 0.500001
Skipped atom 961, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1shkA-orig.a2m
Writing a2m file: tmp/1shkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2209


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2209/tmp -alignfile tmp/1shkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1shkA-orig.a2m (1 sequences, 173 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2209/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2209/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2209/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2209/tmp.a2m (1 sequences, 173 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2209/tmp.mod tmp/1shkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2209 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1shkA-align.mod
tmp/1shkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2209/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1shkA-orig.a2m tmp/1shkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1shkA-align.mod
Running w0.5 tmp/1shkA-orig.a2m tmp/1shkA-align.mod
Running align2model tmp/1shkA-align -i tmp/1shkA-align.mod -db tmp/1shkA-orig.a2m -db tmp/1shkA-pdb.a2m
partial PDB gets fragment 50 through 59 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
ASP    2    5
ILE    3    3
LYS    4   26
LYS    5   26
LYS    6   26
LEU    7    3
GLU    8   15
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 26 rotamers of residue K 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    7     23.8801
Cluster     1 =   3   7
2 clashing residues after turn 
Residue clashes:
3-7
cluster 1 has 2 members and 2.600e+01 combinations:
 3  7 
Energy     94.2906
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 2.600e+01 - Sending to search
0.000000 < 94.290550: keeping 
5.989759 < 33.271832: keeping 
Solved cluster 1: residual clashing 18.75
Still clashes at these sidechain pairs:
Residual clashes =    5.98976
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1shkA.131.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1shkA.132.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1shkA.132.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1shkA.132.1.a2m \
	-target T0124 -template 1shkA \
	-out T0124-1shkA.132.1 -outdir und
Skipped atom 151, because occupancy 0.5 <= existing 0.500001
Skipped atom 153, because occupancy 0.5 <= existing 0.500001
Skipped atom 155, because occupancy 0.5 <= existing 0.500001
Skipped atom 157, because occupancy 0.5 <= existing 0.500001
Skipped atom 177, because occupancy 0.5 <= existing 0.500001
Skipped atom 179, because occupancy 0.5 <= existing 0.500001
Skipped atom 181, because occupancy 0.5 <= existing 0.500001
Skipped atom 183, because occupancy 0.5 <= existing 0.500001
Skipped atom 185, because occupancy 0.5 <= existing 0.500001
Skipped atom 187, because occupancy 0.5 <= existing 0.500001
Skipped atom 455, because occupancy 0.5 <= existing 0.500001
Skipped atom 457, because occupancy 0.5 <= existing 0.500001
Skipped atom 459, because occupancy 0.5 <= existing 0.500001
Skipped atom 461, because occupancy 0.5 <= existing 0.500001
Skipped atom 463, because occupancy 0.5 <= existing 0.500001
Skipped atom 465, because occupancy 0.5 <= existing 0.500001
Skipped atom 498, because occupancy 0.5 <= existing 0.500001
Skipped atom 500, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 524, because occupancy 0.5 <= existing 0.500001
Skipped atom 526, because occupancy 0.5 <= existing 0.500001
Skipped atom 528, because occupancy 0.5 <= existing 0.500001
Skipped atom 530, because occupancy 0.5 <= existing 0.500001
Skipped atom 829, because occupancy 0.5 <= existing 0.500001
Skipped atom 831, because occupancy 0.5 <= existing 0.500001
Skipped atom 833, because occupancy 0.5 <= existing 0.500001
Skipped atom 835, because occupancy 0.5 <= existing 0.500001
Skipped atom 951, because occupancy 0.5 <= existing 0.500001
Skipped atom 953, because occupancy 0.5 <= existing 0.500001
Skipped atom 955, because occupancy 0.5 <= existing 0.500001
Skipped atom 957, because occupancy 0.5 <= existing 0.500001
Skipped atom 959, because occupancy 0.5 <= existing 0.500001
Skipped atom 961, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1shkA-orig.a2m
Writing a2m file: tmp/1shkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10592


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10592/tmp -alignfile tmp/1shkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1shkA-orig.a2m (1 sequences, 173 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10592/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10592/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10592/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10592/tmp.a2m (1 sequences, 173 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10592/tmp.mod tmp/1shkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10592 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1shkA-align.mod
tmp/1shkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10592/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1shkA-orig.a2m tmp/1shkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1shkA-align.mod
Running w0.5 tmp/1shkA-orig.a2m tmp/1shkA-align.mod
Running align2model tmp/1shkA-align -i tmp/1shkA-align.mod -db tmp/1shkA-orig.a2m -db tmp/1shkA-pdb.a2m
partial PDB gets fragment 49 through 58 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
ILE    2    4
LYS    3   30
LYS    4   17
LYS    5   26
LEU    6    3
GLU    7   12
LYS    9   30
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 12 rotamers of residue E 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    8     23.6528
turnclash      4   17    3    0     22.7800
Cluster     1 =   3   4   8
3 clashing residues after turn 
Residue clashes:
4-8
4-3
cluster 1 has 3 members and 7.200e+02 combinations:
 3  8  4 
Energy    119.8875
Searching cluster 3
Combinations for 3 members in cluster 1 OK: 7.200e+02 - Sending to search
73.887222 < 119.887466: keeping 
48.978455 < 117.763580: keeping 
0.000000 < 93.835518: keeping 
6.611811 < 32.728546: keeping 
Solved cluster 1: residual clashing 19.13
Still clashes at these sidechain pairs:
Residual clashes =   12.12363
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1shkA.132.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1shkA.133.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1shkA.133.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1shkA.133.3.a2m \
	-target T0124 -template 1shkA \
	-out T0124-1shkA.133.3 -outdir und
Skipped atom 151, because occupancy 0.5 <= existing 0.500001
Skipped atom 153, because occupancy 0.5 <= existing 0.500001
Skipped atom 155, because occupancy 0.5 <= existing 0.500001
Skipped atom 157, because occupancy 0.5 <= existing 0.500001
Skipped atom 177, because occupancy 0.5 <= existing 0.500001
Skipped atom 179, because occupancy 0.5 <= existing 0.500001
Skipped atom 181, because occupancy 0.5 <= existing 0.500001
Skipped atom 183, because occupancy 0.5 <= existing 0.500001
Skipped atom 185, because occupancy 0.5 <= existing 0.500001
Skipped atom 187, because occupancy 0.5 <= existing 0.500001
Skipped atom 455, because occupancy 0.5 <= existing 0.500001
Skipped atom 457, because occupancy 0.5 <= existing 0.500001
Skipped atom 459, because occupancy 0.5 <= existing 0.500001
Skipped atom 461, because occupancy 0.5 <= existing 0.500001
Skipped atom 463, because occupancy 0.5 <= existing 0.500001
Skipped atom 465, because occupancy 0.5 <= existing 0.500001
Skipped atom 498, because occupancy 0.5 <= existing 0.500001
Skipped atom 500, because occupancy 0.5 <= existing 0.500001
Skipped atom 502, because occupancy 0.5 <= existing 0.500001
Skipped atom 504, because occupancy 0.5 <= existing 0.500001
Skipped atom 524, because occupancy 0.5 <= existing 0.500001
Skipped atom 526, because occupancy 0.5 <= existing 0.500001
Skipped atom 528, because occupancy 0.5 <= existing 0.500001
Skipped atom 530, because occupancy 0.5 <= existing 0.500001
Skipped atom 829, because occupancy 0.5 <= existing 0.500001
Skipped atom 831, because occupancy 0.5 <= existing 0.500001
Skipped atom 833, because occupancy 0.5 <= existing 0.500001
Skipped atom 835, because occupancy 0.5 <= existing 0.500001
Skipped atom 951, because occupancy 0.5 <= existing 0.500001
Skipped atom 953, because occupancy 0.5 <= existing 0.500001
Skipped atom 955, because occupancy 0.5 <= existing 0.500001
Skipped atom 957, because occupancy 0.5 <= existing 0.500001
Skipped atom 959, because occupancy 0.5 <= existing 0.500001
Skipped atom 961, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1shkA-orig.a2m
Writing a2m file: tmp/1shkA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5882


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5882/tmp -alignfile tmp/1shkA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1shkA-orig.a2m (1 sequences, 173 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5882/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5882/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5882/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5882/tmp.a2m (1 sequences, 173 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5882/tmp.mod tmp/1shkA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5882 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1shkA-align.mod
tmp/1shkA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5882/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1shkA-orig.a2m tmp/1shkA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1shkA-align.mod
Running w0.5 tmp/1shkA-orig.a2m tmp/1shkA-align.mod
Running align2model tmp/1shkA-align -i tmp/1shkA-align.mod -db tmp/1shkA-orig.a2m -db tmp/1shkA-pdb.a2m
partial PDB gets fragment 48 through 57 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
LYS    2   26
LYS    3   25
LYS    4   30
LEU    5    2
GLU    6   12
LYS    8   26
ARG    9   27
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 26 rotamers of residue K 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    9     15.6483
Cluster     1 =   5   9
2 clashing residues after turn 
Residue clashes:
5-9
cluster 1 has 2 members and 3.900e+02 combinations:
 9  5 
Energy     84.8236
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 3.900e+02 - Sending to search
10.140974 < 84.823608: keeping 
46.570034 < 81.819298: keeping 
0.071424 < 71.842422: keeping 
6.570035 < 32.108082: keeping 
Solved cluster 1: residual clashing 19.08
Still clashes at these sidechain pairs:
Residual clashes =    6.57003
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1shkA.133.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1sluA.56.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1sluA.56.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1sluA.56.3.a2m \
	-target T0124 -template 1sluA \
	-out T0124-1sluA.56.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1sluA-orig.a2m
Writing a2m file: tmp/1sluA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10442


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10442/tmp -alignfile tmp/1sluA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1sluA-orig.a2m (1 sequences, 142 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10442/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10442/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10442/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10442/tmp.a2m (1 sequences, 142 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10442/tmp.mod tmp/1sluA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10442 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1sluA-align.mod
tmp/1sluA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10442/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1sluA-orig.a2m tmp/1sluA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1sluA-align.mod
Running w0.5 tmp/1sluA-orig.a2m tmp/1sluA-align.mod
Running align2model tmp/1sluA-align -i tmp/1sluA-align.mod -db tmp/1sluA-orig.a2m -db tmp/1sluA-pdb.a2m
partial PDB gets fragment 83 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    5
LEU    3    3
GLU    4   15
PRO    5    2
VAL    6    1
TYR    7    3
PRO    8    2
ARG    9   32
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1sluA.56.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1sluA.57.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1sluA.57.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1sluA.57.1.a2m \
	-target T0124 -template 1sluA \
	-out T0124-1sluA.57.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1sluA-orig.a2m
Writing a2m file: tmp/1sluA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-16894


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-16894/tmp -alignfile tmp/1sluA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1sluA-orig.a2m (1 sequences, 142 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-16894/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16894/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16894/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16894/tmp.a2m (1 sequences, 142 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16894/tmp.mod tmp/1sluA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16894 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1sluA-align.mod
tmp/1sluA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16894/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1sluA-orig.a2m tmp/1sluA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1sluA-align.mod
Running w0.5 tmp/1sluA-orig.a2m tmp/1sluA-align.mod
Running align2model tmp/1sluA-align -i tmp/1sluA-align.mod -db tmp/1sluA-orig.a2m -db tmp/1sluA-pdb.a2m
partial PDB gets fragment 82 through 91 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PHE    1    3
LEU    2    5
GLU    3   12
PRO    4    2
VAL    5    2
TYR    6    3
PRO    7    2
ARG    8   27
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1sluA.57.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1smrA.140.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1smrA.140.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1smrA.140.5.a2m \
	-target T0124 -template 1smrA \
	-out T0124-1smrA.140.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1smrA-orig.a2m
Writing a2m file: tmp/1smrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7633


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7633/tmp -alignfile tmp/1smrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1smrA-orig.a2m (1 sequences, 335 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7633/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7633/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7633/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7633/tmp.a2m (1 sequences, 335 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7633/tmp.mod tmp/1smrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7633 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1smrA-align.mod
tmp/1smrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7633/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1smrA-orig.a2m tmp/1smrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1smrA-align.mod
Running w0.5 tmp/1smrA-orig.a2m tmp/1smrA-align.mod
Running align2model tmp/1smrA-align -i tmp/1smrA-align.mod -db tmp/1smrA-orig.a2m -db tmp/1smrA-pdb.a2m
partial PDB gets fragment 64 through 73 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   21
ARG    2   26
LEU    3    3
ASP    4    4
ARG    5   32
ILE    6    3
GLN    7   14
VAL    8    2
MET    9    9
MET   10   10
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1smrA.140.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1smrA.141.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1smrA.141.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1smrA.141.5.a2m \
	-target T0124 -template 1smrA \
	-out T0124-1smrA.141.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1smrA-orig.a2m
Writing a2m file: tmp/1smrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27792


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27792/tmp -alignfile tmp/1smrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1smrA-orig.a2m (1 sequences, 335 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27792/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27792/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27792/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27792/tmp.a2m (1 sequences, 335 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27792/tmp.mod tmp/1smrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27792 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1smrA-align.mod
tmp/1smrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27792/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1smrA-orig.a2m tmp/1smrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1smrA-align.mod
Running w0.5 tmp/1smrA-orig.a2m tmp/1smrA-align.mod
Running align2model tmp/1smrA-align -i tmp/1smrA-align.mod -db tmp/1smrA-orig.a2m -db tmp/1smrA-pdb.a2m
partial PDB gets fragment 63 through 72 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   32
LEU    2    2
ASP    3    4
ARG    4   32
ILE    5    2
GLN    6   14
VAL    7    1
MET    8   12
MET    9   12
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.87400
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1smrA.141.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1smrA.142.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1smrA.142.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1smrA.142.4.a2m \
	-target T0124 -template 1smrA \
	-out T0124-1smrA.142.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1smrA-orig.a2m
Writing a2m file: tmp/1smrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17404


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17404/tmp -alignfile tmp/1smrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1smrA-orig.a2m (1 sequences, 335 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17404/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17404/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17404/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17404/tmp.a2m (1 sequences, 335 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17404/tmp.mod tmp/1smrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17404 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1smrA-align.mod
tmp/1smrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17404/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1smrA-orig.a2m tmp/1smrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1smrA-align.mod
Running w0.5 tmp/1smrA-orig.a2m tmp/1smrA-align.mod
Running align2model tmp/1smrA-align -i tmp/1smrA-align.mod -db tmp/1smrA-orig.a2m -db tmp/1smrA-pdb.a2m
partial PDB gets fragment 62 through 71 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ASP    2    5
ARG    3   22
ILE    4    2
GLN    5   15
VAL    6    2
MET    7   12
ARG    9   32
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    8     52.6981
Cluster     1 =   2   8
2 clashing residues after turn 
Residue clashes:
2-8
cluster 1 has 2 members and 4.000e+00 combinations:
 2  8 
Energy     54.5119
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
9.553821 < 54.511921: keeping 
0.000000 < 11.630254: keeping 
Solved cluster 1: residual clashing  4.03
Still clashes at these sidechain pairs:
Residual clashes =    2.01487
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1smrA.142.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1smrA.144.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1smrA.144.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1smrA.144.4.a2m \
	-target T0124 -template 1smrA \
	-out T0124-1smrA.144.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1smrA-orig.a2m
Writing a2m file: tmp/1smrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30423


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30423/tmp -alignfile tmp/1smrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1smrA-orig.a2m (1 sequences, 335 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30423/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30423/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30423/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30423/tmp.a2m (1 sequences, 335 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30423/tmp.mod tmp/1smrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30423 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1smrA-align.mod
tmp/1smrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30423/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1smrA-orig.a2m tmp/1smrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1smrA-align.mod
Running w0.5 tmp/1smrA-orig.a2m tmp/1smrA-align.mod
Running align2model tmp/1smrA-align -i tmp/1smrA-align.mod -db tmp/1smrA-orig.a2m -db tmp/1smrA-pdb.a2m
partial PDB gets fragment 60 through 69 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
ILE    2    2
GLN    3   15
VAL    4    3
MET    5    8
MET    6   10
ARG    7   32
THR    9    2
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1smrA.144.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1sra.57.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1sra.57.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1sra.57.4.a2m \
	-target T0124 -template 1sra \
	-out T0124-1sra.57.4 -outdir und
partial PDB gets fragment 94 through 103 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PHE    1    3
LEU    2    2
GLU    3   12
PRO    4    2
VAL    5    3
TYR    6    3
PRO    7    2
ARG    8   32
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue Y 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1sra.57.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1sra.58.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1sra.58.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1sra.58.3.a2m \
	-target T0124 -template 1sra \
	-out T0124-1sra.58.3 -outdir und
partial PDB gets fragment 93 through 102 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   13
PRO    3    2
VAL    4    1
TYR    5    3
PRO    6    2
ARG    7   24
LEU    9    3
ASP   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    7     34.7236
Cluster     1 =   4   7
2 clashing residues after turn 
Residue clashes:
4-7
cluster 1 has 2 members and 4.000e+00 combinations:
 7  4 
Energy     93.0304
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
20.261257 < 93.030388: keeping 
33.501171 < 82.071289: keeping 
21.770966 < 64.709534: keeping 
Solved cluster 1: residual clashing 56.48
Still clashes at these sidechain pairs:
ires=    4 irot=    2 jres=    7 jrot=    2      21.7710
Residual clashes =   25.60971
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1sra.58.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1svy.134.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1svy.134.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1svy.134.1.a2m \
	-target T0124 -template 1svy \
	-out T0124-1svy.134.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1svy-orig.a2m
Writing a2m file: tmp/1svy-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11910


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11910/tmp -alignfile tmp/1svy-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1svy-orig.a2m (1 sequences, 114 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11910/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11910/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11910/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11910/tmp.a2m (1 sequences, 114 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11910/tmp.mod tmp/1svy-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-11910 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1svy-align.mod
tmp/1svy-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11910/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1svy-orig.a2m tmp/1svy-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1svy-align.mod
Running w0.5 tmp/1svy-orig.a2m tmp/1svy-align.mod
Running align2model tmp/1svy-align -i tmp/1svy-align.mod -db tmp/1svy-orig.a2m -db tmp/1svy-pdb.a2m
partial PDB gets fragment 42 through 51 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LYS    2   26
LYS    3   26
LEU    4    3
GLU    5   15
LYS    7   28
ARG    8   27
LEU    9    3
ASP   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1svy.134.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1svy.135.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1svy.135.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1svy.135.0.a2m \
	-target T0124 -template 1svy \
	-out T0124-1svy.135.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1svy-orig.a2m
Writing a2m file: tmp/1svy-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9379


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9379/tmp -alignfile tmp/1svy-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1svy-orig.a2m (1 sequences, 114 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9379/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9379/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9379/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9379/tmp.a2m (1 sequences, 114 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9379/tmp.mod tmp/1svy-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9379 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1svy-align.mod
tmp/1svy-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9379/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1svy-orig.a2m tmp/1svy-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1svy-align.mod
Running w0.5 tmp/1svy-orig.a2m tmp/1svy-align.mod
Running align2model tmp/1svy-align -i tmp/1svy-align.mod -db tmp/1svy-orig.a2m -db tmp/1svy-pdb.a2m
partial PDB gets fragment 41 through 50 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LYS    2   26
LEU    3    3
GLU    4   12
LYS    6   30
ARG    7   20
LEU    8    2
ASP    9    5
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue L 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1svy.135.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1svy.136.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1svy.136.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1svy.136.2.a2m \
	-target T0124 -template 1svy \
	-out T0124-1svy.136.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1svy-orig.a2m
Writing a2m file: tmp/1svy-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25582


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25582/tmp -alignfile tmp/1svy-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1svy-orig.a2m (1 sequences, 114 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25582/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25582/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25582/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25582/tmp.a2m (1 sequences, 114 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25582/tmp.mod tmp/1svy-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25582 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1svy-align.mod
tmp/1svy-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25582/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1svy-orig.a2m tmp/1svy-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1svy-align.mod
Running w0.5 tmp/1svy-orig.a2m tmp/1svy-align.mod
Running align2model tmp/1svy-align -i tmp/1svy-align.mod -db tmp/1svy-orig.a2m -db tmp/1svy-pdb.a2m
partial PDB gets fragment 40 through 49 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LEU    2    3
GLU    3   13
LYS    5   26
ARG    6   32
LEU    7    3
ASP    8    4
ARG    9   30
ILE   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1svy.136.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1svy.137.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1svy.137.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1svy.137.5.a2m \
	-target T0124 -template 1svy \
	-out T0124-1svy.137.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1svy-orig.a2m
Writing a2m file: tmp/1svy-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10227


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10227/tmp -alignfile tmp/1svy-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1svy-orig.a2m (1 sequences, 114 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10227/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10227/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10227/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10227/tmp.a2m (1 sequences, 114 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10227/tmp.mod tmp/1svy-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10227 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1svy-align.mod
tmp/1svy-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10227/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1svy-orig.a2m tmp/1svy-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1svy-align.mod
Running w0.5 tmp/1svy-orig.a2m tmp/1svy-align.mod
Running align2model tmp/1svy-align -i tmp/1svy-align.mod -db tmp/1svy-orig.a2m -db tmp/1svy-pdb.a2m
partial PDB gets fragment 39 through 48 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    4
GLU    2   13
LYS    4   26
ARG    5   27
LEU    6    3
ASP    7    6
ARG    8   32
ILE    9    2
GLN   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1svy.137.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1thx.83.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1thx.83.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1thx.83.4.a2m \
	-target T0124 -template 1thx \
	-out T0124-1thx.83.4 -outdir und
Skipped atom 42, because occupancy 0.5 <= existing 0.500001
Skipped atom 44, because occupancy 0.5 <= existing 0.500001
Skipped atom 46, because occupancy 0.5 <= existing 0.500001
Skipped atom 48, because occupancy 0.5 <= existing 0.500001
Skipped atom 845, because occupancy 0.5 <= existing 0.500001
Skipped atom 847, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1thx-orig.a2m
Writing a2m file: tmp/1thx-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29102


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29102/tmp -alignfile tmp/1thx-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1thx-orig.a2m (1 sequences, 115 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29102/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29102/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29102/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29102/tmp.a2m (1 sequences, 115 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29102/tmp.mod tmp/1thx-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29102 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1thx-align.mod
tmp/1thx-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29102/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1thx-orig.a2m tmp/1thx-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1thx-align.mod
Running w0.5 tmp/1thx-orig.a2m tmp/1thx-align.mod
Running align2model tmp/1thx-align -i tmp/1thx-align.mod -db tmp/1thx-orig.a2m -db tmp/1thx-pdb.a2m
partial PDB gets fragment 72 through 81 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
LEU    2    4
GLU    4   15
GLU    5   16
TYR    6    3
HIS    7    3
ASP    8    5
ILE   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1thx.83.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1tl2A.203.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1tl2A.203.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1tl2A.203.2.a2m \
	-target T0124 -template 1tl2A \
	-out T0124-1tl2A.203.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1tl2A-orig.a2m
Writing a2m file: tmp/1tl2A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22137


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22137/tmp -alignfile tmp/1tl2A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1tl2A-orig.a2m (1 sequences, 236 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22137/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22137/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22137/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22137/tmp.a2m (1 sequences, 236 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22137/tmp.mod tmp/1tl2A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22137 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1tl2A-align.mod
tmp/1tl2A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22137/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1tl2A-orig.a2m tmp/1tl2A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1tl2A-align.mod
Running w0.5 tmp/1tl2A-orig.a2m tmp/1tl2A-align.mod
Running align2model tmp/1tl2A-align -i tmp/1tl2A-align.mod -db tmp/1tl2A-orig.a2m -db tmp/1tl2A-pdb.a2m
partial PDB gets fragment 15 through 25 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   14
LYS    3   30
GLU    4   15
LEU    7    5
GLN    8   15
GLN    9   12
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    3     11.2836
Cluster     1 =   2   3
2 clashing residues after turn 
Residue clashes:
2-3
cluster 1 has 2 members and 0.000e+00 combinations:
 2  3 
Energy     11.2836
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
0.000000 < 11.283617: keeping 
Solved cluster 1: residual clashing  1.24
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1tl2A.203.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1tl2A.204.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1tl2A.204.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1tl2A.204.1.a2m \
	-target T0124 -template 1tl2A \
	-out T0124-1tl2A.204.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1tl2A-orig.a2m
Writing a2m file: tmp/1tl2A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20725


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20725/tmp -alignfile tmp/1tl2A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1tl2A-orig.a2m (1 sequences, 236 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20725/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20725/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20725/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20725/tmp.a2m (1 sequences, 236 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20725/tmp.mod tmp/1tl2A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20725 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1tl2A-align.mod
tmp/1tl2A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20725/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1tl2A-orig.a2m tmp/1tl2A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1tl2A-align.mod
Running w0.5 tmp/1tl2A-orig.a2m tmp/1tl2A-align.mod
Running align2model tmp/1tl2A-align -i tmp/1tl2A-align.mod -db tmp/1tl2A-orig.a2m -db tmp/1tl2A-pdb.a2m
partial PDB gets fragment 14 through 24 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
LYS    2   31
GLU    3   10
GLN    5   15
LEU    6    3
GLN    8    7
GLU    9   15
VAL   11    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1tl2A.204.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1tl2A.206.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1tl2A.206.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1tl2A.206.4.a2m \
	-target T0124 -template 1tl2A \
	-out T0124-1tl2A.206.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1tl2A-orig.a2m
Writing a2m file: tmp/1tl2A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28382


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28382/tmp -alignfile tmp/1tl2A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1tl2A-orig.a2m (1 sequences, 236 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28382/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28382/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28382/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28382/tmp.a2m (1 sequences, 236 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28382/tmp.mod tmp/1tl2A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28382 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1tl2A-align.mod
tmp/1tl2A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28382/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1tl2A-orig.a2m tmp/1tl2A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1tl2A-align.mod
Running w0.5 tmp/1tl2A-orig.a2m tmp/1tl2A-align.mod
Running align2model tmp/1tl2A-align -i tmp/1tl2A-align.mod -db tmp/1tl2A-orig.a2m -db tmp/1tl2A-pdb.a2m
partial PDB gets fragment 14 through 23 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
GLN    3   13
LEU    4    3
GLN    5   15
GLN    6   13
GLU    7   12
VAL    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1tl2A.206.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vfrA.44.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vfrA.44.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vfrA.44.5.a2m \
	-target T0124 -template 1vfrA \
	-out T0124-1vfrA.44.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vfrA-orig.a2m
Writing a2m file: tmp/1vfrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7231


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7231/tmp -alignfile tmp/1vfrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vfrA-orig.a2m (1 sequences, 218 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7231/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7231/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7231/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7231/tmp.a2m (1 sequences, 218 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7231/tmp.mod tmp/1vfrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7231 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vfrA-align.mod
tmp/1vfrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7231/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vfrA-orig.a2m tmp/1vfrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vfrA-align.mod
Running w0.5 tmp/1vfrA-orig.a2m tmp/1vfrA-align.mod
Running align2model tmp/1vfrA-align -i tmp/1vfrA-align.mod -db tmp/1vfrA-orig.a2m -db tmp/1vfrA-pdb.a2m
partial PDB gets fragment 179 through 188 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   31
ARG    3   24
GLU    5   12
LEU    6    2
LEU    7    4
GLN    8   12
LYS    9   25
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vfrA.44.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vfrA.45.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vfrA.45.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vfrA.45.5.a2m \
	-target T0124 -template 1vfrA \
	-out T0124-1vfrA.45.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vfrA-orig.a2m
Writing a2m file: tmp/1vfrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21896


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21896/tmp -alignfile tmp/1vfrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vfrA-orig.a2m (1 sequences, 218 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21896/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21896/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21896/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21896/tmp.a2m (1 sequences, 218 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21896/tmp.mod tmp/1vfrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21896 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vfrA-align.mod
tmp/1vfrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21896/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vfrA-orig.a2m tmp/1vfrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vfrA-align.mod
Running w0.5 tmp/1vfrA-orig.a2m tmp/1vfrA-align.mod
Running align2model tmp/1vfrA-align -i tmp/1vfrA-align.mod -db tmp/1vfrA-orig.a2m -db tmp/1vfrA-pdb.a2m
partial PDB gets fragment 178 through 187 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   20
ARG    2   26
GLU    3   12
GLU    4   13
LEU    5    5
LEU    6    3
GLN    7   12
LYS    8   31
TYR    9    2
SER   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7   10     47.0040
Cluster     1 =   7  10
2 clashing residues after turn 
Residue clashes:
7-10
cluster 1 has 2 members and 6.000e+00 combinations:
 10  7 
Energy     47.0040
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 6.000e+00 - Sending to search
0.000000 < 47.003967: keeping 
0.000000 < 0.600843: keeping 
Solved cluster 1: residual clashing  0.05
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vfrA.45.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vfrA.46.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vfrA.46.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vfrA.46.3.a2m \
	-target T0124 -template 1vfrA \
	-out T0124-1vfrA.46.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vfrA-orig.a2m
Writing a2m file: tmp/1vfrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13277


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13277/tmp -alignfile tmp/1vfrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vfrA-orig.a2m (1 sequences, 218 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13277/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13277/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13277/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13277/tmp.a2m (1 sequences, 218 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13277/tmp.mod tmp/1vfrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13277 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vfrA-align.mod
tmp/1vfrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13277/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vfrA-orig.a2m tmp/1vfrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vfrA-align.mod
Running w0.5 tmp/1vfrA-orig.a2m tmp/1vfrA-align.mod
Running align2model tmp/1vfrA-align -i tmp/1vfrA-align.mod -db tmp/1vfrA-orig.a2m -db tmp/1vfrA-pdb.a2m
partial PDB gets fragment 177 through 186 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
GLU    2   12
GLU    3   12
LEU    4    3
LEU    5    3
GLN    6   15
LYS    7   26
TYR    8    3
SER    9    3
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vfrA.46.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vfrA.47.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vfrA.47.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vfrA.47.4.a2m \
	-target T0124 -template 1vfrA \
	-out T0124-1vfrA.47.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vfrA-orig.a2m
Writing a2m file: tmp/1vfrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27406


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27406/tmp -alignfile tmp/1vfrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vfrA-orig.a2m (1 sequences, 218 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27406/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27406/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27406/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27406/tmp.a2m (1 sequences, 218 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27406/tmp.mod tmp/1vfrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27406 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vfrA-align.mod
tmp/1vfrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27406/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vfrA-orig.a2m tmp/1vfrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vfrA-align.mod
Running w0.5 tmp/1vfrA-orig.a2m tmp/1vfrA-align.mod
Running align2model tmp/1vfrA-align -i tmp/1vfrA-align.mod -db tmp/1vfrA-orig.a2m -db tmp/1vfrA-pdb.a2m
partial PDB gets fragment 176 through 185 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    4    3
GLN    5   11
LYS    6   24
TYR    7    2
SER    8    2
VAL    9    2
LEU   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vfrA.47.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vhh.52.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vhh.52.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vhh.52.1.a2m \
	-target T0124 -template 1vhh \
	-out T0124-1vhh.52.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vhh-orig.a2m
Writing a2m file: tmp/1vhh-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10748


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10748/tmp -alignfile tmp/1vhh-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vhh-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10748/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10748/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10748/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10748/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10748/tmp.mod tmp/1vhh-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10748 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vhh-align.mod
tmp/1vhh-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10748/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vhh-orig.a2m tmp/1vhh-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vhh-align.mod
Running w0.5 tmp/1vhh-orig.a2m tmp/1vhh-align.mod
Running align2model tmp/1vhh-align -i tmp/1vhh-align.mod -db tmp/1vhh-orig.a2m -db tmp/1vhh-pdb.a2m
partial PDB gets fragment 131 through 140 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
TYR    2    2
SER    3    2
VAL    4    2
LEU    5    3
PHE    6    2
LEU    7    3
PRO    9    2
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     9   10     14.3105
Cluster     1 =   9  10
2 clashing residues after turn 
Residue clashes:
9-10
cluster 1 has 2 members and 0.000e+00 combinations:
 9  10 
Energy     14.3105
Searching cluster 9
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
10.000000 < 14.310533: keeping 
Solved cluster 1: residual clashing 10.00
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vhh.52.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vhh.53.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vhh.53.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vhh.53.0.a2m \
	-target T0124 -template 1vhh \
	-out T0124-1vhh.53.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vhh-orig.a2m
Writing a2m file: tmp/1vhh-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31742


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31742/tmp -alignfile tmp/1vhh-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vhh-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31742/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31742/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31742/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31742/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31742/tmp.mod tmp/1vhh-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31742 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vhh-align.mod
tmp/1vhh-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31742/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vhh-orig.a2m tmp/1vhh-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vhh-align.mod
Running w0.5 tmp/1vhh-orig.a2m tmp/1vhh-align.mod
Running align2model tmp/1vhh-align -i tmp/1vhh-align.mod -db tmp/1vhh-orig.a2m -db tmp/1vhh-pdb.a2m
partial PDB gets fragment 130 through 139 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
SER    2    2
VAL    3    3
LEU    4    3
PHE    5    3
LEU    6    3
GLU    7   13
PRO    8    2
VAL    9    1
TYR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vhh.53.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vhh.53.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vhh.53.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vhh.53.3.a2m \
	-target T0124 -template 1vhh \
	-out T0124-1vhh.53.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vhh-orig.a2m
Writing a2m file: tmp/1vhh-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10452


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10452/tmp -alignfile tmp/1vhh-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vhh-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10452/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10452/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10452/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10452/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10452/tmp.mod tmp/1vhh-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10452 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vhh-align.mod
tmp/1vhh-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10452/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vhh-orig.a2m tmp/1vhh-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vhh-align.mod
Running w0.5 tmp/1vhh-orig.a2m tmp/1vhh-align.mod
Running align2model tmp/1vhh-align -i tmp/1vhh-align.mod -db tmp/1vhh-orig.a2m -db tmp/1vhh-pdb.a2m
partial PDB gets fragment 128 through 138 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    2
SER    2    2
VAL    3    3
LEU    4    2
LEU    6    5
GLU    7   14
PRO    8    2
VAL    9    2
PRO   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 12 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    6.28515
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vhh.53.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vhh.54.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vhh.54.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vhh.54.4.a2m \
	-target T0124 -template 1vhh \
	-out T0124-1vhh.54.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vhh-orig.a2m
Writing a2m file: tmp/1vhh-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4575


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4575/tmp -alignfile tmp/1vhh-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vhh-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4575/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4575/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4575/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4575/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4575/tmp.mod tmp/1vhh-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4575 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vhh-align.mod
tmp/1vhh-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4575/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vhh-orig.a2m tmp/1vhh-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vhh-align.mod
Running w0.5 tmp/1vhh-orig.a2m tmp/1vhh-align.mod
Running align2model tmp/1vhh-align -i tmp/1vhh-align.mod -db tmp/1vhh-orig.a2m -db tmp/1vhh-pdb.a2m
partial PDB gets fragment 127 through 137 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
LEU    3    3
PHE    4    3
LEU    5    2
GLU    6   15
PRO    7    2
VAL    8    2
TYR    9    3
PRO   10    2
ARG   11   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vhh.54.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vhh.55.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vhh.55.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vhh.55.4.a2m \
	-target T0124 -template 1vhh \
	-out T0124-1vhh.55.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vhh-orig.a2m
Writing a2m file: tmp/1vhh-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8756


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8756/tmp -alignfile tmp/1vhh-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vhh-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8756/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8756/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8756/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8756/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8756/tmp.mod tmp/1vhh-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8756 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vhh-align.mod
tmp/1vhh-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8756/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vhh-orig.a2m tmp/1vhh-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vhh-align.mod
Running w0.5 tmp/1vhh-orig.a2m tmp/1vhh-align.mod
Running align2model tmp/1vhh-align -i tmp/1vhh-align.mod -db tmp/1vhh-orig.a2m -db tmp/1vhh-pdb.a2m
partial PDB gets fragment 126 through 136 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
LEU    2    3
PHE    3    2
LEU    4    3
GLU    5   14
PRO    6    2
VAL    7    3
TYR    8    3
PRO    9    2
ARG   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vhh.55.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vhh.57.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vhh.57.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vhh.57.2.a2m \
	-target T0124 -template 1vhh \
	-out T0124-1vhh.57.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vhh-orig.a2m
Writing a2m file: tmp/1vhh-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11055


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11055/tmp -alignfile tmp/1vhh-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vhh-orig.a2m (1 sequences, 162 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11055/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11055/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11055/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11055/tmp.a2m (1 sequences, 162 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11055/tmp.mod tmp/1vhh-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-11055 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vhh-align.mod
tmp/1vhh-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11055/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vhh-orig.a2m tmp/1vhh-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vhh-align.mod
Running w0.5 tmp/1vhh-orig.a2m tmp/1vhh-align.mod
Running align2model tmp/1vhh-align -i tmp/1vhh-align.mod -db tmp/1vhh-orig.a2m -db tmp/1vhh-pdb.a2m
partial PDB gets fragment 126 through 135 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PHE    1    3
LEU    2    3
GLU    3   12
PRO    4    2
VAL    5    3
TYR    6    2
PRO    7    2
ARG    8   32
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue V 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    8     18.1220
Cluster     1 =   6   8
2 clashing residues after turn 
Residue clashes:
6-8
cluster 1 has 2 members and 6.000e+00 combinations:
 8  6 
Energy     71.0868
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 6.000e+00 - Sending to search
0.000000 < 71.086823: keeping 
Solved cluster 1: residual clashing 33.33
Still clashes at these sidechain pairs:
Residual clashes =   10.12393
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vhh.57.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vid.39.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vid.39.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vid.39.4.a2m \
	-target T0124 -template 1vid \
	-out T0124-1vid.39.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vid-orig.a2m
Writing a2m file: tmp/1vid-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9869


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9869/tmp -alignfile tmp/1vid-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vid-orig.a2m (1 sequences, 221 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9869/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9869/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9869/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9869/tmp.a2m (1 sequences, 221 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9869/tmp.mod tmp/1vid-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9869 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vid-align.mod
tmp/1vid-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9869/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vid-orig.a2m tmp/1vid-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vid-align.mod
Running w0.5 tmp/1vid-orig.a2m tmp/1vid-align.mod
Running align2model tmp/1vid-align -i tmp/1vid-align.mod -db tmp/1vid-orig.a2m -db tmp/1vid-pdb.a2m
partial PDB gets fragment 201 through 210 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
ARG    2   30
LYS    3   24
SER    5    2
LYS    6   26
ARG    7   27
ARG    8   27
GLU    9   12
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vid.39.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vid.40.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vid.40.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vid.40.2.a2m \
	-target T0124 -template 1vid \
	-out T0124-1vid.40.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vid-orig.a2m
Writing a2m file: tmp/1vid-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5111


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5111/tmp -alignfile tmp/1vid-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vid-orig.a2m (1 sequences, 221 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5111/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5111/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5111/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5111/tmp.a2m (1 sequences, 221 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5111/tmp.mod tmp/1vid-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5111 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vid-align.mod
tmp/1vid-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5111/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vid-orig.a2m tmp/1vid-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vid-align.mod
Running w0.5 tmp/1vid-orig.a2m tmp/1vid-align.mod
Running align2model tmp/1vid-align -i tmp/1vid-align.mod -db tmp/1vid-orig.a2m -db tmp/1vid-pdb.a2m
partial PDB gets fragment 200 through 209 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
LYS    2   28
SER    4    3
LYS    5   27
ARG    6   27
ARG    7   26
GLU    8   13
GLU    9   13
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vid.40.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vid.40.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vid.40.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vid.40.5.a2m \
	-target T0124 -template 1vid \
	-out T0124-1vid.40.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vid-orig.a2m
Writing a2m file: tmp/1vid-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5578


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5578/tmp -alignfile tmp/1vid-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vid-orig.a2m (1 sequences, 221 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5578/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5578/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5578/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5578/tmp.a2m (1 sequences, 221 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5578/tmp.mod tmp/1vid-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5578 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vid-align.mod
tmp/1vid-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5578/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vid-orig.a2m tmp/1vid-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vid-align.mod
Running w0.5 tmp/1vid-orig.a2m tmp/1vid-align.mod
Running align2model tmp/1vid-align -i tmp/1vid-align.mod -db tmp/1vid-orig.a2m -db tmp/1vid-pdb.a2m
partial PDB gets fragment 196 through 207 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   19
LYS    2   22
SER    4    3
LYS    5   26
ARG    6   30
ARG    7   30
GLU    8   15
LEU   10    3
LEU   11    3
GLN   12   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vid.40.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vid.41.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vid.41.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vid.41.1.a2m \
	-target T0124 -template 1vid \
	-out T0124-1vid.41.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vid-orig.a2m
Writing a2m file: tmp/1vid-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12335


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12335/tmp -alignfile tmp/1vid-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vid-orig.a2m (1 sequences, 221 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12335/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12335/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12335/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12335/tmp.a2m (1 sequences, 221 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12335/tmp.mod tmp/1vid-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12335 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vid-align.mod
tmp/1vid-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12335/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vid-orig.a2m tmp/1vid-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vid-align.mod
Running w0.5 tmp/1vid-orig.a2m tmp/1vid-align.mod
Running align2model tmp/1vid-align -i tmp/1vid-align.mod -db tmp/1vid-orig.a2m -db tmp/1vid-pdb.a2m
partial PDB gets fragment 199 through 208 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
SER    3    3
LYS    4   28
ARG    5   28
ARG    6   27
GLU    7   13
GLU    8   14
LEU    9    3
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vid.41.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vid.41.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vid.41.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vid.41.4.a2m \
	-target T0124 -template 1vid \
	-out T0124-1vid.41.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vid-orig.a2m
Writing a2m file: tmp/1vid-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7181


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7181/tmp -alignfile tmp/1vid-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vid-orig.a2m (1 sequences, 221 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7181/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7181/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7181/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7181/tmp.a2m (1 sequences, 221 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7181/tmp.mod tmp/1vid-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7181 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vid-align.mod
tmp/1vid-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7181/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vid-orig.a2m tmp/1vid-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vid-align.mod
Running w0.5 tmp/1vid-orig.a2m tmp/1vid-align.mod
Running align2model tmp/1vid-align -i tmp/1vid-align.mod -db tmp/1vid-orig.a2m -db tmp/1vid-pdb.a2m
partial PDB gets fragment 195 through 206 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   28
SER    3    2
ARG    5   28
ARG    6   26
GLU    7   13
GLU    8   14
LEU   10    3
GLN   11   12
LYS   12   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vid.41.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vid.42.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vid.42.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vid.42.5.a2m \
	-target T0124 -template 1vid \
	-out T0124-1vid.42.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vid-orig.a2m
Writing a2m file: tmp/1vid-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20698


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20698/tmp -alignfile tmp/1vid-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vid-orig.a2m (1 sequences, 221 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20698/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20698/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20698/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20698/tmp.a2m (1 sequences, 221 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20698/tmp.mod tmp/1vid-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20698 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vid-align.mod
tmp/1vid-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20698/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vid-orig.a2m tmp/1vid-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vid-align.mod
Running w0.5 tmp/1vid-orig.a2m tmp/1vid-align.mod
Running align2model tmp/1vid-align -i tmp/1vid-align.mod -db tmp/1vid-orig.a2m -db tmp/1vid-pdb.a2m
partial PDB gets fragment 194 through 205 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
SER    2    3
LYS    3   19
ARG    4   32
ARG    5   21
GLU    6   13
GLU    7   13
LEU    8    4
LEU    9    4
GLN   10   13
LYS   11   27
TYR   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 4 rotamers of residue L 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vid.42.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vid.45.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vid.45.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vid.45.0.a2m \
	-target T0124 -template 1vid \
	-out T0124-1vid.45.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vid-orig.a2m
Writing a2m file: tmp/1vid-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4872


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4872/tmp -alignfile tmp/1vid-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vid-orig.a2m (1 sequences, 221 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4872/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4872/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4872/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4872/tmp.a2m (1 sequences, 221 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4872/tmp.mod tmp/1vid-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4872 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vid-align.mod
tmp/1vid-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4872/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vid-orig.a2m tmp/1vid-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vid-align.mod
Running w0.5 tmp/1vid-orig.a2m tmp/1vid-align.mod
Running align2model tmp/1vid-align -i tmp/1vid-align.mod -db tmp/1vid-orig.a2m -db tmp/1vid-pdb.a2m
partial PDB gets fragment 195 through 204 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   29
ARG    2   19
GLU    3   10
GLU    4   13
LEU    5    3
LEU    6    3
GLN    7   12
LYS    8   28
TYR    9    3
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vid.45.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vid.46.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vid.46.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vid.46.4.a2m \
	-target T0124 -template 1vid \
	-out T0124-1vid.46.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vid-orig.a2m
Writing a2m file: tmp/1vid-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-278


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-278/tmp -alignfile tmp/1vid-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vid-orig.a2m (1 sequences, 221 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-278/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-278/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-278/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-278/tmp.a2m (1 sequences, 221 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-278/tmp.mod tmp/1vid-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-278 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vid-align.mod
tmp/1vid-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-278/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vid-orig.a2m tmp/1vid-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vid-align.mod
Running w0.5 tmp/1vid-orig.a2m tmp/1vid-align.mod
Running align2model tmp/1vid-align -i tmp/1vid-align.mod -db tmp/1vid-orig.a2m -db tmp/1vid-pdb.a2m
partial PDB gets fragment 194 through 203 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   32
GLU    3   12
LEU    4    4
LEU    5    2
GLN    6   12
LYS    7   26
TYR    8    2
SER    9    2
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue Y 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.94792
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vid.46.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vns.189.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vns.189.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vns.189.5.a2m \
	-target T0124 -template 1vns \
	-out T0124-1vns.189.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vns-orig.a2m
Writing a2m file: tmp/1vns-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10037


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10037/tmp -alignfile tmp/1vns-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vns-orig.a2m (1 sequences, 609 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10037/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10037/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10037/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10037/tmp.a2m (1 sequences, 609 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10037/tmp.mod tmp/1vns-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10037 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vns-align.mod
tmp/1vns-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10037/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vns-orig.a2m tmp/1vns-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vns-align.mod
Running w0.5 tmp/1vns-orig.a2m tmp/1vns-align.mod
Running align2model tmp/1vns-align -i tmp/1vns-align.mod -db tmp/1vns-orig.a2m -db tmp/1vns-pdb.a2m
partial PDB gets fragment 19 through 28 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   11
LYS    2   26
LEU    3    3
GLU    4   15
GLU    5   12
LYS    6   26
GLN    7   11
GLU    9   15
ASN   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vns.189.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vns.190.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vns.190.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vns.190.5.a2m \
	-target T0124 -template 1vns \
	-out T0124-1vns.190.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vns-orig.a2m
Writing a2m file: tmp/1vns-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-24366


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-24366/tmp -alignfile tmp/1vns-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vns-orig.a2m (1 sequences, 609 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-24366/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-24366/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-24366/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24366/tmp.a2m (1 sequences, 609 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-24366/tmp.mod tmp/1vns-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-24366 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vns-align.mod
tmp/1vns-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-24366/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vns-orig.a2m tmp/1vns-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vns-align.mod
Running w0.5 tmp/1vns-orig.a2m tmp/1vns-align.mod
Running align2model tmp/1vns-align -i tmp/1vns-align.mod -db tmp/1vns-orig.a2m -db tmp/1vns-pdb.a2m
partial PDB gets fragment 18 through 27 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   30
LEU    2    3
GLU    3   12
GLU    4   12
LYS    5   30
GLN    6   11
GLU    8   12
ASN    9    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vns.190.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vns.191.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vns.191.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vns.191.4.a2m \
	-target T0124 -template 1vns \
	-out T0124-1vns.191.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vns-orig.a2m
Writing a2m file: tmp/1vns-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17467


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17467/tmp -alignfile tmp/1vns-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vns-orig.a2m (1 sequences, 609 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17467/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17467/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17467/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17467/tmp.a2m (1 sequences, 609 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17467/tmp.mod tmp/1vns-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17467 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vns-align.mod
tmp/1vns-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17467/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vns-orig.a2m tmp/1vns-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vns-align.mod
Running w0.5 tmp/1vns-orig.a2m tmp/1vns-align.mod
Running align2model tmp/1vns-align -i tmp/1vns-align.mod -db tmp/1vns-orig.a2m -db tmp/1vns-pdb.a2m
partial PDB gets fragment 17 through 26 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    2   15
GLU    3   12
LYS    4   26
GLN    5   11
GLU    7   12
ASN    8    4
LEU    9    3
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vns.191.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vns.61.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vns.61.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vns.61.0.a2m \
	-target T0124 -template 1vns \
	-out T0124-1vns.61.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vns-orig.a2m
Writing a2m file: tmp/1vns-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9326


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9326/tmp -alignfile tmp/1vns-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vns-orig.a2m (1 sequences, 609 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9326/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9326/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9326/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9326/tmp.a2m (1 sequences, 609 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9326/tmp.mod tmp/1vns-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9326 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vns-align.mod
tmp/1vns-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9326/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vns-orig.a2m tmp/1vns-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vns-align.mod
Running w0.5 tmp/1vns-orig.a2m tmp/1vns-align.mod
Running align2model tmp/1vns-align -i tmp/1vns-align.mod -db tmp/1vns-orig.a2m -db tmp/1vns-pdb.a2m
partial PDB gets fragment 146 through 155 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
TYR    2    3
PRO    3    2
ARG    4   26
LEU    6    3
ASP    7    6
SER    8    3
GLN    9   12
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue V 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vns.61.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vns.61.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vns.61.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vns.61.4.a2m \
	-target T0124 -template 1vns \
	-out T0124-1vns.61.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vns-orig.a2m
Writing a2m file: tmp/1vns-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4905


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4905/tmp -alignfile tmp/1vns-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vns-orig.a2m (1 sequences, 609 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4905/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4905/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4905/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4905/tmp.a2m (1 sequences, 609 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4905/tmp.mod tmp/1vns-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4905 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vns-align.mod
tmp/1vns-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4905/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vns-orig.a2m tmp/1vns-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vns-align.mod
Running w0.5 tmp/1vns-orig.a2m tmp/1vns-align.mod
Running align2model tmp/1vns-align -i tmp/1vns-align.mod -db tmp/1vns-orig.a2m -db tmp/1vns-pdb.a2m
partial PDB gets fragment 142 through 151 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
TYR    2    3
PRO    3    2
ARG    4   29
LEU    6    2
ASP    7    5
SER    8    2
GLN    9   15
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    6.93954
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vns.61.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vns.62.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vns.62.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vns.62.0.a2m \
	-target T0124 -template 1vns \
	-out T0124-1vns.62.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vns-orig.a2m
Writing a2m file: tmp/1vns-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10177


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10177/tmp -alignfile tmp/1vns-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vns-orig.a2m (1 sequences, 609 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10177/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10177/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10177/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10177/tmp.a2m (1 sequences, 609 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10177/tmp.mod tmp/1vns-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10177 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vns-align.mod
tmp/1vns-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10177/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vns-orig.a2m tmp/1vns-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vns-align.mod
Running w0.5 tmp/1vns-orig.a2m tmp/1vns-align.mod
Running align2model tmp/1vns-align -i tmp/1vns-align.mod -db tmp/1vns-orig.a2m -db tmp/1vns-pdb.a2m
partial PDB gets fragment 145 through 154 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    2
PRO    2    2
ARG    3   26
LEU    5    3
ASP    6    5
SER    7    2
GLN    8   14
VAL    9    1
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    3     30.2513
keepclash     6    9     11.1468
Cluster     1 =   2   3
Cluster     2 =   6   9
4 clashing residues after turn 
Residue clashes:
2-3
6-9
cluster 1 has 2 members and 4.000e+00 combinations:
 2  3 
Energy     30.2513
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
18.836479 < 30.251335: keeping 
0.000000 < 18.836479: keeping 
Solved cluster 1: residual clashing  1.30
cluster 2 has 2 members and 3.600e+01 combinations:
 6  9 
Energy     11.1468
Searching cluster 6
Combinations for 2 members in cluster 2 OK: 3.600e+01 - Sending to search
1.554880 < 11.146765: keeping 
0.000000 < 1.663335: keeping 
Solved cluster 2: residual clashing  0.11
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vns.62.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vns.63.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vns.63.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vns.63.0.a2m \
	-target T0124 -template 1vns \
	-out T0124-1vns.63.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vns-orig.a2m
Writing a2m file: tmp/1vns-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1224


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1224/tmp -alignfile tmp/1vns-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vns-orig.a2m (1 sequences, 609 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1224/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1224/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1224/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1224/tmp.a2m (1 sequences, 609 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1224/tmp.mod tmp/1vns-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1224 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vns-align.mod
tmp/1vns-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1224/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vns-orig.a2m tmp/1vns-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vns-align.mod
Running w0.5 tmp/1vns-orig.a2m tmp/1vns-align.mod
Running align2model tmp/1vns-align -i tmp/1vns-align.mod -db tmp/1vns-orig.a2m -db tmp/1vns-pdb.a2m
partial PDB gets fragment 144 through 153 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
ARG    2   29
LEU    4    2
ASP    5    5
SER    6    2
GLN    7   15
VAL    8    3
VAL    9    3
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    6.93954
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vns.63.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.214.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.214.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.214.0.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.214.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28605


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28605/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28605/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28605/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28605/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28605/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28605/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28605 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28605/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 7 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
GLU    3   12
TYR    4    3
GLU    5   12
GLU    6   14
LYS    7   25
LEU    8    3
LYS    9   27
THR   10    3
LEU   11    3
THR   12    2
VAL   13    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    6.92401
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.214.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.214.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.214.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.214.3.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.214.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8607


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8607/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8607/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8607/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8607/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8607/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8607/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8607 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8607/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 9 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
GLU    3   12
GLU    5   15
GLU    6   14
LYS    7   27
LEU    8    3
LYS    9   28
THR   10    2
LEU   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.214.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.214.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.214.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.214.5.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.214.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8390


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8390/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8390/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8390/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8390/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8390/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8390/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8390 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8390/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 11 through 20 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
GLU    3   11
TYR    4    3
GLU    5   13
GLU    6   15
LYS    7   28
LEU    8    2
LYS    9   19
THR   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.214.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.215.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.215.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.215.2.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.215.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21513


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21513/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21513/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21513/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21513/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21513/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21513/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21513 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21513/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 6 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
16 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   16
TYR    3    4
GLU    4   12
GLU    5   12
LEU    7    5
LYS    8   25
THR    9    3
LEU   10    3
THR   11    3
VAL   12    2
GLU   13   15
VAL   14    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.215.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.216.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.216.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.216.2.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.216.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6447


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6447/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6447/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6447/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6447/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6447/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6447/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6447 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6447/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 5 through 18 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
16 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
TYR    2    3
GLU    3   16
GLU    4   15
LYS    5   24
LEU    6    3
THR    8    2
THR   10    3
GLU   12   15
VAL   13    2
GLN   14   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue L 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.216.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.217.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.217.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.217.2.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.217.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21005


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21005/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21005/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21005/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21005/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21005/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21005/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21005 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21005/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 4 through 17 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
16 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    2
GLU    2   15
GLU    3   12
LYS    4   28
LEU    5    3
LYS    6   24
THR    7    2
LEU    8    3
THR    9    2
VAL   10    2
GLU   11   14
GLN   13   11
GLU   14   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.217.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.218.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.218.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.218.2.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.218.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3746


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3746/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3746/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3746/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3746/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3746/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3746/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3746 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3746/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 3 through 16 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
16 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
GLU    2   12
LYS    3   30
LEU    4    2
LYS    5   28
THR    6    2
LEU    7    3
THR    8    2
VAL    9    1
GLU   10   14
VAL   11    2
GLN   12   14
GLU   13   13
MET   14   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 12 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.218.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.219.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.219.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.219.3.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.219.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5507


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5507/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5507/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5507/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5507/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5507/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5507/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5507 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5507/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 2 through 15 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
16 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
LYS    2   24
LEU    3    3
LYS    4   30
LEU    6    2
THR    7    2
VAL    8    1
GLU    9   12
VAL   10    1
GLN   11   13
GLU   12   11
MET   13   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue L 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.219.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.221.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.221.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.221.2.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.221.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11062


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11062/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11062/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11062/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11062/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11062/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11062/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-11062 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11062/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 2 through 12 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   24
THR    3    1
LEU    4    3
VAL    6    2
GLU    7   15
VAL    8    1
GLN    9   12
GLU   10   12
MET   11   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.10050
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.221.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.222.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.222.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.222.2.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.222.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4471


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4471/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4471/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4471/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4471/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4471/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4471/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4471 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4471/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 1 through 11 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   31
THR    2    2
LEU    3    2
THR    4    1
VAL    5    3
GLU    6   12
VAL    7    2
GLN    8   14
GLU    9   12
MET   10   10
VAL   11    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.81021
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.222.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.223.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.223.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.223.5.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.223.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-61


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-61/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-61/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-61/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-61/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-61/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-61/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-61 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-61/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 0 through 10 extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    0    1
LEU    1    3
THR    2    2
VAL    3    2
GLU    4   12
VAL    5    3
GLN    6   11
GLU    7   16
MET    8   10
VAL    9    1
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 16 rotamers of residue E 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    8     16.3980
Cluster     1 =   2   8
2 clashing residues after turn 
Residue clashes:
2-8
cluster 1 has 2 members and 1.600e+01 combinations:
 2  8 
Energy    141.1789
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 1.600e+01 - Sending to search
26.815273 < 141.178894: keeping 
19.856884 < 129.370560: keeping 
18.308929 < 33.545479: keeping 
Solved cluster 1: residual clashing 32.40
Still clashes at these sidechain pairs:
ires=    2 irot=    3 jres=    8 jrot=    6      18.3089
Residual clashes =   18.30893
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.223.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.224.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.224.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.224.1.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.224.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-16332


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-16332/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-16332/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16332/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16332/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16332/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16332/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16332 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16332/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 5 through 14 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
VAL    3    2
GLU    4   15
VAL    5    1
GLN    6   12
GLU    7   12
MET    8   11
VAL    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.10050
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.224.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.225.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.225.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.225.2.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.225.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22750


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22750/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22750/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22750/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22750/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22750/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22750/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22750 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22750/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 0 through 9 extending end
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
THR    0    1
VAL    1    3
GLU    2   15
VAL    3    2
GLN    4   11
GLU    5   15
MET    6   10
VAL    7    2
LYS    8   30
ASN    9    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.225.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vom.225.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vom.225.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vom.225.4.a2m \
	-target T0124 -template 1vom \
	-out T0124-1vom.225.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vom-orig.a2m
Writing a2m file: tmp/1vom-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10390


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10390/tmp -alignfile tmp/1vom-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vom-orig.a2m (1 sequences, 762 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10390/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10390/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10390/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10390/tmp.a2m (1 sequences, 762 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10390/tmp.mod tmp/1vom-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10390 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vom-align.mod
tmp/1vom-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10390/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vom-orig.a2m tmp/1vom-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vom-align.mod
Running w0.5 tmp/1vom-orig.a2m tmp/1vom-align.mod
Running align2model tmp/1vom-align -i tmp/1vom-align.mod -db tmp/1vom-orig.a2m -db tmp/1vom-pdb.a2m
partial PDB gets fragment 4 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    1
VAL    2    3
GLU    3   12
VAL    4    2
GLN    5   14
GLU    6   12
MET    7   10
VAL    8    1
LYS    9   24
ASN   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.26520
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vom.225.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vsrA.207.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vsrA.207.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vsrA.207.4.a2m \
	-target T0124 -template 1vsrA \
	-out T0124-1vsrA.207.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vsrA-orig.a2m
Writing a2m file: tmp/1vsrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4522


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4522/tmp -alignfile tmp/1vsrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vsrA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4522/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4522/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4522/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4522/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4522/tmp.mod tmp/1vsrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4522 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vsrA-align.mod
tmp/1vsrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4522/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vsrA-orig.a2m tmp/1vsrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vsrA-align.mod
Running w0.5 tmp/1vsrA-orig.a2m tmp/1vsrA-align.mod
Running align2model tmp/1vsrA-align -i tmp/1vsrA-align.mod -db tmp/1vsrA-orig.a2m -db tmp/1vsrA-pdb.a2m
partial PDB gets fragment 9 through 18 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    2   12
LEU    3    3
GLN    5   10
GLU    6   15
VAL    8    2
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vsrA.207.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vsrA.208.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vsrA.208.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vsrA.208.5.a2m \
	-target T0124 -template 1vsrA \
	-out T0124-1vsrA.208.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vsrA-orig.a2m
Writing a2m file: tmp/1vsrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28499


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28499/tmp -alignfile tmp/1vsrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vsrA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28499/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28499/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28499/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28499/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28499/tmp.mod tmp/1vsrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28499 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vsrA-align.mod
tmp/1vsrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28499/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vsrA-orig.a2m tmp/1vsrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vsrA-align.mod
Running w0.5 tmp/1vsrA-orig.a2m tmp/1vsrA-align.mod
Running align2model tmp/1vsrA-align -i tmp/1vsrA-align.mod -db tmp/1vsrA-orig.a2m -db tmp/1vsrA-pdb.a2m
partial PDB gets fragment 8 through 17 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
GLN    3   11
GLN    4   14
GLU    5   13
VAL    7    3
GLU    9   14
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vsrA.208.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vsrA.209.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vsrA.209.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vsrA.209.4.a2m \
	-target T0124 -template 1vsrA \
	-out T0124-1vsrA.209.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vsrA-orig.a2m
Writing a2m file: tmp/1vsrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4547


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4547/tmp -alignfile tmp/1vsrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vsrA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4547/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4547/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4547/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4547/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4547/tmp.mod tmp/1vsrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4547 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vsrA-align.mod
tmp/1vsrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4547/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vsrA-orig.a2m tmp/1vsrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vsrA-align.mod
Running w0.5 tmp/1vsrA-orig.a2m tmp/1vsrA-align.mod
Running align2model tmp/1vsrA-align -i tmp/1vsrA-align.mod -db tmp/1vsrA-orig.a2m -db tmp/1vsrA-pdb.a2m
partial PDB gets fragment 7 through 16 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLN    2   12
GLN    3   12
GLU    4   12
VAL    6    2
GLU    8   15
TYR    9    3
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4   11     31.1129
turnclash      4    5    9    0     34.2771
Cluster     1 =   4   9  11
3 clashing residues after turn 
Residue clashes:
4-11
4-9
11-9
cluster 1 has 3 members and 1.650e+03 combinations:
 9  4  11 
Energy     31.1129
Searching cluster 4
Combinations for 3 members in cluster 1 OK: 1.650e+03 - Sending to search
28.121159 < 31.112911: keeping 
19.302996 < 28.253258: keeping 
0.000000 < 19.605417: keeping 
0.000000 < 0.638145: keeping 
Solved cluster 1: residual clashing  0.11
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vsrA.209.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vsrA.88.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vsrA.88.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vsrA.88.5.a2m \
	-target T0124 -template 1vsrA \
	-out T0124-1vsrA.88.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vsrA-orig.a2m
Writing a2m file: tmp/1vsrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9781


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9781/tmp -alignfile tmp/1vsrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vsrA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9781/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9781/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9781/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9781/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9781/tmp.mod tmp/1vsrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9781 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vsrA-align.mod
tmp/1vsrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9781/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vsrA-orig.a2m tmp/1vsrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vsrA-align.mod
Running w0.5 tmp/1vsrA-orig.a2m tmp/1vsrA-align.mod
Running align2model tmp/1vsrA-align -i tmp/1vsrA-align.mod -db tmp/1vsrA-orig.a2m -db tmp/1vsrA-pdb.a2m
partial PDB gets fragment 83 through 92 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
HIS    2    3
ASP    3    4
ILE    5    5
ARG    6   27
ARG    7   27
ARG    8   27
LYS    9   27
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vsrA.88.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vsrA.89.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vsrA.89.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vsrA.89.2.a2m \
	-target T0124 -template 1vsrA \
	-out T0124-1vsrA.89.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vsrA-orig.a2m
Writing a2m file: tmp/1vsrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13332


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13332/tmp -alignfile tmp/1vsrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vsrA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13332/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13332/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13332/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13332/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13332/tmp.mod tmp/1vsrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13332 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vsrA-align.mod
tmp/1vsrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13332/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vsrA-orig.a2m tmp/1vsrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vsrA-align.mod
Running w0.5 tmp/1vsrA-orig.a2m tmp/1vsrA-align.mod
Running align2model tmp/1vsrA-align -i tmp/1vsrA-align.mod -db tmp/1vsrA-orig.a2m -db tmp/1vsrA-pdb.a2m
partial PDB gets fragment 82 through 91 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    4
ASP    2    4
ILE    4    2
ARG    5   29
ARG    7   27
LYS    8   27
GLU    9   12
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vsrA.89.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vsrA.90.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vsrA.90.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vsrA.90.2.a2m \
	-target T0124 -template 1vsrA \
	-out T0124-1vsrA.90.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vsrA-orig.a2m
Writing a2m file: tmp/1vsrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4262


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4262/tmp -alignfile tmp/1vsrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vsrA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4262/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4262/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4262/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4262/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4262/tmp.mod tmp/1vsrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4262 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vsrA-align.mod
tmp/1vsrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4262/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vsrA-orig.a2m tmp/1vsrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vsrA-align.mod
Running w0.5 tmp/1vsrA-orig.a2m tmp/1vsrA-align.mod
Running align2model tmp/1vsrA-align -i tmp/1vsrA-align.mod -db tmp/1vsrA-orig.a2m -db tmp/1vsrA-pdb.a2m
partial PDB gets fragment 81 through 90 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    4
ILE    3    5
ARG    4   27
ARG    5   25
ARG    6   29
LYS    7   25
GLU    8   12
GLN    9   13
HIS   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     9   11     10.2282
Cluster     1 =   9  11
2 clashing residues after turn 
Residue clashes:
9-11
cluster 1 has 2 members and 3.600e+01 combinations:
 11  9 
Energy     10.2282
Searching cluster 9
Combinations for 2 members in cluster 1 OK: 3.600e+01 - Sending to search
0.000000 < 10.228216: keeping 
Solved cluster 1: residual clashing  0.10
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vsrA.90.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vsrA.91.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vsrA.91.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vsrA.91.4.a2m \
	-target T0124 -template 1vsrA \
	-out T0124-1vsrA.91.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vsrA-orig.a2m
Writing a2m file: tmp/1vsrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-28435


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-28435/tmp -alignfile tmp/1vsrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vsrA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-28435/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-28435/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-28435/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28435/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-28435/tmp.mod tmp/1vsrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-28435 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vsrA-align.mod
tmp/1vsrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-28435/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vsrA-orig.a2m tmp/1vsrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vsrA-align.mod
Running w0.5 tmp/1vsrA-orig.a2m tmp/1vsrA-align.mod
Running align2model tmp/1vsrA-align -i tmp/1vsrA-align.mod -db tmp/1vsrA-orig.a2m -db tmp/1vsrA-pdb.a2m
partial PDB gets fragment 80 through 89 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    2    2
ARG    3   27
ARG    4   32
ARG    5   27
LYS    6   24
GLU    7   14
GLN    8   14
HIS    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue I 3 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vsrA.91.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vsrA.92.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vsrA.92.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vsrA.92.1.a2m \
	-target T0124 -template 1vsrA \
	-out T0124-1vsrA.92.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vsrA-orig.a2m
Writing a2m file: tmp/1vsrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8156


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8156/tmp -alignfile tmp/1vsrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vsrA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8156/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8156/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8156/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8156/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8156/tmp.mod tmp/1vsrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8156 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vsrA-align.mod
tmp/1vsrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8156/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vsrA-orig.a2m tmp/1vsrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vsrA-align.mod
Running w0.5 tmp/1vsrA-orig.a2m tmp/1vsrA-align.mod
Running align2model tmp/1vsrA-align -i tmp/1vsrA-align.mod -db tmp/1vsrA-orig.a2m -db tmp/1vsrA-pdb.a2m
partial PDB gets fragment 79 through 88 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
ARG    3   25
ARG    4   27
LYS    5   30
GLU    6   14
GLN    7   12
HIS    8    3
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vsrA.92.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vsrA.93.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vsrA.93.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vsrA.93.2.a2m \
	-target T0124 -template 1vsrA \
	-out T0124-1vsrA.93.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vsrA-orig.a2m
Writing a2m file: tmp/1vsrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13502


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13502/tmp -alignfile tmp/1vsrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vsrA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13502/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13502/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13502/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13502/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13502/tmp.mod tmp/1vsrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13502 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vsrA-align.mod
tmp/1vsrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13502/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vsrA-orig.a2m tmp/1vsrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vsrA-align.mod
Running w0.5 tmp/1vsrA-orig.a2m tmp/1vsrA-align.mod
Running align2model tmp/1vsrA-align -i tmp/1vsrA-align.mod -db tmp/1vsrA-orig.a2m -db tmp/1vsrA-pdb.a2m
partial PDB gets fragment 78 through 87 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
ARG    2   27
LYS    4   24
GLU    5   12
GLN    6   14
HIS    7    3
THR    9    2
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.77987
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vsrA.93.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1vsrA.94.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1vsrA.94.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1vsrA.94.4.a2m \
	-target T0124 -template 1vsrA \
	-out T0124-1vsrA.94.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vsrA-orig.a2m
Writing a2m file: tmp/1vsrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12262


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12262/tmp -alignfile tmp/1vsrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vsrA-orig.a2m (1 sequences, 136 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12262/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12262/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12262/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12262/tmp.a2m (1 sequences, 136 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12262/tmp.mod tmp/1vsrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12262 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vsrA-align.mod
tmp/1vsrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12262/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vsrA-orig.a2m tmp/1vsrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vsrA-align.mod
Running w0.5 tmp/1vsrA-orig.a2m tmp/1vsrA-align.mod
Running align2model tmp/1vsrA-align -i tmp/1vsrA-align.mod -db tmp/1vsrA-orig.a2m -db tmp/1vsrA-pdb.a2m
partial PDB gets fragment 77 through 86 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
ARG    2   27
LYS    3   26
GLU    4   12
GLN    5   11
HIS    6    4
THR    8    1
GLU    9   13
GLN   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1vsrA.94.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1yge.125.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1yge.125.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1yge.125.5.a2m \
	-target T0124 -template 1yge \
	-out T0124-1yge.125.5 -outdir und
partial PDB gets fragment 69 through 78 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    2    2
GLU    3   12
SER    4    3
ASN    5    3
ILE    6    3
LYS    7   21
ASP    8    5
ILE    9    5
LYS   10   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1yge.125.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1yge.126.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1yge.126.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1yge.126.5.a2m \
	-target T0124 -template 1yge \
	-out T0124-1yge.126.5 -outdir und
partial PDB gets fragment 68 through 78 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
GLU    2   12
SER    3    3
ASN    4    4
ILE    5    3
LYS    6   22
ASP    7    5
ILE    8    3
LYS    9   18
LYS   10   21
LYS   11   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     9   11     46.1366
Cluster     1 =   9  11
2 clashing residues after turn 
Residue clashes:
9-11
cluster 1 has 2 members and 4.800e+01 combinations:
 9  11 
Energy     46.1366
Searching cluster 9
Combinations for 2 members in cluster 1 OK: 4.800e+01 - Sending to search
17.422211 < 46.136604: keeping 
0.000000 < 18.402906: keeping 
0.000000 < 2.987167: keeping 
Solved cluster 1: residual clashing  1.06
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1yge.126.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1yge.129.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1yge.129.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1yge.129.5.a2m \
	-target T0124 -template 1yge \
	-out T0124-1yge.129.5 -outdir und
partial PDB gets fragment 67 through 76 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    2    4
LYS    3   24
ASP    4    5
ILE    5    3
LYS    6   30
LYS    7   22
LYS    8   21
LEU    9    3
GLU   10    7
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1yge.129.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1yge.130.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1yge.130.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1yge.130.5.a2m \
	-target T0124 -template 1yge \
	-out T0124-1yge.130.5 -outdir und
partial PDB gets fragment 66 through 75 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   28
ASP    3    3
ILE    4    2
LYS    5   26
LYS    6   26
LYS    7   30
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1yge.130.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1yge.198.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1yge.198.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1yge.198.5.a2m \
	-target T0124 -template 1yge \
	-out T0124-1yge.198.5 -outdir und
partial PDB gets fragment 22 through 31 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    3
ARG    3   27
ILE    5    4
GLN    6    7
GLU    7   13
LYS    8   18
GLU    9   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1yge.198.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1yge.199.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1yge.199.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1yge.199.2.a2m \
	-target T0124 -template 1yge \
	-out T0124-1yge.199.2 -outdir und
partial PDB gets fragment 21 through 30 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
ARG    2   32
ILE    4    3
GLN    5   16
GLU    6   11
LYS    7   28
GLU    8   13
GLN   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1yge.199.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1yge.199.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1yge.199.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1yge.199.5.a2m \
	-target T0124 -template 1yge \
	-out T0124-1yge.199.5 -outdir und
partial PDB gets fragment 19 through 29 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
ARG    2   27
ILE    4    4
GLN    5   12
GLU    6   11
LYS    7   29
GLU    8   11
GLN   10    9
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1yge.199.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1yge.201.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1yge.201.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1yge.201.5.a2m \
	-target T0124 -template 1yge \
	-out T0124-1yge.201.5 -outdir und
partial PDB gets fragment 19 through 28 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    2    4
GLN    3   13
GLU    4   15
LYS    5   28
GLU    6   11
GLN    8   10
LEU    9    2
GLN   10    9
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1yge.201.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1zpdA.145.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1zpdA.145.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1zpdA.145.3.a2m \
	-target T0124 -template 1zpdA \
	-out T0124-1zpdA.145.3 -outdir und
Skipped atom 3555, because occupancy 0.5 <= existing 0.500001
Skipped atom 3557, because occupancy 0.5 <= existing 0.500001
Skipped atom 3559, because occupancy 0.5 <= existing 0.500001
Skipped atom 3561, because occupancy 0.5 <= existing 0.500001
Skipped atom 4169, because occupancy 0.4 <= existing 0.600001
Skipped atom 4171, because occupancy 0.4 <= existing 0.600001
Skipped atom 4173, because occupancy 0.4 <= existing 0.600001
Skipped atom 4175, because occupancy 0.4 <= existing 0.600001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1zpdA-orig.a2m
Writing a2m file: tmp/1zpdA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25473


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25473/tmp -alignfile tmp/1zpdA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1zpdA-orig.a2m (1 sequences, 568 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25473/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25473/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25473/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25473/tmp.a2m (1 sequences, 568 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25473/tmp.mod tmp/1zpdA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-25473 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1zpdA-align.mod
tmp/1zpdA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25473/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1zpdA-orig.a2m tmp/1zpdA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1zpdA-align.mod
Running w0.5 tmp/1zpdA-orig.a2m tmp/1zpdA-align.mod
Running align2model tmp/1zpdA-align -i tmp/1zpdA-align.mod -db tmp/1zpdA-orig.a2m -db tmp/1zpdA-pdb.a2m
partial PDB gets fragment 33 through 42 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
GLN    2   12
VAL    3    3
MET    4   10
MET    5   10
ARG    6   20
SER    7    2
THR    8    2
SER    9    3
ASP   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1zpdA.145.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1zpdA.146.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1zpdA.146.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1zpdA.146.0.a2m \
	-target T0124 -template 1zpdA \
	-out T0124-1zpdA.146.0 -outdir und
Skipped atom 3555, because occupancy 0.5 <= existing 0.500001
Skipped atom 3557, because occupancy 0.5 <= existing 0.500001
Skipped atom 3559, because occupancy 0.5 <= existing 0.500001
Skipped atom 3561, because occupancy 0.5 <= existing 0.500001
Skipped atom 4169, because occupancy 0.4 <= existing 0.600001
Skipped atom 4171, because occupancy 0.4 <= existing 0.600001
Skipped atom 4173, because occupancy 0.4 <= existing 0.600001
Skipped atom 4175, because occupancy 0.4 <= existing 0.600001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1zpdA-orig.a2m
Writing a2m file: tmp/1zpdA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12156


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12156/tmp -alignfile tmp/1zpdA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1zpdA-orig.a2m (1 sequences, 568 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12156/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12156/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12156/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12156/tmp.a2m (1 sequences, 568 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12156/tmp.mod tmp/1zpdA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12156 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1zpdA-align.mod
tmp/1zpdA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12156/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1zpdA-orig.a2m tmp/1zpdA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1zpdA-align.mod
Running w0.5 tmp/1zpdA-orig.a2m tmp/1zpdA-align.mod
Running align2model tmp/1zpdA-align -i tmp/1zpdA-align.mod -db tmp/1zpdA-orig.a2m -db tmp/1zpdA-pdb.a2m
partial PDB gets fragment 32 through 41 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
VAL    2    1
MET    3   10
MET    4   11
ARG    5   32
SER    6    2
THR    7    1
SER    8    2
ASP    9    7
LYS   10   23
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1zpdA.146.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-1zpdA.147.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-1zpdA.147.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-1zpdA.147.3.a2m \
	-target T0124 -template 1zpdA \
	-out T0124-1zpdA.147.3 -outdir und
Skipped atom 3555, because occupancy 0.5 <= existing 0.500001
Skipped atom 3557, because occupancy 0.5 <= existing 0.500001
Skipped atom 3559, because occupancy 0.5 <= existing 0.500001
Skipped atom 3561, because occupancy 0.5 <= existing 0.500001
Skipped atom 4169, because occupancy 0.4 <= existing 0.600001
Skipped atom 4171, because occupancy 0.4 <= existing 0.600001
Skipped atom 4173, because occupancy 0.4 <= existing 0.600001
Skipped atom 4175, because occupancy 0.4 <= existing 0.600001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1zpdA-orig.a2m
Writing a2m file: tmp/1zpdA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3482


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3482/tmp -alignfile tmp/1zpdA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1zpdA-orig.a2m (1 sequences, 568 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3482/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3482/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3482/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3482/tmp.a2m (1 sequences, 568 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3482/tmp.mod tmp/1zpdA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3482 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1zpdA-align.mod
tmp/1zpdA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3482/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1zpdA-orig.a2m tmp/1zpdA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1zpdA-align.mod
Running w0.5 tmp/1zpdA-orig.a2m tmp/1zpdA-align.mod
Running align2model tmp/1zpdA-align -i tmp/1zpdA-align.mod -db tmp/1zpdA-orig.a2m -db tmp/1zpdA-pdb.a2m
partial PDB gets fragment 31 through 40 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
MET    2   10
MET    3   10
ARG    4   27
SER    5    2
THR    6    2
SER    7    2
ASP    8    4
LYS    9   22
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-1zpdA.147.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.59.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.59.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.59.4.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.59.4 -outdir und
partial PDB gets fragment 49 through 58 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
PRO    2    2
VAL    3    3
TYR    4    1
ARG    6   31
LEU    8    3
ASP    9    4
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue Y 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   10    117.7518
Cluster     1 =   5  10
2 clashing residues after turn 
Residue clashes:
5-10
cluster 1 has 2 members and 2.000e+00 combinations:
 5  10 
Energy    295.0446
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search
32.729523 < 295.044617: keeping 
Solved cluster 1: residual clashing 211.54
Still clashes at these sidechain pairs:
ires=    5 irot=    1 jres=   10 jrot=    3      32.7295
Residual clashes =   39.84080
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.59.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.60.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.60.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.60.1.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.60.1 -outdir und
partial PDB gets fragment 48 through 57 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
VAL    2    3
TYR    3    3
PRO    4    2
ARG    5   32
LEU    7    3
ASP    8    4
SER    9    3
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    8.12381
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.60.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.65.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.65.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.65.4.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.65.4 -outdir und
partial PDB gets fragment 53 through 62 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    3
ASP    3    4
SER    4    3
GLN    5   12
VAL    6    1
VAL    7    2
GLU    8   12
LEU    9    3
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.65.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.66.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.66.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.66.1.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.66.1 -outdir und
partial PDB gets fragment 52 through 61 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
ASP    2    5
SER    3    3
GLN    4   12
VAL    5    2
GLU    7   13
LEU    8    3
LYS    9   26
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue L 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.24062
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.66.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.67.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.67.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.67.1.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.67.1 -outdir und
partial PDB gets fragment 51 through 60 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    6
SER    2    3
GLN    3   14
VAL    4    2
VAL    5    2
GLU    6   13
LEU    7    3
LYS    8   26
GLU    9   12
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.32180
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.67.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.68.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.68.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.68.0.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.68.0 -outdir und
partial PDB gets fragment 50 through 60 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
VAL    3    1
VAL    4    3
GLU    5   13
LEU    6    3
GLU    8   13
LEU   10    3
GLU   11   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    4     14.2264
Cluster     1 =   3   4
2 clashing residues after turn 
Residue clashes:
3-4
cluster 1 has 2 members and 0.000e+00 combinations:
 3  4 
Energy     14.2264
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
Solved cluster 1: residual clashing 14.23
Still clashes at these sidechain pairs:
ires=    3 irot=    1 jres=    4 jrot=    1      14.2264
Residual clashes =   33.43410
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.68.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.69.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.69.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.69.0.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.69.0 -outdir und
partial PDB gets fragment 49 through 60 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
VAL    2    3
VAL    3    3
GLU    4   14
LEU    5    3
LYS    6   27
GLU    7   12
ARG    8   29
LEU    9    3
GLU   10   12
MET   11   10
GLU   12   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5   10     15.8051
Cluster     1 =   5  10
2 clashing residues after turn 
Residue clashes:
5-10
cluster 1 has 2 members and 1.300e+01 combinations:
 10  5 
Energy     15.8051
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 1.300e+01 - Sending to search
0.000000 < 15.805059: keeping 
Solved cluster 1: residual clashing  0.75
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.69.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.70.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.70.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.70.0.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.70.0 -outdir und
partial PDB gets fragment 48 through 59 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
VAL    2    3
GLU    3   15
LEU    4    4
LYS    5   30
GLU    6   15
ARG    7   29
LEU    8    3
GLU    9   13
MET   10   10
GLU   11   12
LEU   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6   10     26.2758
Cluster     1 =   6  10
2 clashing residues after turn 
Residue clashes:
6-10
cluster 1 has 2 members and 2.880e+02 combinations:
 10  6 
Energy     26.2758
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 2.880e+02 - Sending to search
0.000000 < 26.275810: keeping 
Solved cluster 1: residual clashing  0.43
Still clashes at these sidechain pairs:
Residual clashes =    7.98377
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.70.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.71.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.71.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.71.0.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.71.0 -outdir und
partial PDB gets fragment 47 through 58 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
GLU    2    9
LEU    3    4
LYS    4   27
GLU    5   16
ARG    6   32
LEU    7    3
GLU    8   13
MET    9   10
GLU   10   13
LEU   11    3
ILE   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7   12     14.3250
turnclash      7   13   11    0     41.5107
Cluster     1 =   7  11  12
3 clashing residues after turn 
Residue clashes:
7-12
7-11
cluster 1 has 3 members and 2.880e+02 combinations:
 11  12  7 
Energy     16.2239
Searching cluster 7
Combinations for 3 members in cluster 1 OK: 2.880e+02 - Sending to search
14.495273 < 16.223881: keeping 
0.000000 < 14.929930: keeping 
Solved cluster 1: residual clashing  0.62
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.71.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.72.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.72.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.72.0.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.72.0 -outdir und
partial PDB gets fragment 46 through 57 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
LEU    2    4
LYS    3   27
GLU    4   15
ARG    5   29
LEU    6    4
GLU    7   14
MET    8   12
GLU    9   13
LEU   10    3
ILE   11    4
HIS   12    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.96144
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.72.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.73.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.73.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.73.1.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.73.1 -outdir und
partial PDB gets fragment 45 through 56 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
LYS    2   30
GLU    3   13
ARG    4   32
LEU    5    4
GLU    6   15
MET    7   13
GLU    8   14
LEU    9    3
ILE   10    4
HIS   11    4
LEU   12    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.73.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.74.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.74.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.74.1.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.74.1 -outdir und
partial PDB gets fragment 44 through 55 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   16
GLU    2   13
ARG    3   31
LEU    4    4
GLU    5    9
MET    6   12
GLU    7   15
LEU    8    4
ILE    9    1
HIS   10    3
LEU   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.74.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.75.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.75.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.75.1.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.75.1 -outdir und
partial PDB gets fragment 43 through 54 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   11
ARG    2   27
LEU    3    2
GLU    4   15
MET    5    9
GLU    6    9
LEU    7    4
ILE    8    5
HIS    9    4
LEU   10    2
GLU   12   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   10     17.6704
Cluster     1 =   8  10
2 clashing residues after turn 
Residue clashes:
8-10
cluster 1 has 2 members and 1.600e+01 combinations:
 10  8 
Energy     17.6704
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 1.600e+01 - Sending to search
0.000000 < 17.670383: keeping 
0.000000 < 0.280102: keeping 
Solved cluster 1: residual clashing  0.26
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.75.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.76.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.76.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.76.2.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.76.2 -outdir und
partial PDB gets fragment 42 through 54 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   24
LEU    2    2
GLU    3    9
MET    4    8
GLU    5   15
LEU    6    4
ILE    7    2
HIS    8    4
GLU   11   14
GLU   12   15
TYR   13    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.76.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.77.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.77.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.77.3.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.77.3 -outdir und
partial PDB gets fragment 41 through 53 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
GLU    2   13
MET    3    7
GLU    4    9
LEU    5    2
ILE    6    4
HIS    7    3
LEU    8    4
GLU   10   15
GLU   11   16
TYR   12    1
HIS   13    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    8     37.8756
Cluster     1 =   2   8
2 clashing residues after turn 
Residue clashes:
2-8
cluster 1 has 2 members and 6.000e+00 combinations:
 2  8 
Energy     37.8756
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 6.000e+00 - Sending to search
34.141026 < 37.875580: keeping 
24.636448 < 34.327705: keeping 
Solved cluster 1: residual clashing 26.20
Still clashes at these sidechain pairs:
ires=    2 irot=    1 jres=    8 jrot=    3      24.6364
Residual clashes =   24.63645
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.77.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.79.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.79.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.79.0.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.79.0 -outdir und
partial PDB gets fragment 41 through 53 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
15 residues read 
Measuring phi and psi 
Getting chi values
MET    1    9
GLU    2   13
LEU    3    2
ILE    4    2
HIS    5    3
LEU    6    3
GLU    8    9
GLU    9   15
TYR   10    3
HIS   11    4
ASP   12    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    6.71621
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.79.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.81.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.81.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.81.4.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.81.4 -outdir und
partial PDB gets fragment 41 through 50 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
ILE    2    3
HIS    3    2
LEU    4    2
GLU    6   15
GLU    7   13
TYR    8    2
HIS    9    4
ASP   10    7
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    8     18.3117
Cluster     1 =   2   8
2 clashing residues after turn 
Residue clashes:
2-8
cluster 1 has 2 members and 2.600e+01 combinations:
 2  8 
Energy     18.3117
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 2.600e+01 - Sending to search
4.634421 < 18.311680: keeping 
Solved cluster 1: residual clashing  5.39
Still clashes at these sidechain pairs:
Residual clashes =   10.00965
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.81.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2acy.83.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2acy.83.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2acy.83.5.a2m \
	-target T0124 -template 2acy \
	-out T0124-2acy.83.5 -outdir und
partial PDB gets fragment 43 through 52 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    2
LEU    2    2
GLU    4   15
GLU    5   13
TYR    6    2
HIS    7    4
ASP    8    7
ILE   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.37523
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2acy.83.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2ae2A.0.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2ae2A.0.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2ae2A.0.0.a2m \
	-target T0124 -template 2ae2A \
	-out T0124-2ae2A.0.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2ae2A-orig.a2m
Writing a2m file: tmp/2ae2A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10935


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10935/tmp -alignfile tmp/2ae2A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2ae2A-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10935/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10935/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10935/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10935/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10935/tmp.mod tmp/2ae2A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10935 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2ae2A-align.mod
tmp/2ae2A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10935/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2ae2A-orig.a2m tmp/2ae2A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2ae2A-align.mod
Running w0.5 tmp/2ae2A-orig.a2m tmp/2ae2A-align.mod
Running align2model tmp/2ae2A-align -i tmp/2ae2A-align.mod -db tmp/2ae2A-orig.a2m -db tmp/2ae2A-pdb.a2m
partial PDB gets fragment 248 through 258 extending start
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
MET    2   12
LYS    3   15
GLU    4   13
VAL    5    1
THR    6    2
GLN    7   10
LEU    8    3
PRO    9    2
GLU   10   12
PRO   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2ae2A.0.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2ae2A.0.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2ae2A.0.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2ae2A.0.1.a2m \
	-target T0124 -template 2ae2A \
	-out T0124-2ae2A.0.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2ae2A-orig.a2m
Writing a2m file: tmp/2ae2A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9561


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9561/tmp -alignfile tmp/2ae2A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2ae2A-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9561/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9561/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9561/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9561/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9561/tmp.mod tmp/2ae2A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9561 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2ae2A-align.mod
tmp/2ae2A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9561/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2ae2A-orig.a2m tmp/2ae2A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2ae2A-align.mod
Running w0.5 tmp/2ae2A-orig.a2m tmp/2ae2A-align.mod
Running align2model tmp/2ae2A-align -i tmp/2ae2A-align.mod -db tmp/2ae2A-orig.a2m -db tmp/2ae2A-pdb.a2m
partial PDB gets fragment 246 through 257 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    5
MET    2   10
LYS    3   23
GLU    4   12
VAL    5    2
THR    6    1
GLN    7   12
LEU    8    3
PRO    9    2
GLU   10   14
PRO   11    2
GLN   12   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    5     22.2149
Cluster     1 =   3   5
2 clashing residues after turn 
Residue clashes:
3-5
cluster 1 has 2 members and 2.000e+01 combinations:
 3  5 
Energy     22.2625
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 2.000e+01 - Sending to search
17.963577 < 22.262516: keeping 
2.232396 < 18.608305: keeping 
0.000000 < 3.038949: keeping 
Solved cluster 1: residual clashing  1.44
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2ae2A.0.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2ae2A.0.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2ae2A.0.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2ae2A.0.2.a2m \
	-target T0124 -template 2ae2A \
	-out T0124-2ae2A.0.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2ae2A-orig.a2m
Writing a2m file: tmp/2ae2A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11880


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11880/tmp -alignfile tmp/2ae2A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2ae2A-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11880/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11880/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11880/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11880/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11880/tmp.mod tmp/2ae2A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-11880 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2ae2A-align.mod
tmp/2ae2A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11880/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2ae2A-orig.a2m tmp/2ae2A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2ae2A-align.mod
Running w0.5 tmp/2ae2A-orig.a2m tmp/2ae2A-align.mod
Running align2model tmp/2ae2A-align -i tmp/2ae2A-align.mod -db tmp/2ae2A-orig.a2m -db tmp/2ae2A-pdb.a2m
partial PDB gets fragment 244 through 255 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    6
MET    2   10
LYS    3   27
GLU    4   13
THR    6    1
GLN    7   11
LEU    8    2
PRO    9    2
GLU   10   15
PRO   11    2
GLN   12   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 12 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    7     30.1870
turnclash      5    5   11    1     22.2193
Cluster     1 =   5   7  11
3 clashing residues after turn 
Residue clashes:
5-7
5-11
7-11
cluster 1 has 3 members and 8.000e+01 combinations:
 11  7  5 
Energy     46.7360
Searching cluster 5
Combinations for 3 members in cluster 1 OK: 8.000e+01 - Sending to search
22.219341 < 46.735966: keeping 
0.733589 < 29.171516: keeping 
0.000000 < 5.573034: keeping 
Solved cluster 1: residual clashing  1.77
Still clashes at these sidechain pairs:
Residual clashes =    4.96186
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2ae2A.0.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2ae2A.2.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2ae2A.2.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2ae2A.2.2.a2m \
	-target T0124 -template 2ae2A \
	-out T0124-2ae2A.2.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2ae2A-orig.a2m
Writing a2m file: tmp/2ae2A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10968


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10968/tmp -alignfile tmp/2ae2A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2ae2A-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10968/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10968/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10968/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10968/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10968/tmp.mod tmp/2ae2A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10968 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2ae2A-align.mod
tmp/2ae2A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10968/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2ae2A-orig.a2m tmp/2ae2A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2ae2A-align.mod
Running w0.5 tmp/2ae2A-orig.a2m tmp/2ae2A-align.mod
Running align2model tmp/2ae2A-align -i tmp/2ae2A-align.mod -db tmp/2ae2A-orig.a2m -db tmp/2ae2A-pdb.a2m
partial PDB gets fragment 244 through 254 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   23
GLU    2   12
VAL    3    1
THR    4    2
GLN    5   12
LEU    6    4
PRO    7    2
GLU    8   13
PRO    9    2
GLN   10   15
THR   11    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    7     20.0000
Cluster     1 =   5   7
2 clashing residues after turn 
Residue clashes:
5-7
cluster 1 has 2 members and 4.000e+00 combinations:
 5  7 
Energy     20.0000
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
0.000000 < 20.000000: keeping 
Solved cluster 1: residual clashing  2.01
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2ae2A.2.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2ae2A.4.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2ae2A.4.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2ae2A.4.5.a2m \
	-target T0124 -template 2ae2A \
	-out T0124-2ae2A.4.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2ae2A-orig.a2m
Writing a2m file: tmp/2ae2A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-16337


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-16337/tmp -alignfile tmp/2ae2A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2ae2A-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-16337/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-16337/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-16337/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16337/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-16337/tmp.mod tmp/2ae2A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-16337 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2ae2A-align.mod
tmp/2ae2A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-16337/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2ae2A-orig.a2m tmp/2ae2A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2ae2A-align.mod
Running w0.5 tmp/2ae2A-orig.a2m tmp/2ae2A-align.mod
Running align2model tmp/2ae2A-align -i tmp/2ae2A-align.mod -db tmp/2ae2A-orig.a2m -db tmp/2ae2A-pdb.a2m
partial PDB gets fragment 242 through 251 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
THR    2    1
LEU    4    3
PRO    5    2
GLU    6   13
PRO    7    2
GLN    8   16
THR    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     7    9     69.0582
Cluster     1 =   7   9
2 clashing residues after turn 
Residue clashes:
7-9
cluster 1 has 2 members and 1.320e+02 combinations:
 9  7 
Energy     69.0582
Searching cluster 7
Combinations for 2 members in cluster 1 OK: 1.320e+02 - Sending to search
0.000000 < 69.058243: keeping 
Solved cluster 1: residual clashing  0.25
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2ae2A.4.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2ahjB.123.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2ahjB.123.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2ahjB.123.3.a2m \
	-target T0124 -template 2ahjB \
	-out T0124-2ahjB.123.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2ahjB-orig.a2m
Writing a2m file: tmp/2ahjB-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-938


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-938/tmp -alignfile tmp/2ahjB-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2ahjB-orig.a2m (1 sequences, 212 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-938/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-938/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-938/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-938/tmp.a2m (1 sequences, 212 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-938/tmp.mod tmp/2ahjB-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-938 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2ahjB-align.mod
tmp/2ahjB-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-938/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2ahjB-orig.a2m tmp/2ahjB-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2ahjB-align.mod
Running w0.5 tmp/2ahjB-orig.a2m tmp/2ahjB-align.mod
Running align2model tmp/2ahjB-align -i tmp/2ahjB-align.mod -db tmp/2ahjB-orig.a2m -db tmp/2ahjB-pdb.a2m
partial PDB gets fragment 106 through 115 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   29
GLU    2   15
SER    4    2
GLU    5   16
SER    6    2
ASN    7    5
ILE    8    5
LYS    9   28
ASP   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2ahjB.123.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2ahjB.124.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2ahjB.124.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2ahjB.124.4.a2m \
	-target T0124 -template 2ahjB \
	-out T0124-2ahjB.124.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2ahjB-orig.a2m
Writing a2m file: tmp/2ahjB-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12290


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12290/tmp -alignfile tmp/2ahjB-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2ahjB-orig.a2m (1 sequences, 212 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12290/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12290/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12290/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12290/tmp.a2m (1 sequences, 212 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12290/tmp.mod tmp/2ahjB-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12290 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2ahjB-align.mod
tmp/2ahjB-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12290/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2ahjB-orig.a2m tmp/2ahjB-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2ahjB-align.mod
Running w0.5 tmp/2ahjB-orig.a2m tmp/2ahjB-align.mod
Running align2model tmp/2ahjB-align -i tmp/2ahjB-align.mod -db tmp/2ahjB-orig.a2m -db tmp/2ahjB-pdb.a2m
partial PDB gets fragment 105 through 114 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   16
SER    2    3
SER    3    3
GLU    4   14
SER    5    2
ASN    6    6
ILE    7    3
LYS    8   20
ASP    9    6
ILE   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2ahjB.124.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2bbkH.10.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2bbkH.10.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2bbkH.10.5.a2m \
	-target T0124 -template 2bbkH \
	-out T0124-2bbkH.10.5 -outdir und
partial PDB gets fragment 342 through 351 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
GLN    2   13
THR    3    3
SER    5    3
LEU    6    3
GLU    8   15
LEU    9    5
GLN   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2bbkH.10.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2bbkH.9.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2bbkH.9.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2bbkH.9.5.a2m \
	-target T0124 -template 2bbkH \
	-out T0124-2bbkH.9.5 -outdir und
partial PDB gets fragment 343 through 352 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
PRO    2    2
GLN    3   14
THR    4    3
SER    6    2
LEU    7    3
GLU    9   15
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2bbkH.9.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2bc2A.51.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2bc2A.51.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2bc2A.51.4.a2m \
	-target T0124 -template 2bc2A \
	-out T0124-2bc2A.51.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2bc2A-orig.a2m
Writing a2m file: tmp/2bc2A-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9592


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9592/tmp -alignfile tmp/2bc2A-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2bc2A-orig.a2m (1 sequences, 227 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9592/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9592/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9592/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9592/tmp.a2m (1 sequences, 227 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9592/tmp.mod tmp/2bc2A-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9592 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2bc2A-align.mod
tmp/2bc2A-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9592/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2bc2A-orig.a2m tmp/2bc2A-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2bc2A-align.mod
Running w0.5 tmp/2bc2A-orig.a2m tmp/2bc2A-align.mod
Running align2model tmp/2bc2A-align -i tmp/2bc2A-align.mod -db tmp/2bc2A-orig.a2m -db tmp/2bc2A-pdb.a2m
partial PDB gets fragment 174 through 183 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
LYS    2   25
TYR    3    3
SER    4    2
VAL    5    2
LEU    6    3
PHE    7    3
LEU    8    3
GLU    9   12
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2bc2A.51.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2cxbA.60.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2cxbA.60.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2cxbA.60.4.a2m \
	-target T0124 -template 2cxbA \
	-out T0124-2cxbA.60.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2cxbA-orig.a2m
Writing a2m file: tmp/2cxbA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12623


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12623/tmp -alignfile tmp/2cxbA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2cxbA-orig.a2m (1 sequences, 124 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12623/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12623/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12623/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12623/tmp.a2m (1 sequences, 124 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12623/tmp.mod tmp/2cxbA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12623 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2cxbA-align.mod
tmp/2cxbA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12623/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2cxbA-orig.a2m tmp/2cxbA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2cxbA-align.mod
Running w0.5 tmp/2cxbA-orig.a2m tmp/2cxbA-align.mod
Running align2model tmp/2cxbA-align -i tmp/2cxbA-align.mod -db tmp/2cxbA-orig.a2m -db tmp/2cxbA-pdb.a2m
partial PDB gets fragment 71 through 80 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
VAL    2    1
TYR    3    3
PRO    4    2
ARG    5   27
LEU    7    3
ASP    8    5
SER    9    2
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2cxbA.60.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2cxbA.64.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2cxbA.64.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2cxbA.64.3.a2m \
	-target T0124 -template 2cxbA \
	-out T0124-2cxbA.64.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2cxbA-orig.a2m
Writing a2m file: tmp/2cxbA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-19733


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-19733/tmp -alignfile tmp/2cxbA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2cxbA-orig.a2m (1 sequences, 124 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-19733/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-19733/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-19733/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19733/tmp.a2m (1 sequences, 124 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-19733/tmp.mod tmp/2cxbA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-19733 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2cxbA-align.mod
tmp/2cxbA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19733/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2cxbA-orig.a2m tmp/2cxbA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2cxbA-align.mod
Running w0.5 tmp/2cxbA-orig.a2m tmp/2cxbA-align.mod
Running align2model tmp/2cxbA-align -i tmp/2cxbA-align.mod -db tmp/2cxbA-orig.a2m -db tmp/2cxbA-pdb.a2m
partial PDB gets fragment 71 through 80 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
LEU    3    3
ASP    4    4
SER    5    3
VAL    7    2
GLU    9   13
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2cxbA.64.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2cxbA.65.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2cxbA.65.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2cxbA.65.2.a2m \
	-target T0124 -template 2cxbA \
	-out T0124-2cxbA.65.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2cxbA-orig.a2m
Writing a2m file: tmp/2cxbA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-23693


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-23693/tmp -alignfile tmp/2cxbA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2cxbA-orig.a2m (1 sequences, 124 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-23693/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23693/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23693/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23693/tmp.a2m (1 sequences, 124 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23693/tmp.mod tmp/2cxbA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23693 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2cxbA-align.mod
tmp/2cxbA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23693/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2cxbA-orig.a2m tmp/2cxbA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2cxbA-align.mod
Running w0.5 tmp/2cxbA-orig.a2m tmp/2cxbA-align.mod
Running align2model tmp/2cxbA-align -i tmp/2cxbA-align.mod -db tmp/2cxbA-orig.a2m -db tmp/2cxbA-pdb.a2m
partial PDB gets fragment 70 through 79 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    2    3
ASP    3    4
SER    4    3
GLN    5   11
VAL    7    3
GLU    8   12
LEU    9    3
LYS   10   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2cxbA.65.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2cxbA.66.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2cxbA.66.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2cxbA.66.2.a2m \
	-target T0124 -template 2cxbA \
	-out T0124-2cxbA.66.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2cxbA-orig.a2m
Writing a2m file: tmp/2cxbA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12017


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12017/tmp -alignfile tmp/2cxbA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2cxbA-orig.a2m (1 sequences, 124 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12017/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12017/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12017/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12017/tmp.a2m (1 sequences, 124 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12017/tmp.mod tmp/2cxbA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12017 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2cxbA-align.mod
tmp/2cxbA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12017/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2cxbA-orig.a2m tmp/2cxbA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2cxbA-align.mod
Running w0.5 tmp/2cxbA-orig.a2m tmp/2cxbA-align.mod
Running align2model tmp/2cxbA-align -i tmp/2cxbA-align.mod -db tmp/2cxbA-orig.a2m -db tmp/2cxbA-pdb.a2m
partial PDB gets fragment 69 through 78 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
SER    3    3
GLN    4   11
VAL    5    2
VAL    6    1
GLU    7   12
LEU    8    3
LYS    9   25
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    7     22.6847
Cluster     1 =   2   7
2 clashing residues after turn 
Residue clashes:
2-7
cluster 1 has 2 members and 3.000e+00 combinations:
 7  2 
Energy     23.6393
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 3.000e+00 - Sending to search
0.000000 < 23.639326: keeping 
Solved cluster 1: residual clashing  0.57
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2cxbA.66.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2cxbA.67.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2cxbA.67.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2cxbA.67.4.a2m \
	-target T0124 -template 2cxbA \
	-out T0124-2cxbA.67.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2cxbA-orig.a2m
Writing a2m file: tmp/2cxbA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1787


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1787/tmp -alignfile tmp/2cxbA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2cxbA-orig.a2m (1 sequences, 124 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1787/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1787/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1787/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1787/tmp.a2m (1 sequences, 124 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1787/tmp.mod tmp/2cxbA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1787 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2cxbA-align.mod
tmp/2cxbA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1787/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2cxbA-orig.a2m tmp/2cxbA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2cxbA-align.mod
Running w0.5 tmp/2cxbA-orig.a2m tmp/2cxbA-align.mod
Running align2model tmp/2cxbA-align -i tmp/2cxbA-align.mod -db tmp/2cxbA-orig.a2m -db tmp/2cxbA-pdb.a2m
partial PDB gets fragment 68 through 77 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    7
SER    2    2
GLN    3   12
VAL    4    1
VAL    5    1
GLU    6   12
LEU    7    3
LYS    8   26
GLU    9   12
ARG   10   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2cxbA.67.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.194.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.194.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.194.4.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.194.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10368


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10368/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10368/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10368/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10368/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10368/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10368/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10368 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10368/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 19 through 28 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
GLN    2   11
GLU    4   13
ASN    5    4
LEU    6    3
ARG    7   26
GLN   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.194.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.195.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.195.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.195.0.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.195.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9624


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9624/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9624/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9624/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9624/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9624/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9624/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9624 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9624/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 18 through 29 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
14 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
GLU    3   12
ASN    4    4
LEU    5    3
ARG    6   27
ILE    8    2
GLN    9   11
GLU   10   12
LYS   11   26
GLU   12   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.195.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.196.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.196.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.196.1.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.196.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12366


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12366/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12366/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12366/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12366/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12366/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12366/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12366 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12366/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 17 through 26 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   15
ASN    3    4
ARG    5   26
ILE    7    3
GLN    8   11
GLU    9   12
LYS   10   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.02975
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.196.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.197.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.197.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.197.1.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.197.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11259


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11259/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11259/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11259/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11259/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11259/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11259/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-11259 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11259/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 16 through 25 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    3    4
ARG    4   26
ILE    6    3
GLN    7   12
GLU    8   12
LYS    9   24
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue I 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.197.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.198.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.198.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.198.1.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.198.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1867


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1867/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1867/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1867/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1867/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1867/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1867/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-1867 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1867/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 15 through 24 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    5
LEU    2    2
ARG    3   27
ILE    5    2
GLN    6   11
GLU    7   12
LYS    8   26
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.13535
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.198.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.199.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.199.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.199.1.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.199.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13743


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13743/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13743/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13743/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13743/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13743/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13743/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13743 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13743/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 22 through 31 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ARG    2   27
ILE    4    2
GLN    5   11
GLU    6   12
LYS    7   26
GLU    8   15
GLN   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.199.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.199.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.199.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.199.3.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.199.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21211


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21211/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21211/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21211/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21211/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21211/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21211/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21211 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21211/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 14 through 23 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ARG    2   32
ILE    4    2
GLN    5   14
GLU    6   12
LYS    7   24
GLU    8   12
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.60120
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.199.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.200.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.200.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.200.1.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.200.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13723


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13723/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13723/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13723/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13723/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13723/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13723/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13723 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13723/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 21 through 30 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
ILE    3    3
GLN    4   11
GLU    5   12
LYS    6   24
GLU    7   12
GLN    9   15
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.200.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.200.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.200.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.200.3.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.200.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30363


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30363/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30363/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30363/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30363/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30363/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30363/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30363 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30363/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 13 through 22 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   26
ILE    3    4
GLN    4   12
GLU    5   12
LYS    6   30
GLU    7   12
GLN    9   12
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.200.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.201.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.201.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.201.1.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.201.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4854


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4854/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4854/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4854/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4854/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4854/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4854/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4854 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4854/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 20 through 29 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    2    3
GLN    3   12
GLU    4   12
LYS    5   24
GLU    6   12
GLN    8   11
LEU    9    3
GLN   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.201.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.202.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.202.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.202.0.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.202.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18155


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18155/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18155/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18155/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18155/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18155/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18155/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18155 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18155/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 19 through 28 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
GLN    2   11
GLU    3   12
LYS    4   26
GLU    5   12
GLN    7   11
LEU    8    3
GLN    9   11
GLN   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.202.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.202.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.202.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.202.5.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.202.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8325


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8325/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8325/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8325/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8325/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8325/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8325/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8325 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8325/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 11 through 20 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
GLN    2   12
GLU    3   12
GLU    5   14
GLN    7   12
LEU    8    3
GLN    9   11
GLN   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     8   11     24.2406
Cluster     1 =   8  11
2 clashing residues after turn 
Residue clashes:
8-11
cluster 1 has 2 members and 7.700e+01 combinations:
 11  8 
Energy     24.2406
Searching cluster 8
Combinations for 2 members in cluster 1 OK: 7.700e+01 - Sending to search
0.000000 < 24.240561: keeping 
Solved cluster 1: residual clashing  0.07
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.202.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.203.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.203.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.203.0.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.203.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21541


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21541/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21541/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21541/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21541/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21541/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21541/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21541 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21541/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 18 through 27 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
GLU    2   12
LYS    3   24
GLU    4   12
GLN    6   12
LEU    7    3
GLN    8   11
GLN    9   11
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.203.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.204.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.204.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.204.0.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.204.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13745


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13745/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13745/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13745/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13745/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13745/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13745/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13745 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13745/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 17 through 26 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LYS    2   30
GLU    3   12
GLN    5   12
LEU    6    3
GLN    7   12
GLN    8   11
GLU    9   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.204.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.205.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.205.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.205.0.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.205.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18371


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18371/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18371/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18371/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18371/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18371/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18371/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18371 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18371/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 16 through 25 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   21
GLU    2   12
GLN    4   11
GLN    6   12
GLN    7   12
GLU    8   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.205.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.206.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.206.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.206.0.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.206.0 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13697


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13697/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13697/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13697/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13697/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13697/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13697/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13697 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13697/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 15 through 24 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
GLN    3   12
LEU    4    3
GLN    5   11
GLN    6   11
GLU    7   12
VAL    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    7     24.2406
Cluster     1 =   4   7
2 clashing residues after turn 
Residue clashes:
4-7
cluster 1 has 2 members and 8.800e+01 combinations:
 7  4 
Energy     24.2406
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 8.800e+01 - Sending to search
0.000000 < 24.240561: keeping 
Solved cluster 1: residual clashing  0.07
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.206.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2dnjA.207.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2dnjA.207.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2dnjA.207.2.a2m \
	-target T0124 -template 2dnjA \
	-out T0124-2dnjA.207.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2dnjA-orig.a2m
Writing a2m file: tmp/2dnjA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6314


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6314/tmp -alignfile tmp/2dnjA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2dnjA-orig.a2m (1 sequences, 260 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6314/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6314/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6314/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6314/tmp.a2m (1 sequences, 260 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6314/tmp.mod tmp/2dnjA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6314 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2dnjA-align.mod
tmp/2dnjA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6314/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2dnjA-orig.a2m tmp/2dnjA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2dnjA-align.mod
Running w0.5 tmp/2dnjA-orig.a2m tmp/2dnjA-align.mod
Running align2model tmp/2dnjA-align -i tmp/2dnjA-align.mod -db tmp/2dnjA-orig.a2m -db tmp/2dnjA-pdb.a2m
partial PDB gets fragment 14 through 23 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    2   15
LEU    3    2
GLN    4   12
GLN    5   14
GLU    6   12
VAL    8    1
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue V 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2dnjA.207.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2fcbA.220.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2fcbA.220.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2fcbA.220.4.a2m \
	-target T0124 -template 2fcbA \
	-out T0124-2fcbA.220.4 -outdir und
partial PDB gets fragment 8 through 17 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
LEU    2    3
LYS    3   24
THR    4    1
LEU    5    3
THR    6    1
VAL    7    1
GLU    8   13
VAL    9    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2fcbA.220.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2fcbA.221.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2fcbA.221.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2fcbA.221.3.a2m \
	-target T0124 -template 2fcbA \
	-out T0124-2fcbA.221.3 -outdir und
partial PDB gets fragment 7 through 16 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
LYS    2   27
THR    3    2
LEU    4    2
THR    5    1
VAL    6    2
GLU    7   12
VAL    8    1
GLN    9   11
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2fcbA.221.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2fcbA.222.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2fcbA.222.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2fcbA.222.3.a2m \
	-target T0124 -template 2fcbA \
	-out T0124-2fcbA.222.3 -outdir und
partial PDB gets fragment 6 through 15 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
THR    2    3
THR    4    2
VAL    5    2
GLU    6   15
VAL    7    2
GLN    8   12
GLU    9   13
MET   10    9
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2fcbA.222.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2fcbA.223.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2fcbA.223.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2fcbA.223.3.a2m \
	-target T0124 -template 2fcbA \
	-out T0124-2fcbA.223.3 -outdir und
partial PDB gets fragment 5 through 14 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
THR    3    3
VAL    4    2
VAL    6    2
GLU    8   13
MET    9    9
VAL   10    1
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2fcbA.223.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2fcbA.224.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2fcbA.224.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2fcbA.224.3.a2m \
	-target T0124 -template 2fcbA \
	-out T0124-2fcbA.224.3 -outdir und
partial PDB gets fragment 4 through 13 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
THR    2    2
VAL    3    1
GLU    4   14
VAL    5    2
GLN    6   13
GLU    7   15
MET    8   11
VAL    9    2
LYS   10   21
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2fcbA.224.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2fcbA.225.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2fcbA.225.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2fcbA.225.3.a2m \
	-target T0124 -template 2fcbA \
	-out T0124-2fcbA.225.3 -outdir und
partial PDB gets fragment 3 through 12 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    3
VAL    2    2
GLU    3   12
VAL    4    1
GLN    5   14
GLU    6   12
MET    7   12
VAL    8    2
LYS    9   28
ASN   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2fcbA.225.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2fcbA.226.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2fcbA.226.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2fcbA.226.4.a2m \
	-target T0124 -template 2fcbA \
	-out T0124-2fcbA.226.4 -outdir und
partial PDB gets fragment 2 through 11 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
GLU    2   15
VAL    3    2
GLN    4   13
GLU    5   13
MET    6   12
VAL    7    2
LYS    8   27
ASN    9    5
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2fcbA.226.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2mcm.47.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2mcm.47.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2mcm.47.0.a2m \
	-target T0124 -template 2mcm \
	-out T0124-2mcm.47.0 -outdir und
Skipped atom 23, because occupancy 0.25 <= existing 0.750001
Skipped atom 25, because occupancy 0.25 <= existing 0.750001
Skipped atom 32, because occupancy 0.5 <= existing 0.500001
Skipped atom 34, because occupancy 0.5 <= existing 0.500001
Skipped atom 86, because occupancy 0.2 <= existing 0.800001
Skipped atom 300, because occupancy 0.3 <= existing 0.700001
Skipped atom 344, because occupancy 0.5 <= existing 0.500001
Skipped atom 485, because occupancy 0.4 <= existing 0.600001
Skipped atom 539, because occupancy 0.25 <= existing 0.750001
Skipped atom 541, because occupancy 0.25 <= existing 0.750001
Skipped atom 543, because occupancy 0.25 <= existing 0.750001
Skipped atom 545, because occupancy 0.25 <= existing 0.750001
Skipped atom 632, because occupancy 0.4 <= existing 0.600001
Skipped atom 634, because occupancy 0.4 <= existing 0.600001
Skipped atom 669, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 696, because occupancy 0.3 <= existing 0.700001
partial PDB gets fragment 92 through 101 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
GLU    2   13
LEU    3    3
LEU    4    4
GLN    5   17
LYS    6   32
TYR    7    3
SER    8    2
VAL    9    2
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2mcm.47.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2mcm.48.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2mcm.48.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2mcm.48.0.a2m \
	-target T0124 -template 2mcm \
	-out T0124-2mcm.48.0 -outdir und
Skipped atom 23, because occupancy 0.25 <= existing 0.750001
Skipped atom 25, because occupancy 0.25 <= existing 0.750001
Skipped atom 32, because occupancy 0.5 <= existing 0.500001
Skipped atom 34, because occupancy 0.5 <= existing 0.500001
Skipped atom 86, because occupancy 0.2 <= existing 0.800001
Skipped atom 300, because occupancy 0.3 <= existing 0.700001
Skipped atom 344, because occupancy 0.5 <= existing 0.500001
Skipped atom 485, because occupancy 0.4 <= existing 0.600001
Skipped atom 539, because occupancy 0.25 <= existing 0.750001
Skipped atom 541, because occupancy 0.25 <= existing 0.750001
Skipped atom 543, because occupancy 0.25 <= existing 0.750001
Skipped atom 545, because occupancy 0.25 <= existing 0.750001
Skipped atom 632, because occupancy 0.4 <= existing 0.600001
Skipped atom 634, because occupancy 0.4 <= existing 0.600001
Skipped atom 669, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 696, because occupancy 0.3 <= existing 0.700001
partial PDB gets fragment 91 through 100 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   13
LEU    2    2
LEU    3    4
GLN    4   14
LYS    5   25
TYR    6    3
SER    7    3
VAL    8    2
LEU    9    3
PHE   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2mcm.48.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2mcm.49.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2mcm.49.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2mcm.49.0.a2m \
	-target T0124 -template 2mcm \
	-out T0124-2mcm.49.0 -outdir und
Skipped atom 23, because occupancy 0.25 <= existing 0.750001
Skipped atom 25, because occupancy 0.25 <= existing 0.750001
Skipped atom 32, because occupancy 0.5 <= existing 0.500001
Skipped atom 34, because occupancy 0.5 <= existing 0.500001
Skipped atom 86, because occupancy 0.2 <= existing 0.800001
Skipped atom 300, because occupancy 0.3 <= existing 0.700001
Skipped atom 344, because occupancy 0.5 <= existing 0.500001
Skipped atom 485, because occupancy 0.4 <= existing 0.600001
Skipped atom 539, because occupancy 0.25 <= existing 0.750001
Skipped atom 541, because occupancy 0.25 <= existing 0.750001
Skipped atom 543, because occupancy 0.25 <= existing 0.750001
Skipped atom 545, because occupancy 0.25 <= existing 0.750001
Skipped atom 632, because occupancy 0.4 <= existing 0.600001
Skipped atom 634, because occupancy 0.4 <= existing 0.600001
Skipped atom 669, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 696, because occupancy 0.3 <= existing 0.700001
partial PDB gets fragment 90 through 99 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
LEU    2    3
GLN    3   11
LYS    4   28
TYR    5    3
SER    6    3
VAL    7    3
LEU    8    5
PHE    9    3
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2mcm.49.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2mcm.50.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2mcm.50.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2mcm.50.0.a2m \
	-target T0124 -template 2mcm \
	-out T0124-2mcm.50.0 -outdir und
Skipped atom 23, because occupancy 0.25 <= existing 0.750001
Skipped atom 25, because occupancy 0.25 <= existing 0.750001
Skipped atom 32, because occupancy 0.5 <= existing 0.500001
Skipped atom 34, because occupancy 0.5 <= existing 0.500001
Skipped atom 86, because occupancy 0.2 <= existing 0.800001
Skipped atom 300, because occupancy 0.3 <= existing 0.700001
Skipped atom 344, because occupancy 0.5 <= existing 0.500001
Skipped atom 485, because occupancy 0.4 <= existing 0.600001
Skipped atom 539, because occupancy 0.25 <= existing 0.750001
Skipped atom 541, because occupancy 0.25 <= existing 0.750001
Skipped atom 543, because occupancy 0.25 <= existing 0.750001
Skipped atom 545, because occupancy 0.25 <= existing 0.750001
Skipped atom 632, because occupancy 0.4 <= existing 0.600001
Skipped atom 634, because occupancy 0.4 <= existing 0.600001
Skipped atom 669, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 696, because occupancy 0.3 <= existing 0.700001
partial PDB gets fragment 89 through 98 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLN    2   11
LYS    3   26
TYR    4    3
VAL    6    3
LEU    7    4
PHE    8    3
LEU    9    5
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2mcm.50.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2mcm.51.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2mcm.51.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2mcm.51.0.a2m \
	-target T0124 -template 2mcm \
	-out T0124-2mcm.51.0 -outdir und
Skipped atom 23, because occupancy 0.25 <= existing 0.750001
Skipped atom 25, because occupancy 0.25 <= existing 0.750001
Skipped atom 32, because occupancy 0.5 <= existing 0.500001
Skipped atom 34, because occupancy 0.5 <= existing 0.500001
Skipped atom 86, because occupancy 0.2 <= existing 0.800001
Skipped atom 300, because occupancy 0.3 <= existing 0.700001
Skipped atom 344, because occupancy 0.5 <= existing 0.500001
Skipped atom 485, because occupancy 0.4 <= existing 0.600001
Skipped atom 539, because occupancy 0.25 <= existing 0.750001
Skipped atom 541, because occupancy 0.25 <= existing 0.750001
Skipped atom 543, because occupancy 0.25 <= existing 0.750001
Skipped atom 545, because occupancy 0.25 <= existing 0.750001
Skipped atom 632, because occupancy 0.4 <= existing 0.600001
Skipped atom 634, because occupancy 0.4 <= existing 0.600001
Skipped atom 669, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 696, because occupancy 0.3 <= existing 0.700001
partial PDB gets fragment 88 through 97 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   11
LYS    2   25
TYR    3    3
VAL    5    2
LEU    6    4
PHE    7    3
LEU    8    4
GLU    9   16
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    8.01653
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2mcm.51.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2mcm.52.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2mcm.52.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2mcm.52.0.a2m \
	-target T0124 -template 2mcm \
	-out T0124-2mcm.52.0 -outdir und
Skipped atom 23, because occupancy 0.25 <= existing 0.750001
Skipped atom 25, because occupancy 0.25 <= existing 0.750001
Skipped atom 32, because occupancy 0.5 <= existing 0.500001
Skipped atom 34, because occupancy 0.5 <= existing 0.500001
Skipped atom 86, because occupancy 0.2 <= existing 0.800001
Skipped atom 300, because occupancy 0.3 <= existing 0.700001
Skipped atom 344, because occupancy 0.5 <= existing 0.500001
Skipped atom 485, because occupancy 0.4 <= existing 0.600001
Skipped atom 539, because occupancy 0.25 <= existing 0.750001
Skipped atom 541, because occupancy 0.25 <= existing 0.750001
Skipped atom 543, because occupancy 0.25 <= existing 0.750001
Skipped atom 545, because occupancy 0.25 <= existing 0.750001
Skipped atom 632, because occupancy 0.4 <= existing 0.600001
Skipped atom 634, because occupancy 0.4 <= existing 0.600001
Skipped atom 669, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 696, because occupancy 0.3 <= existing 0.700001
partial PDB gets fragment 87 through 96 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   22
TYR    2    3
SER    3    3
LEU    5    4
PHE    6    3
LEU    7    4
GLU    8   14
PRO    9    2
VAL   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue F 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    7     40.5013
Cluster     1 =   2   7
2 clashing residues after turn 
Residue clashes:
2-7
cluster 1 has 2 members and 3.300e+01 combinations:
 7  2 
Energy    105.8514
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 3.300e+01 - Sending to search
37.403881 < 105.851364: keeping 
0.000000 < 104.261536: keeping 
33.718903 < 66.174149: keeping 
5.507779 < 51.696747: keeping 
Solved cluster 1: residual clashing 24.31
Still clashes at these sidechain pairs:
Residual clashes =    5.50778
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2mcm.52.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2mcm.54.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2mcm.54.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2mcm.54.5.a2m \
	-target T0124 -template 2mcm \
	-out T0124-2mcm.54.5 -outdir und
Skipped atom 23, because occupancy 0.25 <= existing 0.750001
Skipped atom 25, because occupancy 0.25 <= existing 0.750001
Skipped atom 32, because occupancy 0.5 <= existing 0.500001
Skipped atom 34, because occupancy 0.5 <= existing 0.500001
Skipped atom 86, because occupancy 0.2 <= existing 0.800001
Skipped atom 300, because occupancy 0.3 <= existing 0.700001
Skipped atom 344, because occupancy 0.5 <= existing 0.500001
Skipped atom 485, because occupancy 0.4 <= existing 0.600001
Skipped atom 539, because occupancy 0.25 <= existing 0.750001
Skipped atom 541, because occupancy 0.25 <= existing 0.750001
Skipped atom 543, because occupancy 0.25 <= existing 0.750001
Skipped atom 545, because occupancy 0.25 <= existing 0.750001
Skipped atom 632, because occupancy 0.4 <= existing 0.600001
Skipped atom 634, because occupancy 0.4 <= existing 0.600001
Skipped atom 669, because occupancy 0.5 <= existing 0.500001
Skipped atom 671, because occupancy 0.5 <= existing 0.500001
Skipped atom 696, because occupancy 0.3 <= existing 0.700001
partial PDB gets fragment 85 through 94 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
VAL    2    1
LEU    3    2
PHE    4    3
LEU    5    3
GLU    6   14
PRO    7    2
VAL    8    2
TYR    9    2
PRO   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    9     24.9204
Cluster     1 =   4   9
2 clashing residues after turn 
Residue clashes:
4-9
cluster 1 has 2 members and 2.000e+00 combinations:
 4  9 
Energy     29.0125
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search
15.387688 < 29.012522: keeping 
Solved cluster 1: residual clashing 21.76
Still clashes at these sidechain pairs:
ires=    4 irot=    2 jres=    9 jrot=    2      15.3877
Residual clashes =   15.38769
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2mcm.54.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2pia.30.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2pia.30.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2pia.30.4.a2m \
	-target T0124 -template 2pia \
	-out T0124-2pia.30.4 -outdir und
partial PDB gets fragment 299 through 308 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   23
GLN    2   15
GLU    3   12
LYS    4   25
GLU    5   14
LEU    6    3
LYS    7   25
GLU    8   15
LEU    9    3
GLU   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.54239
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2pia.30.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2pia.31.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2pia.31.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2pia.31.2.a2m \
	-target T0124 -template 2pia \
	-out T0124-2pia.31.2 -outdir und
partial PDB gets fragment 298 through 308 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
GLU    4   14
LEU    5    4
LYS    6   25
GLU    7   14
LEU    8    4
GLU    9   15
ARG   10   32
LYS   11   28
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2pia.31.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2pia.33.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2pia.33.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2pia.33.5.a2m \
	-target T0124 -template 2pia \
	-out T0124-2pia.33.5 -outdir und
partial PDB gets fragment 298 through 307 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   27
LEU    3    2
LYS    4   24
GLU    5   12
LEU    6    3
GLU    7   14
ARG    8   27
LYS    9   31
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2pia.33.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2pia.34.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2pia.34.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2pia.34.5.a2m \
	-target T0124 -template 2pia \
	-out T0124-2pia.34.5 -outdir und
partial PDB gets fragment 297 through 307 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   16
LEU    2    3
LYS    3   23
GLU    4   14
LEU    5    2
GLU    6   12
ARG    7   26
LYS    8   28
SER   10    2
LYS   11   29
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    8     18.3532
Cluster     1 =   4   8
2 clashing residues after turn 
Residue clashes:
4-8
cluster 1 has 2 members and 4.140e+02 combinations:
 8  4 
Energy     18.3532
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 4.140e+02 - Sending to search
0.000000 < 18.353199: keeping 
Solved cluster 1: residual clashing  0.98
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2pia.34.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2rspA.20.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2rspA.20.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2rspA.20.2.a2m \
	-target T0124 -template 2rspA \
	-out T0124-2rspA.20.2 -outdir und
Skipped atom 869, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2rspA-orig.a2m
Writing a2m file: tmp/2rspA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14863


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14863/tmp -alignfile tmp/2rspA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2rspA-orig.a2m (1 sequences, 124 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14863/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14863/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14863/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14863/tmp.a2m (1 sequences, 124 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14863/tmp.mod tmp/2rspA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14863 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2rspA-align.mod
tmp/2rspA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14863/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2rspA-orig.a2m tmp/2rspA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2rspA-align.mod
Running w0.5 tmp/2rspA-orig.a2m tmp/2rspA-align.mod
Running align2model tmp/2rspA-align -i tmp/2rspA-align.mod -db tmp/2rspA-orig.a2m -db tmp/2rspA-pdb.a2m
partial PDB gets fragment 105 through 114 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
MET    2   10
LYS    3   21
LEU    4    2
PHE    5    3
LEU    6    3
LYS    7   26
LEU    8    5
LEU    9    2
LYS   10   19
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2rspA.20.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2rspA.21.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2rspA.21.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2rspA.21.3.a2m \
	-target T0124 -template 2rspA \
	-out T0124-2rspA.21.3 -outdir und
Skipped atom 869, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2rspA-orig.a2m
Writing a2m file: tmp/2rspA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8341


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8341/tmp -alignfile tmp/2rspA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2rspA-orig.a2m (1 sequences, 124 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8341/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8341/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8341/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8341/tmp.a2m (1 sequences, 124 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8341/tmp.mod tmp/2rspA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8341 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2rspA-align.mod
tmp/2rspA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8341/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2rspA-orig.a2m tmp/2rspA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2rspA-align.mod
Running w0.5 tmp/2rspA-orig.a2m tmp/2rspA-align.mod
Running align2model tmp/2rspA-align -i tmp/2rspA-align.mod -db tmp/2rspA-orig.a2m -db tmp/2rspA-pdb.a2m
partial PDB gets fragment 104 through 113 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
LYS    2   26
LEU    3    3
PHE    4    3
LEU    5    2
LYS    6   24
LEU    7    3
LYS    9   27
LYS   10   18
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    7     13.4689
Cluster     1 =   2   7
2 clashing residues after turn 
Residue clashes:
2-7
cluster 1 has 2 members and 1.440e+02 combinations:
 2  7 
Energy     13.4689
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 1.440e+02 - Sending to search
0.000000 < 13.468881: keeping 
0.000000 < 0.980699: keeping 
Solved cluster 1: residual clashing  0.03
Still clashes at these sidechain pairs:
Residual clashes =    0.29889
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2rspA.21.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2rspA.22.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2rspA.22.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2rspA.22.4.a2m \
	-target T0124 -template 2rspA \
	-out T0124-2rspA.22.4 -outdir und
Skipped atom 869, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2rspA-orig.a2m
Writing a2m file: tmp/2rspA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-26668


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-26668/tmp -alignfile tmp/2rspA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2rspA-orig.a2m (1 sequences, 124 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-26668/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26668/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26668/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26668/tmp.a2m (1 sequences, 124 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26668/tmp.mod tmp/2rspA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26668 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2rspA-align.mod
tmp/2rspA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26668/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2rspA-orig.a2m tmp/2rspA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2rspA-align.mod
Running w0.5 tmp/2rspA-orig.a2m tmp/2rspA-align.mod
Running align2model tmp/2rspA-align -i tmp/2rspA-align.mod -db tmp/2rspA-orig.a2m -db tmp/2rspA-pdb.a2m
partial PDB gets fragment 103 through 112 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   29
PHE    3    4
LEU    4    3
LYS    5   21
LEU    6    2
LYS    8   31
LYS    9   26
GLN   10   16
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2rspA.22.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2rspA.26.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2rspA.26.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2rspA.26.5.a2m \
	-target T0124 -template 2rspA \
	-out T0124-2rspA.26.5 -outdir und
Skipped atom 869, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2rspA-orig.a2m
Writing a2m file: tmp/2rspA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27805


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27805/tmp -alignfile tmp/2rspA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2rspA-orig.a2m (1 sequences, 124 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27805/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27805/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27805/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27805/tmp.a2m (1 sequences, 124 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27805/tmp.mod tmp/2rspA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27805 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2rspA-align.mod
tmp/2rspA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27805/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2rspA-orig.a2m tmp/2rspA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2rspA-align.mod
Running w0.5 tmp/2rspA-orig.a2m tmp/2rspA-align.mod
Running align2model tmp/2rspA-align -i tmp/2rspA-align.mod -db tmp/2rspA-orig.a2m -db tmp/2rspA-pdb.a2m
partial PDB gets fragment 101 through 110 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   28
LEU    2    3
LEU    3    3
LYS    4   26
LYS    5   26
GLN    6   14
GLU    7   12
LYS    8   17
GLU    9   15
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2rspA.26.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2scpA.168.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2scpA.168.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2scpA.168.4.a2m \
	-target T0124 -template 2scpA \
	-out T0124-2scpA.168.4 -outdir und
partial PDB gets fragment 49 through 58 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
HIS    2    3
ILE    3    3
GLN    4   12
GLU    5   15
VAL    6    3
GLN    8   14
THR    9    2
ILE   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue V 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2scpA.168.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2scpA.169.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2scpA.169.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2scpA.169.5.a2m \
	-target T0124 -template 2scpA \
	-out T0124-2scpA.169.5 -outdir und
partial PDB gets fragment 48 through 57 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
ILE    2    2
GLN    3   11
GLU    4   12
VAL    5    2
VAL    6    3
GLN    7   15
THR    8    1
ILE    9    2
LYS   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2scpA.169.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2scpA.179.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2scpA.179.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2scpA.179.4.a2m \
	-target T0124 -template 2scpA \
	-out T0124-2scpA.179.4 -outdir und
partial PDB gets fragment 40 through 49 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    4
LEU    2    3
THR    3    1
LYS    5   25
THR    6    2
ARG    8   26
TYR    9    2
GLN   10   11
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2scpA.179.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2scpA.180.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2scpA.180.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2scpA.180.5.a2m \
	-target T0124 -template 2scpA \
	-out T0124-2scpA.180.5 -outdir und
partial PDB gets fragment 39 through 49 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
THR    2    2
GLU    3   14
LYS    4   25
THR    5    2
ARG    7   27
TYR    8    3
GLN    9   12
GLN   10   12
LYS   11   24
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2scpA.180.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2scpA.182.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2scpA.182.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2scpA.182.5.a2m \
	-target T0124 -template 2scpA \
	-out T0124-2scpA.182.5 -outdir und
partial PDB gets fragment 39 through 48 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    2   22
THR    3    2
ARG    5   32
TYR    6    3
GLN    7   12
GLN    8   12
LYS    9   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   20.82790
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2scpA.182.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2scpA.183.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2scpA.183.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2scpA.183.5.a2m \
	-target T0124 -template 2scpA \
	-out T0124-2scpA.183.5 -outdir und
partial PDB gets fragment 38 through 47 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   23
THR    2    2
ARG    4   30
TYR    5    2
GLN    6   15
GLN    7   15
LYS    8   26
LEU    9    3
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2scpA.183.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2scpA.216.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2scpA.216.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2scpA.216.3.a2m \
	-target T0124 -template 2scpA \
	-out T0124-2scpA.216.3 -outdir und
partial PDB gets fragment 11 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
TYR    2    2
GLU    3   12
GLU    4   15
LYS    5   20
LEU    6    3
LYS    7   22
THR    8    2
LEU    9    2
THR   10    1
VAL   11    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 20 rotamers of residue K 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    6     14.5381
Cluster     1 =   2   6
2 clashing residues after turn 
Residue clashes:
2-6
cluster 1 has 2 members and 2.400e+02 combinations:
 6  2 
Energy     22.7829
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 2.400e+02 - Sending to search
0.000000 < 22.782913: keeping 
0.000000 < 8.470917: keeping 
0.000000 < 6.765862: keeping 
Solved cluster 1: residual clashing  6.28
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2scpA.216.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2scpA.217.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2scpA.217.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2scpA.217.4.a2m \
	-target T0124 -template 2scpA \
	-out T0124-2scpA.217.4 -outdir und
partial PDB gets fragment 10 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   12
GLU    3   12
LYS    4   26
LEU    5    3
LYS    6   20
THR    7    1
LEU    8    2
THR    9    2
VAL   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    6     13.6425
Cluster     1 =   2   6
2 clashing residues after turn 
Residue clashes:
2-6
cluster 1 has 2 members and 0.000e+00 combinations:
 2  6 
Energy     13.6425
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search
0.000000 < 13.642529: keeping 
Solved cluster 1: residual clashing  2.60
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2scpA.217.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2scpA.218.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2scpA.218.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2scpA.218.5.a2m \
	-target T0124 -template 2scpA \
	-out T0124-2scpA.218.5 -outdir und
partial PDB gets fragment 9 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
GLU    2   12
LYS    3   25
LEU    4    3
LYS    5   26
THR    6    2
LEU    7    3
THR    8    1
VAL    9    2
GLU   10    7
VAL   11    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2scpA.218.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2scpA.220.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2scpA.220.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2scpA.220.5.a2m \
	-target T0124 -template 2scpA \
	-out T0124-2scpA.220.5 -outdir und
partial PDB gets fragment 9 through 18 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   25
LEU    2    3
LYS    3   25
THR    4    1
LEU    5    3
THR    6    2
VAL    7    1
GLU    8   12
VAL    9    2
GLN   10    7
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue V 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2scpA.220.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2sicI.52.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2sicI.52.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2sicI.52.4.a2m \
	-target T0124 -template 2sicI \
	-out T0124-2sicI.52.4 -outdir und
partial PDB gets fragment 76 through 85 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   31
TYR    2    3
SER    3    3
VAL    4    1
LEU    5    3
PHE    6    2
LEU    7    3
GLU    8   15
PRO    9    2
VAL   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 10 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2sicI.52.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2sicI.53.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2sicI.53.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2sicI.53.1.a2m \
	-target T0124 -template 2sicI \
	-out T0124-2sicI.53.1 -outdir und
partial PDB gets fragment 75 through 84 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
TYR    1    3
SER    2    3
VAL    3    2
LEU    4    4
PHE    5    3
LEU    6    3
GLU    7    7
PRO    8    2
VAL    9    3
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 3 rotamers of residue Y 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2sicI.53.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2sicI.55.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2sicI.55.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2sicI.55.5.a2m \
	-target T0124 -template 2sicI \
	-out T0124-2sicI.55.5 -outdir und
partial PDB gets fragment 73 through 82 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
LEU    2    3
PHE    3    3
LEU    4    4
GLU    5   15
PRO    6    2
VAL    7    1
TYR    8    2
PRO    9    2
ARG   10   27
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.20593
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2sicI.55.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2sicI.56.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2sicI.56.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2sicI.56.4.a2m \
	-target T0124 -template 2sicI \
	-out T0124-2sicI.56.4 -outdir und
partial PDB gets fragment 72 through 81 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PHE    2    2
LEU    3    3
GLU    4   13
PRO    5    2
VAL    6    2
TYR    7    3
PRO    8    2
ARG    9   19
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2sicI.56.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2sqcA.131.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2sqcA.131.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2sqcA.131.4.a2m \
	-target T0124 -template 2sqcA \
	-out T0124-2sqcA.131.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2sqcA-orig.a2m
Writing a2m file: tmp/2sqcA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14630


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14630/tmp -alignfile tmp/2sqcA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2sqcA-orig.a2m (1 sequences, 631 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14630/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14630/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14630/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14630/tmp.a2m (1 sequences, 631 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14630/tmp.mod tmp/2sqcA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14630 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2sqcA-align.mod
tmp/2sqcA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14630/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2sqcA-orig.a2m tmp/2sqcA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2sqcA-align.mod
Running w0.5 tmp/2sqcA-orig.a2m tmp/2sqcA-align.mod
Running align2model tmp/2sqcA-align -i tmp/2sqcA-align.mod -db tmp/2sqcA-orig.a2m -db tmp/2sqcA-pdb.a2m
partial PDB gets fragment 73 through 82 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   28
ASP    2    5
ILE    3    3
LYS    4   24
LYS    5   29
LYS    6   28
LEU    7    3
GLU    8   12
LYS   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2sqcA.131.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2sqcA.132.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2sqcA.132.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2sqcA.132.4.a2m \
	-target T0124 -template 2sqcA \
	-out T0124-2sqcA.132.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2sqcA-orig.a2m
Writing a2m file: tmp/2sqcA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14458


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14458/tmp -alignfile tmp/2sqcA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2sqcA-orig.a2m (1 sequences, 631 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14458/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14458/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14458/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14458/tmp.a2m (1 sequences, 631 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14458/tmp.mod tmp/2sqcA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14458 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2sqcA-align.mod
tmp/2sqcA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14458/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2sqcA-orig.a2m tmp/2sqcA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2sqcA-align.mod
Running w0.5 tmp/2sqcA-orig.a2m tmp/2sqcA-align.mod
Running align2model tmp/2sqcA-align -i tmp/2sqcA-align.mod -db tmp/2sqcA-orig.a2m -db tmp/2sqcA-pdb.a2m
partial PDB gets fragment 72 through 81 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ASP    1    5
ILE    2    3
LYS    3   28
LYS    4   17
LYS    5   24
LEU    6    3
GLU    7   13
LYS    9   24
ARG   10   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    6     29.9313
Cluster     1 =   3   6
2 clashing residues after turn 
Residue clashes:
3-6
cluster 1 has 2 members and 6.000e+00 combinations:
 6  3 
Energy     34.7035
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 6.000e+00 - Sending to search
0.000000 < 34.703468: keeping 
Solved cluster 1: residual clashing  2.78
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2sqcA.132.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2sqcA.133.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2sqcA.133.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2sqcA.133.5.a2m \
	-target T0124 -template 2sqcA \
	-out T0124-2sqcA.133.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2sqcA-orig.a2m
Writing a2m file: tmp/2sqcA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-29561


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-29561/tmp -alignfile tmp/2sqcA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2sqcA-orig.a2m (1 sequences, 631 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-29561/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-29561/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-29561/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29561/tmp.a2m (1 sequences, 631 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-29561/tmp.mod tmp/2sqcA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-29561 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2sqcA-align.mod
tmp/2sqcA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-29561/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2sqcA-orig.a2m tmp/2sqcA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2sqcA-align.mod
Running w0.5 tmp/2sqcA-orig.a2m tmp/2sqcA-align.mod
Running align2model tmp/2sqcA-align -i tmp/2sqcA-align.mod -db tmp/2sqcA-orig.a2m -db tmp/2sqcA-pdb.a2m
partial PDB gets fragment 71 through 80 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
LYS    2   27
LYS    3   28
LYS    4   28
LEU    5    2
GLU    6   15
LYS    8   28
ARG    9   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue I 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    7     64.5632
Cluster     1 =   4   7
2 clashing residues after turn 
Residue clashes:
4-7
cluster 1 has 2 members and 1.200e+02 combinations:
 7  4 
Energy     68.9516
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 1.200e+02 - Sending to search
45.680912 < 68.951591: keeping 
43.782646 < 51.342468: keeping 
0.000000 < 49.477249: keeping 
0.000000 < 6.004161: keeping 
Solved cluster 1: residual clashing  1.19
Still clashes at these sidechain pairs:
Residual clashes =    7.87625
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2sqcA.133.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2tpsA.145.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2tpsA.145.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2tpsA.145.5.a2m \
	-target T0124 -template 2tpsA \
	-out T0124-2tpsA.145.5 -outdir und
Skipped atom 464, because occupancy 0.27 <= existing 0.730001
Skipped atom 466, because occupancy 0.27 <= existing 0.730001
Skipped atom 468, because occupancy 0.27 <= existing 0.730001
Skipped atom 470, because occupancy 0.27 <= existing 0.730001
Skipped atom 931, because occupancy 0.47 <= existing 0.530001
Skipped atom 933, because occupancy 0.47 <= existing 0.530001
Skipped atom 935, because occupancy 0.47 <= existing 0.530001
Skipped atom 937, because occupancy 0.47 <= existing 0.530001
Skipped atom 939, because occupancy 0.47 <= existing 0.530001
Skipped atom 941, because occupancy 0.47 <= existing 0.530001
Skipped atom 1474, because occupancy 0.39 <= existing 0.610001
Skipped atom 1569, because occupancy 0.44 <= existing 0.560001
Skipped atom 1586, because occupancy 0.44 <= existing 0.560001
Skipped atom 1588, because occupancy 0.44 <= existing 0.560001
Skipped atom 1590, because occupancy 0.44 <= existing 0.560001
Skipped atom 1592, because occupancy 0.44 <= existing 0.560001
Skipped atom 1594, because occupancy 0.44 <= existing 0.560001
Skipped atom 1596, because occupancy 0.44 <= existing 0.560001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2tpsA-orig.a2m
Writing a2m file: tmp/2tpsA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27255


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27255/tmp -alignfile tmp/2tpsA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2tpsA-orig.a2m (1 sequences, 227 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27255/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27255/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27255/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27255/tmp.a2m (1 sequences, 227 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27255/tmp.mod tmp/2tpsA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-27255 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2tpsA-align.mod
tmp/2tpsA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27255/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2tpsA-orig.a2m tmp/2tpsA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2tpsA-align.mod
Running w0.5 tmp/2tpsA-orig.a2m tmp/2tpsA-align.mod
Running align2model tmp/2tpsA-align -i tmp/2tpsA-align.mod -db tmp/2tpsA-orig.a2m -db tmp/2tpsA-pdb.a2m
partial PDB gets fragment 69 through 78 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    3
GLN    2   12
VAL    3    1
MET    4   10
MET    5   10
ARG    6   32
SER    7    2
THR    8    1
SER    9    3
ASP   10    6
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2tpsA.145.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2tpsA.168.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2tpsA.168.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2tpsA.168.5.a2m \
	-target T0124 -template 2tpsA \
	-out T0124-2tpsA.168.5 -outdir und
Skipped atom 464, because occupancy 0.27 <= existing 0.730001
Skipped atom 466, because occupancy 0.27 <= existing 0.730001
Skipped atom 468, because occupancy 0.27 <= existing 0.730001
Skipped atom 470, because occupancy 0.27 <= existing 0.730001
Skipped atom 931, because occupancy 0.47 <= existing 0.530001
Skipped atom 933, because occupancy 0.47 <= existing 0.530001
Skipped atom 935, because occupancy 0.47 <= existing 0.530001
Skipped atom 937, because occupancy 0.47 <= existing 0.530001
Skipped atom 939, because occupancy 0.47 <= existing 0.530001
Skipped atom 941, because occupancy 0.47 <= existing 0.530001
Skipped atom 1474, because occupancy 0.39 <= existing 0.610001
Skipped atom 1569, because occupancy 0.44 <= existing 0.560001
Skipped atom 1586, because occupancy 0.44 <= existing 0.560001
Skipped atom 1588, because occupancy 0.44 <= existing 0.560001
Skipped atom 1590, because occupancy 0.44 <= existing 0.560001
Skipped atom 1592, because occupancy 0.44 <= existing 0.560001
Skipped atom 1594, because occupancy 0.44 <= existing 0.560001
Skipped atom 1596, because occupancy 0.44 <= existing 0.560001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2tpsA-orig.a2m
Writing a2m file: tmp/2tpsA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2153


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2153/tmp -alignfile tmp/2tpsA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2tpsA-orig.a2m (1 sequences, 227 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2153/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2153/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2153/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2153/tmp.a2m (1 sequences, 227 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2153/tmp.mod tmp/2tpsA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2153 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2tpsA-align.mod
tmp/2tpsA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2153/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2tpsA-orig.a2m tmp/2tpsA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2tpsA-align.mod
Running w0.5 tmp/2tpsA-orig.a2m tmp/2tpsA-align.mod
Running align2model tmp/2tpsA-align -i tmp/2tpsA-align.mod -db tmp/2tpsA-orig.a2m -db tmp/2tpsA-pdb.a2m
partial PDB gets fragment 50 through 59 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    2
HIS    2    4
ILE    3    3
GLN    4   12
GLU    5   13
VAL    6    2
VAL    7    3
GLN    8   14
THR    9    3
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue V 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2tpsA.168.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2tpsA.169.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2tpsA.169.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2tpsA.169.4.a2m \
	-target T0124 -template 2tpsA \
	-out T0124-2tpsA.169.4 -outdir und
Skipped atom 464, because occupancy 0.27 <= existing 0.730001
Skipped atom 466, because occupancy 0.27 <= existing 0.730001
Skipped atom 468, because occupancy 0.27 <= existing 0.730001
Skipped atom 470, because occupancy 0.27 <= existing 0.730001
Skipped atom 931, because occupancy 0.47 <= existing 0.530001
Skipped atom 933, because occupancy 0.47 <= existing 0.530001
Skipped atom 935, because occupancy 0.47 <= existing 0.530001
Skipped atom 937, because occupancy 0.47 <= existing 0.530001
Skipped atom 939, because occupancy 0.47 <= existing 0.530001
Skipped atom 941, because occupancy 0.47 <= existing 0.530001
Skipped atom 1474, because occupancy 0.39 <= existing 0.610001
Skipped atom 1569, because occupancy 0.44 <= existing 0.560001
Skipped atom 1586, because occupancy 0.44 <= existing 0.560001
Skipped atom 1588, because occupancy 0.44 <= existing 0.560001
Skipped atom 1590, because occupancy 0.44 <= existing 0.560001
Skipped atom 1592, because occupancy 0.44 <= existing 0.560001
Skipped atom 1594, because occupancy 0.44 <= existing 0.560001
Skipped atom 1596, because occupancy 0.44 <= existing 0.560001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2tpsA-orig.a2m
Writing a2m file: tmp/2tpsA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-12961


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-12961/tmp -alignfile tmp/2tpsA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2tpsA-orig.a2m (1 sequences, 227 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-12961/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-12961/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-12961/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12961/tmp.a2m (1 sequences, 227 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-12961/tmp.mod tmp/2tpsA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-12961 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2tpsA-align.mod
tmp/2tpsA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-12961/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2tpsA-orig.a2m tmp/2tpsA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2tpsA-align.mod
Running w0.5 tmp/2tpsA-orig.a2m tmp/2tpsA-align.mod
Running align2model tmp/2tpsA-align -i tmp/2tpsA-align.mod -db tmp/2tpsA-orig.a2m -db tmp/2tpsA-pdb.a2m
partial PDB gets fragment 49 through 58 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    4
ILE    2    3
GLN    3   16
GLU    4    9
VAL    5    3
VAL    6    2
GLN    7   15
THR    8    3
ILE    9    2
LYS   10   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 15 rotamers of residue Q 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    4     36.3538
Cluster     1 =   2   4
2 clashing residues after turn 
Residue clashes:
2-4
cluster 1 has 2 members and 6.400e+01 combinations:
 2  4 
Energy     36.3538
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 6.400e+01 - Sending to search
21.052042 < 36.353752: keeping 
0.000000 < 21.093521: keeping 
0.000000 < 0.244156: keeping 
Solved cluster 1: residual clashing  0.22
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2tpsA.169.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-2tpsA.170.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-2tpsA.170.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-2tpsA.170.5.a2m \
	-target T0124 -template 2tpsA \
	-out T0124-2tpsA.170.5 -outdir und
Skipped atom 464, because occupancy 0.27 <= existing 0.730001
Skipped atom 466, because occupancy 0.27 <= existing 0.730001
Skipped atom 468, because occupancy 0.27 <= existing 0.730001
Skipped atom 470, because occupancy 0.27 <= existing 0.730001
Skipped atom 931, because occupancy 0.47 <= existing 0.530001
Skipped atom 933, because occupancy 0.47 <= existing 0.530001
Skipped atom 935, because occupancy 0.47 <= existing 0.530001
Skipped atom 937, because occupancy 0.47 <= existing 0.530001
Skipped atom 939, because occupancy 0.47 <= existing 0.530001
Skipped atom 941, because occupancy 0.47 <= existing 0.530001
Skipped atom 1474, because occupancy 0.39 <= existing 0.610001
Skipped atom 1569, because occupancy 0.44 <= existing 0.560001
Skipped atom 1586, because occupancy 0.44 <= existing 0.560001
Skipped atom 1588, because occupancy 0.44 <= existing 0.560001
Skipped atom 1590, because occupancy 0.44 <= existing 0.560001
Skipped atom 1592, because occupancy 0.44 <= existing 0.560001
Skipped atom 1594, because occupancy 0.44 <= existing 0.560001
Skipped atom 1596, because occupancy 0.44 <= existing 0.560001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2tpsA-orig.a2m
Writing a2m file: tmp/2tpsA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14997


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14997/tmp -alignfile tmp/2tpsA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2tpsA-orig.a2m (1 sequences, 227 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14997/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14997/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14997/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14997/tmp.a2m (1 sequences, 227 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14997/tmp.mod tmp/2tpsA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14997 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2tpsA-align.mod
tmp/2tpsA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14997/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2tpsA-orig.a2m tmp/2tpsA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2tpsA-align.mod
Running w0.5 tmp/2tpsA-orig.a2m tmp/2tpsA-align.mod
Running align2model tmp/2tpsA-align -i tmp/2tpsA-align.mod -db tmp/2tpsA-orig.a2m -db tmp/2tpsA-pdb.a2m
partial PDB gets fragment 48 through 57 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
GLN    2   11
VAL    4    3
VAL    5    2
GLN    6   12
THR    7    2
ILE    8    4
LYS    9   29
LEU   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 4 rotamers of residue I 9 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-2tpsA.170.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3c2c.58.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3c2c.58.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3c2c.58.2.a2m \
	-target T0124 -template 3c2c \
	-out T0124-3c2c.58.2 -outdir und
partial PDB gets fragment 82 through 91 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
GLU    2   12
VAL    4    2
TYR    5    2
PRO    6    2
ARG    7   31
LEU    9    3
ASP   10    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    5.39697
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3c2c.58.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3cla.14.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3cla.14.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3cla.14.5.a2m \
	-target T0124 -template 3cla \
	-out T0124-3cla.14.5 -outdir und
partial PDB gets fragment 198 through 207 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
SER    1    3
LEU    2    3
GLU    4   12
LEU    5    3
GLN    6   11
MET    8   10
LYS    9   26
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3cla.14.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3cla.15.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3cla.15.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3cla.15.2.a2m \
	-target T0124 -template 3cla \
	-out T0124-3cla.15.2 -outdir und
partial PDB gets fragment 197 through 206 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    3   12
LEU    4    3
GLN    5   12
GLN    6   12
MET    7   10
LYS    8   26
LEU    9    3
PHE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3cla.15.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3cla.17.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3cla.17.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3cla.17.4.a2m \
	-target T0124 -template 3cla \
	-out T0124-3cla.17.4 -outdir und
partial PDB gets fragment 195 through 204 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
LEU    2    3
GLN    3   12
GLN    4   11
MET    5   10
LYS    6   24
LEU    7    3
PHE    8    3
LYS   10   23
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3cla.17.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3cla.18.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3cla.18.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3cla.18.5.a2m \
	-target T0124 -template 3cla \
	-out T0124-3cla.18.5 -outdir und
partial PDB gets fragment 194 through 203 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLN    2   12
GLN    3   12
MET    4   10
LYS    5   24
LEU    6    3
PHE    7    2
LEU    8    3
LYS    9   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3cla.18.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3csuA.163.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3csuA.163.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3csuA.163.5.a2m \
	-target T0124 -template 3csuA \
	-out T0124-3csuA.163.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3csuA-orig.a2m
Writing a2m file: tmp/3csuA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11525


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11525/tmp -alignfile tmp/3csuA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3csuA-orig.a2m (1 sequences, 310 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11525/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11525/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11525/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11525/tmp.a2m (1 sequences, 310 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11525/tmp.mod tmp/3csuA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-11525 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3csuA-align.mod
tmp/3csuA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11525/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3csuA-orig.a2m tmp/3csuA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3csuA-align.mod
Running w0.5 tmp/3csuA-orig.a2m tmp/3csuA-align.mod
Running align2model tmp/3csuA-align -i tmp/3csuA-align.mod -db tmp/3csuA-orig.a2m -db tmp/3csuA-pdb.a2m
partial PDB gets fragment 58 through 67 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
ILE    3    4
ASN    4    4
ASN    5    4
SER    6    3
HIS    7    3
ILE    8    3
GLN    9   11
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    3.52721
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3csuA.163.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3csuA.164.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3csuA.164.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3csuA.164.5.a2m \
	-target T0124 -template 3csuA \
	-out T0124-3csuA.164.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3csuA-orig.a2m
Writing a2m file: tmp/3csuA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13954


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13954/tmp -alignfile tmp/3csuA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3csuA-orig.a2m (1 sequences, 310 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13954/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13954/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13954/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13954/tmp.a2m (1 sequences, 310 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13954/tmp.mod tmp/3csuA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13954 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3csuA-align.mod
tmp/3csuA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13954/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3csuA-orig.a2m tmp/3csuA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3csuA-align.mod
Running w0.5 tmp/3csuA-orig.a2m tmp/3csuA-align.mod
Running align2model tmp/3csuA-align -i tmp/3csuA-align.mod -db tmp/3csuA-orig.a2m -db tmp/3csuA-pdb.a2m
partial PDB gets fragment 57 through 66 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   12
ILE    2    2
ASN    3    4
ASN    4    4
HIS    6    3
ILE    7    3
GLN    8   15
GLU    9   12
VAL   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3csuA.164.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3csuA.175.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3csuA.175.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3csuA.175.4.a2m \
	-target T0124 -template 3csuA \
	-out T0124-3csuA.175.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3csuA-orig.a2m
Writing a2m file: tmp/3csuA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18112


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18112/tmp -alignfile tmp/3csuA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3csuA-orig.a2m (1 sequences, 310 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18112/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18112/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18112/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18112/tmp.a2m (1 sequences, 310 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18112/tmp.mod tmp/3csuA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18112 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3csuA-align.mod
tmp/3csuA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18112/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3csuA-orig.a2m tmp/3csuA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3csuA-align.mod
Running w0.5 tmp/3csuA-orig.a2m tmp/3csuA-align.mod
Running align2model tmp/3csuA-align -i tmp/3csuA-align.mod -db tmp/3csuA-orig.a2m -db tmp/3csuA-pdb.a2m
partial PDB gets fragment 46 through 55 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
THR    2    2
ILE    3    5
LYS    4   29
LEU    5    3
LEU    6    3
GLU    8   13
LYS    9   26
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    4.26388
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3csuA.175.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3csuA.176.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3csuA.176.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3csuA.176.4.a2m \
	-target T0124 -template 3csuA \
	-out T0124-3csuA.176.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3csuA-orig.a2m
Writing a2m file: tmp/3csuA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-19767


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-19767/tmp -alignfile tmp/3csuA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3csuA-orig.a2m (1 sequences, 310 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-19767/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-19767/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-19767/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19767/tmp.a2m (1 sequences, 310 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-19767/tmp.mod tmp/3csuA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-19767 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3csuA-align.mod
tmp/3csuA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-19767/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3csuA-orig.a2m tmp/3csuA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3csuA-align.mod
Running w0.5 tmp/3csuA-orig.a2m tmp/3csuA-align.mod
Running align2model tmp/3csuA-align -i tmp/3csuA-align.mod -db tmp/3csuA-orig.a2m -db tmp/3csuA-pdb.a2m
partial PDB gets fragment 45 through 54 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
ILE    2    3
LYS    3   26
LEU    4    3
LEU    5    3
THR    6    1
GLU    7   15
LYS    8   27
THR    9    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3csuA.176.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3csuA.177.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3csuA.177.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3csuA.177.5.a2m \
	-target T0124 -template 3csuA \
	-out T0124-3csuA.177.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3csuA-orig.a2m
Writing a2m file: tmp/3csuA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13269


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13269/tmp -alignfile tmp/3csuA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3csuA-orig.a2m (1 sequences, 310 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13269/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13269/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13269/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13269/tmp.a2m (1 sequences, 310 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13269/tmp.mod tmp/3csuA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13269 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3csuA-align.mod
tmp/3csuA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13269/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3csuA-orig.a2m tmp/3csuA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3csuA-align.mod
Running w0.5 tmp/3csuA-orig.a2m tmp/3csuA-align.mod
Running align2model tmp/3csuA-align -i tmp/3csuA-align.mod -db tmp/3csuA-orig.a2m -db tmp/3csuA-pdb.a2m
partial PDB gets fragment 44 through 53 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    2
LYS    2   23
LEU    3    3
LEU    4    3
THR    5    2
LYS    7   18
THR    8    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    7.03701
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3csuA.177.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3lck.100.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3lck.100.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3lck.100.1.a2m \
	-target T0124 -template 3lck \
	-out T0124-3lck.100.1 -outdir und
Skipped atom 153, because occupancy 0.4 <= existing 0.600001
Skipped atom 155, because occupancy 0.4 <= existing 0.600001
Skipped atom 157, because occupancy 0.4 <= existing 0.600001
Skipped atom 159, because occupancy 0.4 <= existing 0.600001
Skipped atom 161, because occupancy 0.4 <= existing 0.600001
Skipped atom 163, because occupancy 0.4 <= existing 0.600001
Skipped atom 165, because occupancy 0.4 <= existing 0.600001
Skipped atom 167, because occupancy 0.4 <= existing 0.600001
Skipped atom 250, because occupancy 0.23 <= existing 0.770001
Skipped atom 252, because occupancy 0.23 <= existing 0.770001
Skipped atom 254, because occupancy 0.23 <= existing 0.770001
Skipped atom 256, because occupancy 0.23 <= existing 0.770001
Skipped atom 258, because occupancy 0.23 <= existing 0.770001
Skipped atom 260, because occupancy 0.23 <= existing 0.770001
Skipped atom 262, because occupancy 0.23 <= existing 0.770001
Skipped atom 390, because occupancy 0.35 <= existing 0.650001
Skipped atom 392, because occupancy 0.35 <= existing 0.650001
Skipped atom 394, because occupancy 0.35 <= existing 0.650001
Skipped atom 396, because occupancy 0.35 <= existing 0.650001
Skipped atom 398, because occupancy 0.35 <= existing 0.650001
Skipped atom 400, because occupancy 0.35 <= existing 0.650001
Skipped atom 419, because occupancy 0.36 <= existing 0.640001
Skipped atom 421, because occupancy 0.36 <= existing 0.640001
Skipped atom 423, because occupancy 0.36 <= existing 0.640001
Skipped atom 425, because occupancy 0.36 <= existing 0.640001
Skipped atom 427, because occupancy 0.36 <= existing 0.640001
Skipped atom 429, because occupancy 0.36 <= existing 0.640001
Skipped atom 431, because occupancy 0.36 <= existing 0.640001
Skipped atom 433, because occupancy 0.36 <= existing 0.640001
Skipped atom 435, because occupancy 0.36 <= existing 0.640001
Skipped atom 461, because occupancy 0.49 <= existing 0.510001
Skipped atom 463, because occupancy 0.49 <= existing 0.510001
Skipped atom 465, because occupancy 0.49 <= existing 0.510001
Skipped atom 467, because occupancy 0.49 <= existing 0.510001
Skipped atom 469, because occupancy 0.49 <= existing 0.510001
Skipped atom 471, because occupancy 0.49 <= existing 0.510001
Skipped atom 473, because occupancy 0.49 <= existing 0.510001
Skipped atom 666, because occupancy 0.25 <= existing 0.750001
Skipped atom 668, because occupancy 0.25 <= existing 0.750001
Skipped atom 670, because occupancy 0.25 <= existing 0.750001
Skipped atom 672, because occupancy 0.25 <= existing 0.750001
Skipped atom 674, because occupancy 0.25 <= existing 0.750001
Skipped atom 676, because occupancy 0.25 <= existing 0.750001
Skipped atom 678, because occupancy 0.25 <= existing 0.750001
Skipped atom 739, because occupancy 0.18 <= existing 0.820001
Skipped atom 741, because occupancy 0.18 <= existing 0.820001
Skipped atom 743, because occupancy 0.18 <= existing 0.820001
Skipped atom 745, because occupancy 0.18 <= existing 0.820001
Skipped atom 747, because occupancy 0.18 <= existing 0.820001
Skipped atom 749, because occupancy 0.18 <= existing 0.820001
Skipped atom 751, because occupancy 0.18 <= existing 0.820001
Skipped atom 753, because occupancy 0.18 <= existing 0.820001
Skipped atom 1618, because occupancy 0.16 <= existing 0.840001
Skipped atom 1620, because occupancy 0.16 <= existing 0.840001
Skipped atom 1622, because occupancy 0.16 <= existing 0.840001
Skipped atom 1624, because occupancy 0.16 <= existing 0.840001
Skipped atom 1626, because occupancy 0.16 <= existing 0.840001
Skipped atom 1628, because occupancy 0.16 <= existing 0.840001
Skipped atom 1659, because occupancy 0.26 <= existing 0.740001
Skipped atom 1661, because occupancy 0.26 <= existing 0.740001
Skipped atom 1663, because occupancy 0.26 <= existing 0.740001
Skipped atom 1665, because occupancy 0.26 <= existing 0.740001
Skipped atom 1667, because occupancy 0.26 <= existing 0.740001
Skipped atom 1669, because occupancy 0.26 <= existing 0.740001
Skipped atom 1762, because occupancy 0.42 <= existing 0.580001
Skipped atom 1764, because occupancy 0.42 <= existing 0.580001
Skipped atom 1766, because occupancy 0.42 <= existing 0.580001
Skipped atom 1768, because occupancy 0.42 <= existing 0.580001
Skipped atom 1770, because occupancy 0.42 <= existing 0.580001
Skipped atom 1772, because occupancy 0.42 <= existing 0.580001
Skipped atom 1774, because occupancy 0.42 <= existing 0.580001
Skipped atom 1776, because occupancy 0.42 <= existing 0.580001
Skipped atom 1778, because occupancy 0.42 <= existing 0.580001
Skipped atom 1780, because occupancy 0.42 <= existing 0.580001
Skipped atom 1782, because occupancy 0.42 <= existing 0.580001
Skipped atom 1875, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1883, because occupancy 0.4 <= existing 0.600001
Skipped atom 1885, because occupancy 0.4 <= existing 0.600001
Skipped atom 1887, because occupancy 0.4 <= existing 0.600001
Skipped atom 1889, because occupancy 0.4 <= existing 0.600001
Skipped atom 2034, because occupancy 0.49 <= existing 0.510001
Skipped atom 2036, because occupancy 0.49 <= existing 0.510001
Skipped atom 2038, because occupancy 0.49 <= existing 0.510001
Skipped atom 2040, because occupancy 0.49 <= existing 0.510001
Skipped atom 2042, because occupancy 0.49 <= existing 0.510001
Skipped atom 2044, because occupancy 0.49 <= existing 0.510001
Skipped atom 2046, because occupancy 0.49 <= existing 0.510001
Skipped atom 2048, because occupancy 0.49 <= existing 0.510001
Skipped atom 2050, because occupancy 0.49 <= existing 0.510001
Skipped atom 2264, because occupancy 0.29 <= existing 0.710001
Skipped atom 2266, because occupancy 0.29 <= existing 0.710001
Skipped atom 2268, because occupancy 0.29 <= existing 0.710001
Skipped atom 2270, because occupancy 0.29 <= existing 0.710001
Skipped atom 2272, because occupancy 0.29 <= existing 0.710001
Skipped atom 2274, because occupancy 0.29 <= existing 0.710001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3lck-orig.a2m
Writing a2m file: tmp/3lck-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14219


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14219/tmp -alignfile tmp/3lck-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3lck-orig.a2m (1 sequences, 271 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14219/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14219/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14219/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14219/tmp.a2m (1 sequences, 271 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14219/tmp.mod tmp/3lck-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14219 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3lck-align.mod
tmp/3lck-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14219/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3lck-orig.a2m tmp/3lck-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3lck-align.mod
Running w0.5 tmp/3lck-orig.a2m tmp/3lck-align.mod
Running align2model tmp/3lck-align -i tmp/3lck-align.mod -db tmp/3lck-orig.a2m -db tmp/3lck-pdb.a2m
partial PDB gets fragment 125 through 134 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
THR    2    2
GLU    3   13
GLN    4    8
THR    5    2
LYS    7   24
ILE    8    3
THR    9    1
GLU   10   12
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3lck.100.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3lck.100.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3lck.100.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3lck.100.4.a2m \
	-target T0124 -template 3lck \
	-out T0124-3lck.100.4 -outdir und
Skipped atom 153, because occupancy 0.4 <= existing 0.600001
Skipped atom 155, because occupancy 0.4 <= existing 0.600001
Skipped atom 157, because occupancy 0.4 <= existing 0.600001
Skipped atom 159, because occupancy 0.4 <= existing 0.600001
Skipped atom 161, because occupancy 0.4 <= existing 0.600001
Skipped atom 163, because occupancy 0.4 <= existing 0.600001
Skipped atom 165, because occupancy 0.4 <= existing 0.600001
Skipped atom 167, because occupancy 0.4 <= existing 0.600001
Skipped atom 250, because occupancy 0.23 <= existing 0.770001
Skipped atom 252, because occupancy 0.23 <= existing 0.770001
Skipped atom 254, because occupancy 0.23 <= existing 0.770001
Skipped atom 256, because occupancy 0.23 <= existing 0.770001
Skipped atom 258, because occupancy 0.23 <= existing 0.770001
Skipped atom 260, because occupancy 0.23 <= existing 0.770001
Skipped atom 262, because occupancy 0.23 <= existing 0.770001
Skipped atom 390, because occupancy 0.35 <= existing 0.650001
Skipped atom 392, because occupancy 0.35 <= existing 0.650001
Skipped atom 394, because occupancy 0.35 <= existing 0.650001
Skipped atom 396, because occupancy 0.35 <= existing 0.650001
Skipped atom 398, because occupancy 0.35 <= existing 0.650001
Skipped atom 400, because occupancy 0.35 <= existing 0.650001
Skipped atom 419, because occupancy 0.36 <= existing 0.640001
Skipped atom 421, because occupancy 0.36 <= existing 0.640001
Skipped atom 423, because occupancy 0.36 <= existing 0.640001
Skipped atom 425, because occupancy 0.36 <= existing 0.640001
Skipped atom 427, because occupancy 0.36 <= existing 0.640001
Skipped atom 429, because occupancy 0.36 <= existing 0.640001
Skipped atom 431, because occupancy 0.36 <= existing 0.640001
Skipped atom 433, because occupancy 0.36 <= existing 0.640001
Skipped atom 435, because occupancy 0.36 <= existing 0.640001
Skipped atom 461, because occupancy 0.49 <= existing 0.510001
Skipped atom 463, because occupancy 0.49 <= existing 0.510001
Skipped atom 465, because occupancy 0.49 <= existing 0.510001
Skipped atom 467, because occupancy 0.49 <= existing 0.510001
Skipped atom 469, because occupancy 0.49 <= existing 0.510001
Skipped atom 471, because occupancy 0.49 <= existing 0.510001
Skipped atom 473, because occupancy 0.49 <= existing 0.510001
Skipped atom 666, because occupancy 0.25 <= existing 0.750001
Skipped atom 668, because occupancy 0.25 <= existing 0.750001
Skipped atom 670, because occupancy 0.25 <= existing 0.750001
Skipped atom 672, because occupancy 0.25 <= existing 0.750001
Skipped atom 674, because occupancy 0.25 <= existing 0.750001
Skipped atom 676, because occupancy 0.25 <= existing 0.750001
Skipped atom 678, because occupancy 0.25 <= existing 0.750001
Skipped atom 739, because occupancy 0.18 <= existing 0.820001
Skipped atom 741, because occupancy 0.18 <= existing 0.820001
Skipped atom 743, because occupancy 0.18 <= existing 0.820001
Skipped atom 745, because occupancy 0.18 <= existing 0.820001
Skipped atom 747, because occupancy 0.18 <= existing 0.820001
Skipped atom 749, because occupancy 0.18 <= existing 0.820001
Skipped atom 751, because occupancy 0.18 <= existing 0.820001
Skipped atom 753, because occupancy 0.18 <= existing 0.820001
Skipped atom 1618, because occupancy 0.16 <= existing 0.840001
Skipped atom 1620, because occupancy 0.16 <= existing 0.840001
Skipped atom 1622, because occupancy 0.16 <= existing 0.840001
Skipped atom 1624, because occupancy 0.16 <= existing 0.840001
Skipped atom 1626, because occupancy 0.16 <= existing 0.840001
Skipped atom 1628, because occupancy 0.16 <= existing 0.840001
Skipped atom 1659, because occupancy 0.26 <= existing 0.740001
Skipped atom 1661, because occupancy 0.26 <= existing 0.740001
Skipped atom 1663, because occupancy 0.26 <= existing 0.740001
Skipped atom 1665, because occupancy 0.26 <= existing 0.740001
Skipped atom 1667, because occupancy 0.26 <= existing 0.740001
Skipped atom 1669, because occupancy 0.26 <= existing 0.740001
Skipped atom 1762, because occupancy 0.42 <= existing 0.580001
Skipped atom 1764, because occupancy 0.42 <= existing 0.580001
Skipped atom 1766, because occupancy 0.42 <= existing 0.580001
Skipped atom 1768, because occupancy 0.42 <= existing 0.580001
Skipped atom 1770, because occupancy 0.42 <= existing 0.580001
Skipped atom 1772, because occupancy 0.42 <= existing 0.580001
Skipped atom 1774, because occupancy 0.42 <= existing 0.580001
Skipped atom 1776, because occupancy 0.42 <= existing 0.580001
Skipped atom 1778, because occupancy 0.42 <= existing 0.580001
Skipped atom 1780, because occupancy 0.42 <= existing 0.580001
Skipped atom 1782, because occupancy 0.42 <= existing 0.580001
Skipped atom 1875, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1883, because occupancy 0.4 <= existing 0.600001
Skipped atom 1885, because occupancy 0.4 <= existing 0.600001
Skipped atom 1887, because occupancy 0.4 <= existing 0.600001
Skipped atom 1889, because occupancy 0.4 <= existing 0.600001
Skipped atom 2034, because occupancy 0.49 <= existing 0.510001
Skipped atom 2036, because occupancy 0.49 <= existing 0.510001
Skipped atom 2038, because occupancy 0.49 <= existing 0.510001
Skipped atom 2040, because occupancy 0.49 <= existing 0.510001
Skipped atom 2042, because occupancy 0.49 <= existing 0.510001
Skipped atom 2044, because occupancy 0.49 <= existing 0.510001
Skipped atom 2046, because occupancy 0.49 <= existing 0.510001
Skipped atom 2048, because occupancy 0.49 <= existing 0.510001
Skipped atom 2050, because occupancy 0.49 <= existing 0.510001
Skipped atom 2264, because occupancy 0.29 <= existing 0.710001
Skipped atom 2266, because occupancy 0.29 <= existing 0.710001
Skipped atom 2268, because occupancy 0.29 <= existing 0.710001
Skipped atom 2270, because occupancy 0.29 <= existing 0.710001
Skipped atom 2272, because occupancy 0.29 <= existing 0.710001
Skipped atom 2274, because occupancy 0.29 <= existing 0.710001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3lck-orig.a2m
Writing a2m file: tmp/3lck-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14689


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14689/tmp -alignfile tmp/3lck-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3lck-orig.a2m (1 sequences, 271 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14689/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14689/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14689/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14689/tmp.a2m (1 sequences, 271 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14689/tmp.mod tmp/3lck-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14689 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3lck-align.mod
tmp/3lck-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14689/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3lck-orig.a2m tmp/3lck-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3lck-align.mod
Running w0.5 tmp/3lck-orig.a2m tmp/3lck-align.mod
Running align2model tmp/3lck-align -i tmp/3lck-align.mod -db tmp/3lck-orig.a2m -db tmp/3lck-pdb.a2m
partial PDB gets fragment 123 through 133 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
THR    2    2
GLN    4   15
THR    5    1
LYS    7   23
THR    9    1
GLU   10   10
LEU   11    4
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3lck.100.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3lck.101.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3lck.101.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3lck.101.4.a2m \
	-target T0124 -template 3lck \
	-out T0124-3lck.101.4 -outdir und
Skipped atom 153, because occupancy 0.4 <= existing 0.600001
Skipped atom 155, because occupancy 0.4 <= existing 0.600001
Skipped atom 157, because occupancy 0.4 <= existing 0.600001
Skipped atom 159, because occupancy 0.4 <= existing 0.600001
Skipped atom 161, because occupancy 0.4 <= existing 0.600001
Skipped atom 163, because occupancy 0.4 <= existing 0.600001
Skipped atom 165, because occupancy 0.4 <= existing 0.600001
Skipped atom 167, because occupancy 0.4 <= existing 0.600001
Skipped atom 250, because occupancy 0.23 <= existing 0.770001
Skipped atom 252, because occupancy 0.23 <= existing 0.770001
Skipped atom 254, because occupancy 0.23 <= existing 0.770001
Skipped atom 256, because occupancy 0.23 <= existing 0.770001
Skipped atom 258, because occupancy 0.23 <= existing 0.770001
Skipped atom 260, because occupancy 0.23 <= existing 0.770001
Skipped atom 262, because occupancy 0.23 <= existing 0.770001
Skipped atom 390, because occupancy 0.35 <= existing 0.650001
Skipped atom 392, because occupancy 0.35 <= existing 0.650001
Skipped atom 394, because occupancy 0.35 <= existing 0.650001
Skipped atom 396, because occupancy 0.35 <= existing 0.650001
Skipped atom 398, because occupancy 0.35 <= existing 0.650001
Skipped atom 400, because occupancy 0.35 <= existing 0.650001
Skipped atom 419, because occupancy 0.36 <= existing 0.640001
Skipped atom 421, because occupancy 0.36 <= existing 0.640001
Skipped atom 423, because occupancy 0.36 <= existing 0.640001
Skipped atom 425, because occupancy 0.36 <= existing 0.640001
Skipped atom 427, because occupancy 0.36 <= existing 0.640001
Skipped atom 429, because occupancy 0.36 <= existing 0.640001
Skipped atom 431, because occupancy 0.36 <= existing 0.640001
Skipped atom 433, because occupancy 0.36 <= existing 0.640001
Skipped atom 435, because occupancy 0.36 <= existing 0.640001
Skipped atom 461, because occupancy 0.49 <= existing 0.510001
Skipped atom 463, because occupancy 0.49 <= existing 0.510001
Skipped atom 465, because occupancy 0.49 <= existing 0.510001
Skipped atom 467, because occupancy 0.49 <= existing 0.510001
Skipped atom 469, because occupancy 0.49 <= existing 0.510001
Skipped atom 471, because occupancy 0.49 <= existing 0.510001
Skipped atom 473, because occupancy 0.49 <= existing 0.510001
Skipped atom 666, because occupancy 0.25 <= existing 0.750001
Skipped atom 668, because occupancy 0.25 <= existing 0.750001
Skipped atom 670, because occupancy 0.25 <= existing 0.750001
Skipped atom 672, because occupancy 0.25 <= existing 0.750001
Skipped atom 674, because occupancy 0.25 <= existing 0.750001
Skipped atom 676, because occupancy 0.25 <= existing 0.750001
Skipped atom 678, because occupancy 0.25 <= existing 0.750001
Skipped atom 739, because occupancy 0.18 <= existing 0.820001
Skipped atom 741, because occupancy 0.18 <= existing 0.820001
Skipped atom 743, because occupancy 0.18 <= existing 0.820001
Skipped atom 745, because occupancy 0.18 <= existing 0.820001
Skipped atom 747, because occupancy 0.18 <= existing 0.820001
Skipped atom 749, because occupancy 0.18 <= existing 0.820001
Skipped atom 751, because occupancy 0.18 <= existing 0.820001
Skipped atom 753, because occupancy 0.18 <= existing 0.820001
Skipped atom 1618, because occupancy 0.16 <= existing 0.840001
Skipped atom 1620, because occupancy 0.16 <= existing 0.840001
Skipped atom 1622, because occupancy 0.16 <= existing 0.840001
Skipped atom 1624, because occupancy 0.16 <= existing 0.840001
Skipped atom 1626, because occupancy 0.16 <= existing 0.840001
Skipped atom 1628, because occupancy 0.16 <= existing 0.840001
Skipped atom 1659, because occupancy 0.26 <= existing 0.740001
Skipped atom 1661, because occupancy 0.26 <= existing 0.740001
Skipped atom 1663, because occupancy 0.26 <= existing 0.740001
Skipped atom 1665, because occupancy 0.26 <= existing 0.740001
Skipped atom 1667, because occupancy 0.26 <= existing 0.740001
Skipped atom 1669, because occupancy 0.26 <= existing 0.740001
Skipped atom 1762, because occupancy 0.42 <= existing 0.580001
Skipped atom 1764, because occupancy 0.42 <= existing 0.580001
Skipped atom 1766, because occupancy 0.42 <= existing 0.580001
Skipped atom 1768, because occupancy 0.42 <= existing 0.580001
Skipped atom 1770, because occupancy 0.42 <= existing 0.580001
Skipped atom 1772, because occupancy 0.42 <= existing 0.580001
Skipped atom 1774, because occupancy 0.42 <= existing 0.580001
Skipped atom 1776, because occupancy 0.42 <= existing 0.580001
Skipped atom 1778, because occupancy 0.42 <= existing 0.580001
Skipped atom 1780, because occupancy 0.42 <= existing 0.580001
Skipped atom 1782, because occupancy 0.42 <= existing 0.580001
Skipped atom 1875, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1883, because occupancy 0.4 <= existing 0.600001
Skipped atom 1885, because occupancy 0.4 <= existing 0.600001
Skipped atom 1887, because occupancy 0.4 <= existing 0.600001
Skipped atom 1889, because occupancy 0.4 <= existing 0.600001
Skipped atom 2034, because occupancy 0.49 <= existing 0.510001
Skipped atom 2036, because occupancy 0.49 <= existing 0.510001
Skipped atom 2038, because occupancy 0.49 <= existing 0.510001
Skipped atom 2040, because occupancy 0.49 <= existing 0.510001
Skipped atom 2042, because occupancy 0.49 <= existing 0.510001
Skipped atom 2044, because occupancy 0.49 <= existing 0.510001
Skipped atom 2046, because occupancy 0.49 <= existing 0.510001
Skipped atom 2048, because occupancy 0.49 <= existing 0.510001
Skipped atom 2050, because occupancy 0.49 <= existing 0.510001
Skipped atom 2264, because occupancy 0.29 <= existing 0.710001
Skipped atom 2266, because occupancy 0.29 <= existing 0.710001
Skipped atom 2268, because occupancy 0.29 <= existing 0.710001
Skipped atom 2270, because occupancy 0.29 <= existing 0.710001
Skipped atom 2272, because occupancy 0.29 <= existing 0.710001
Skipped atom 2274, because occupancy 0.29 <= existing 0.710001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3lck-orig.a2m
Writing a2m file: tmp/3lck-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-20990


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-20990/tmp -alignfile tmp/3lck-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3lck-orig.a2m (1 sequences, 271 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-20990/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-20990/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-20990/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20990/tmp.a2m (1 sequences, 271 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-20990/tmp.mod tmp/3lck-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-20990 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3lck-align.mod
tmp/3lck-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-20990/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3lck-orig.a2m tmp/3lck-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3lck-align.mod
Running w0.5 tmp/3lck-orig.a2m tmp/3lck-align.mod
Running align2model tmp/3lck-align -i tmp/3lck-align.mod -db tmp/3lck-orig.a2m -db tmp/3lck-pdb.a2m
partial PDB gets fragment 122 through 132 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
THR    1    2
GLU    2   12
GLN    3   12
THR    4    1
LYS    6   17
ILE    7    3
THR    8    2
GLU    9   14
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4   11     16.5907
Cluster     1 =   4  11
2 clashing residues after turn 
Residue clashes:
4-11
cluster 1 has 2 members and 3.000e+01 combinations:
 11  4 
Energy     16.5907
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 3.000e+01 - Sending to search
0.000000 < 16.590725: keeping 
Solved cluster 1: residual clashing  0.11
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3lck.101.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3lck.102.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3lck.102.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3lck.102.2.a2m \
	-target T0124 -template 3lck \
	-out T0124-3lck.102.2 -outdir und
Skipped atom 153, because occupancy 0.4 <= existing 0.600001
Skipped atom 155, because occupancy 0.4 <= existing 0.600001
Skipped atom 157, because occupancy 0.4 <= existing 0.600001
Skipped atom 159, because occupancy 0.4 <= existing 0.600001
Skipped atom 161, because occupancy 0.4 <= existing 0.600001
Skipped atom 163, because occupancy 0.4 <= existing 0.600001
Skipped atom 165, because occupancy 0.4 <= existing 0.600001
Skipped atom 167, because occupancy 0.4 <= existing 0.600001
Skipped atom 250, because occupancy 0.23 <= existing 0.770001
Skipped atom 252, because occupancy 0.23 <= existing 0.770001
Skipped atom 254, because occupancy 0.23 <= existing 0.770001
Skipped atom 256, because occupancy 0.23 <= existing 0.770001
Skipped atom 258, because occupancy 0.23 <= existing 0.770001
Skipped atom 260, because occupancy 0.23 <= existing 0.770001
Skipped atom 262, because occupancy 0.23 <= existing 0.770001
Skipped atom 390, because occupancy 0.35 <= existing 0.650001
Skipped atom 392, because occupancy 0.35 <= existing 0.650001
Skipped atom 394, because occupancy 0.35 <= existing 0.650001
Skipped atom 396, because occupancy 0.35 <= existing 0.650001
Skipped atom 398, because occupancy 0.35 <= existing 0.650001
Skipped atom 400, because occupancy 0.35 <= existing 0.650001
Skipped atom 419, because occupancy 0.36 <= existing 0.640001
Skipped atom 421, because occupancy 0.36 <= existing 0.640001
Skipped atom 423, because occupancy 0.36 <= existing 0.640001
Skipped atom 425, because occupancy 0.36 <= existing 0.640001
Skipped atom 427, because occupancy 0.36 <= existing 0.640001
Skipped atom 429, because occupancy 0.36 <= existing 0.640001
Skipped atom 431, because occupancy 0.36 <= existing 0.640001
Skipped atom 433, because occupancy 0.36 <= existing 0.640001
Skipped atom 435, because occupancy 0.36 <= existing 0.640001
Skipped atom 461, because occupancy 0.49 <= existing 0.510001
Skipped atom 463, because occupancy 0.49 <= existing 0.510001
Skipped atom 465, because occupancy 0.49 <= existing 0.510001
Skipped atom 467, because occupancy 0.49 <= existing 0.510001
Skipped atom 469, because occupancy 0.49 <= existing 0.510001
Skipped atom 471, because occupancy 0.49 <= existing 0.510001
Skipped atom 473, because occupancy 0.49 <= existing 0.510001
Skipped atom 666, because occupancy 0.25 <= existing 0.750001
Skipped atom 668, because occupancy 0.25 <= existing 0.750001
Skipped atom 670, because occupancy 0.25 <= existing 0.750001
Skipped atom 672, because occupancy 0.25 <= existing 0.750001
Skipped atom 674, because occupancy 0.25 <= existing 0.750001
Skipped atom 676, because occupancy 0.25 <= existing 0.750001
Skipped atom 678, because occupancy 0.25 <= existing 0.750001
Skipped atom 739, because occupancy 0.18 <= existing 0.820001
Skipped atom 741, because occupancy 0.18 <= existing 0.820001
Skipped atom 743, because occupancy 0.18 <= existing 0.820001
Skipped atom 745, because occupancy 0.18 <= existing 0.820001
Skipped atom 747, because occupancy 0.18 <= existing 0.820001
Skipped atom 749, because occupancy 0.18 <= existing 0.820001
Skipped atom 751, because occupancy 0.18 <= existing 0.820001
Skipped atom 753, because occupancy 0.18 <= existing 0.820001
Skipped atom 1618, because occupancy 0.16 <= existing 0.840001
Skipped atom 1620, because occupancy 0.16 <= existing 0.840001
Skipped atom 1622, because occupancy 0.16 <= existing 0.840001
Skipped atom 1624, because occupancy 0.16 <= existing 0.840001
Skipped atom 1626, because occupancy 0.16 <= existing 0.840001
Skipped atom 1628, because occupancy 0.16 <= existing 0.840001
Skipped atom 1659, because occupancy 0.26 <= existing 0.740001
Skipped atom 1661, because occupancy 0.26 <= existing 0.740001
Skipped atom 1663, because occupancy 0.26 <= existing 0.740001
Skipped atom 1665, because occupancy 0.26 <= existing 0.740001
Skipped atom 1667, because occupancy 0.26 <= existing 0.740001
Skipped atom 1669, because occupancy 0.26 <= existing 0.740001
Skipped atom 1762, because occupancy 0.42 <= existing 0.580001
Skipped atom 1764, because occupancy 0.42 <= existing 0.580001
Skipped atom 1766, because occupancy 0.42 <= existing 0.580001
Skipped atom 1768, because occupancy 0.42 <= existing 0.580001
Skipped atom 1770, because occupancy 0.42 <= existing 0.580001
Skipped atom 1772, because occupancy 0.42 <= existing 0.580001
Skipped atom 1774, because occupancy 0.42 <= existing 0.580001
Skipped atom 1776, because occupancy 0.42 <= existing 0.580001
Skipped atom 1778, because occupancy 0.42 <= existing 0.580001
Skipped atom 1780, because occupancy 0.42 <= existing 0.580001
Skipped atom 1782, because occupancy 0.42 <= existing 0.580001
Skipped atom 1875, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1883, because occupancy 0.4 <= existing 0.600001
Skipped atom 1885, because occupancy 0.4 <= existing 0.600001
Skipped atom 1887, because occupancy 0.4 <= existing 0.600001
Skipped atom 1889, because occupancy 0.4 <= existing 0.600001
Skipped atom 2034, because occupancy 0.49 <= existing 0.510001
Skipped atom 2036, because occupancy 0.49 <= existing 0.510001
Skipped atom 2038, because occupancy 0.49 <= existing 0.510001
Skipped atom 2040, because occupancy 0.49 <= existing 0.510001
Skipped atom 2042, because occupancy 0.49 <= existing 0.510001
Skipped atom 2044, because occupancy 0.49 <= existing 0.510001
Skipped atom 2046, because occupancy 0.49 <= existing 0.510001
Skipped atom 2048, because occupancy 0.49 <= existing 0.510001
Skipped atom 2050, because occupancy 0.49 <= existing 0.510001
Skipped atom 2264, because occupancy 0.29 <= existing 0.710001
Skipped atom 2266, because occupancy 0.29 <= existing 0.710001
Skipped atom 2268, because occupancy 0.29 <= existing 0.710001
Skipped atom 2270, because occupancy 0.29 <= existing 0.710001
Skipped atom 2272, because occupancy 0.29 <= existing 0.710001
Skipped atom 2274, because occupancy 0.29 <= existing 0.710001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3lck-orig.a2m
Writing a2m file: tmp/3lck-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13328


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13328/tmp -alignfile tmp/3lck-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3lck-orig.a2m (1 sequences, 271 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13328/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13328/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13328/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13328/tmp.a2m (1 sequences, 271 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13328/tmp.mod tmp/3lck-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13328 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3lck-align.mod
tmp/3lck-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13328/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3lck-orig.a2m tmp/3lck-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3lck-align.mod
Running w0.5 tmp/3lck-orig.a2m tmp/3lck-align.mod
Running align2model tmp/3lck-align -i tmp/3lck-align.mod -db tmp/3lck-orig.a2m -db tmp/3lck-pdb.a2m
partial PDB gets fragment 121 through 131 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
GLN    2   14
THR    3    2
LYS    5   24
ILE    6    5
THR    7    1
GLU    8    7
LEU    9    2
ARG   11   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3lck.102.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3lck.103.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3lck.103.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3lck.103.4.a2m \
	-target T0124 -template 3lck \
	-out T0124-3lck.103.4 -outdir und
Skipped atom 153, because occupancy 0.4 <= existing 0.600001
Skipped atom 155, because occupancy 0.4 <= existing 0.600001
Skipped atom 157, because occupancy 0.4 <= existing 0.600001
Skipped atom 159, because occupancy 0.4 <= existing 0.600001
Skipped atom 161, because occupancy 0.4 <= existing 0.600001
Skipped atom 163, because occupancy 0.4 <= existing 0.600001
Skipped atom 165, because occupancy 0.4 <= existing 0.600001
Skipped atom 167, because occupancy 0.4 <= existing 0.600001
Skipped atom 250, because occupancy 0.23 <= existing 0.770001
Skipped atom 252, because occupancy 0.23 <= existing 0.770001
Skipped atom 254, because occupancy 0.23 <= existing 0.770001
Skipped atom 256, because occupancy 0.23 <= existing 0.770001
Skipped atom 258, because occupancy 0.23 <= existing 0.770001
Skipped atom 260, because occupancy 0.23 <= existing 0.770001
Skipped atom 262, because occupancy 0.23 <= existing 0.770001
Skipped atom 390, because occupancy 0.35 <= existing 0.650001
Skipped atom 392, because occupancy 0.35 <= existing 0.650001
Skipped atom 394, because occupancy 0.35 <= existing 0.650001
Skipped atom 396, because occupancy 0.35 <= existing 0.650001
Skipped atom 398, because occupancy 0.35 <= existing 0.650001
Skipped atom 400, because occupancy 0.35 <= existing 0.650001
Skipped atom 419, because occupancy 0.36 <= existing 0.640001
Skipped atom 421, because occupancy 0.36 <= existing 0.640001
Skipped atom 423, because occupancy 0.36 <= existing 0.640001
Skipped atom 425, because occupancy 0.36 <= existing 0.640001
Skipped atom 427, because occupancy 0.36 <= existing 0.640001
Skipped atom 429, because occupancy 0.36 <= existing 0.640001
Skipped atom 431, because occupancy 0.36 <= existing 0.640001
Skipped atom 433, because occupancy 0.36 <= existing 0.640001
Skipped atom 435, because occupancy 0.36 <= existing 0.640001
Skipped atom 461, because occupancy 0.49 <= existing 0.510001
Skipped atom 463, because occupancy 0.49 <= existing 0.510001
Skipped atom 465, because occupancy 0.49 <= existing 0.510001
Skipped atom 467, because occupancy 0.49 <= existing 0.510001
Skipped atom 469, because occupancy 0.49 <= existing 0.510001
Skipped atom 471, because occupancy 0.49 <= existing 0.510001
Skipped atom 473, because occupancy 0.49 <= existing 0.510001
Skipped atom 666, because occupancy 0.25 <= existing 0.750001
Skipped atom 668, because occupancy 0.25 <= existing 0.750001
Skipped atom 670, because occupancy 0.25 <= existing 0.750001
Skipped atom 672, because occupancy 0.25 <= existing 0.750001
Skipped atom 674, because occupancy 0.25 <= existing 0.750001
Skipped atom 676, because occupancy 0.25 <= existing 0.750001
Skipped atom 678, because occupancy 0.25 <= existing 0.750001
Skipped atom 739, because occupancy 0.18 <= existing 0.820001
Skipped atom 741, because occupancy 0.18 <= existing 0.820001
Skipped atom 743, because occupancy 0.18 <= existing 0.820001
Skipped atom 745, because occupancy 0.18 <= existing 0.820001
Skipped atom 747, because occupancy 0.18 <= existing 0.820001
Skipped atom 749, because occupancy 0.18 <= existing 0.820001
Skipped atom 751, because occupancy 0.18 <= existing 0.820001
Skipped atom 753, because occupancy 0.18 <= existing 0.820001
Skipped atom 1618, because occupancy 0.16 <= existing 0.840001
Skipped atom 1620, because occupancy 0.16 <= existing 0.840001
Skipped atom 1622, because occupancy 0.16 <= existing 0.840001
Skipped atom 1624, because occupancy 0.16 <= existing 0.840001
Skipped atom 1626, because occupancy 0.16 <= existing 0.840001
Skipped atom 1628, because occupancy 0.16 <= existing 0.840001
Skipped atom 1659, because occupancy 0.26 <= existing 0.740001
Skipped atom 1661, because occupancy 0.26 <= existing 0.740001
Skipped atom 1663, because occupancy 0.26 <= existing 0.740001
Skipped atom 1665, because occupancy 0.26 <= existing 0.740001
Skipped atom 1667, because occupancy 0.26 <= existing 0.740001
Skipped atom 1669, because occupancy 0.26 <= existing 0.740001
Skipped atom 1762, because occupancy 0.42 <= existing 0.580001
Skipped atom 1764, because occupancy 0.42 <= existing 0.580001
Skipped atom 1766, because occupancy 0.42 <= existing 0.580001
Skipped atom 1768, because occupancy 0.42 <= existing 0.580001
Skipped atom 1770, because occupancy 0.42 <= existing 0.580001
Skipped atom 1772, because occupancy 0.42 <= existing 0.580001
Skipped atom 1774, because occupancy 0.42 <= existing 0.580001
Skipped atom 1776, because occupancy 0.42 <= existing 0.580001
Skipped atom 1778, because occupancy 0.42 <= existing 0.580001
Skipped atom 1780, because occupancy 0.42 <= existing 0.580001
Skipped atom 1782, because occupancy 0.42 <= existing 0.580001
Skipped atom 1875, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1883, because occupancy 0.4 <= existing 0.600001
Skipped atom 1885, because occupancy 0.4 <= existing 0.600001
Skipped atom 1887, because occupancy 0.4 <= existing 0.600001
Skipped atom 1889, because occupancy 0.4 <= existing 0.600001
Skipped atom 2034, because occupancy 0.49 <= existing 0.510001
Skipped atom 2036, because occupancy 0.49 <= existing 0.510001
Skipped atom 2038, because occupancy 0.49 <= existing 0.510001
Skipped atom 2040, because occupancy 0.49 <= existing 0.510001
Skipped atom 2042, because occupancy 0.49 <= existing 0.510001
Skipped atom 2044, because occupancy 0.49 <= existing 0.510001
Skipped atom 2046, because occupancy 0.49 <= existing 0.510001
Skipped atom 2048, because occupancy 0.49 <= existing 0.510001
Skipped atom 2050, because occupancy 0.49 <= existing 0.510001
Skipped atom 2264, because occupancy 0.29 <= existing 0.710001
Skipped atom 2266, because occupancy 0.29 <= existing 0.710001
Skipped atom 2268, because occupancy 0.29 <= existing 0.710001
Skipped atom 2270, because occupancy 0.29 <= existing 0.710001
Skipped atom 2272, because occupancy 0.29 <= existing 0.710001
Skipped atom 2274, because occupancy 0.29 <= existing 0.710001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3lck-orig.a2m
Writing a2m file: tmp/3lck-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15723


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15723/tmp -alignfile tmp/3lck-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3lck-orig.a2m (1 sequences, 271 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15723/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15723/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15723/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15723/tmp.a2m (1 sequences, 271 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15723/tmp.mod tmp/3lck-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15723 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3lck-align.mod
tmp/3lck-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15723/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3lck-orig.a2m tmp/3lck-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3lck-align.mod
Running w0.5 tmp/3lck-orig.a2m tmp/3lck-align.mod
Running align2model tmp/3lck-align -i tmp/3lck-align.mod -db tmp/3lck-orig.a2m -db tmp/3lck-pdb.a2m
partial PDB gets fragment 120 through 130 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
THR    2    2
LYS    4   23
THR    6    2
LEU    8    4
ARG   10   26
GLU   11   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3lck.103.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3lck.99.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3lck.99.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3lck.99.2.a2m \
	-target T0124 -template 3lck \
	-out T0124-3lck.99.2 -outdir und
Skipped atom 153, because occupancy 0.4 <= existing 0.600001
Skipped atom 155, because occupancy 0.4 <= existing 0.600001
Skipped atom 157, because occupancy 0.4 <= existing 0.600001
Skipped atom 159, because occupancy 0.4 <= existing 0.600001
Skipped atom 161, because occupancy 0.4 <= existing 0.600001
Skipped atom 163, because occupancy 0.4 <= existing 0.600001
Skipped atom 165, because occupancy 0.4 <= existing 0.600001
Skipped atom 167, because occupancy 0.4 <= existing 0.600001
Skipped atom 250, because occupancy 0.23 <= existing 0.770001
Skipped atom 252, because occupancy 0.23 <= existing 0.770001
Skipped atom 254, because occupancy 0.23 <= existing 0.770001
Skipped atom 256, because occupancy 0.23 <= existing 0.770001
Skipped atom 258, because occupancy 0.23 <= existing 0.770001
Skipped atom 260, because occupancy 0.23 <= existing 0.770001
Skipped atom 262, because occupancy 0.23 <= existing 0.770001
Skipped atom 390, because occupancy 0.35 <= existing 0.650001
Skipped atom 392, because occupancy 0.35 <= existing 0.650001
Skipped atom 394, because occupancy 0.35 <= existing 0.650001
Skipped atom 396, because occupancy 0.35 <= existing 0.650001
Skipped atom 398, because occupancy 0.35 <= existing 0.650001
Skipped atom 400, because occupancy 0.35 <= existing 0.650001
Skipped atom 419, because occupancy 0.36 <= existing 0.640001
Skipped atom 421, because occupancy 0.36 <= existing 0.640001
Skipped atom 423, because occupancy 0.36 <= existing 0.640001
Skipped atom 425, because occupancy 0.36 <= existing 0.640001
Skipped atom 427, because occupancy 0.36 <= existing 0.640001
Skipped atom 429, because occupancy 0.36 <= existing 0.640001
Skipped atom 431, because occupancy 0.36 <= existing 0.640001
Skipped atom 433, because occupancy 0.36 <= existing 0.640001
Skipped atom 435, because occupancy 0.36 <= existing 0.640001
Skipped atom 461, because occupancy 0.49 <= existing 0.510001
Skipped atom 463, because occupancy 0.49 <= existing 0.510001
Skipped atom 465, because occupancy 0.49 <= existing 0.510001
Skipped atom 467, because occupancy 0.49 <= existing 0.510001
Skipped atom 469, because occupancy 0.49 <= existing 0.510001
Skipped atom 471, because occupancy 0.49 <= existing 0.510001
Skipped atom 473, because occupancy 0.49 <= existing 0.510001
Skipped atom 666, because occupancy 0.25 <= existing 0.750001
Skipped atom 668, because occupancy 0.25 <= existing 0.750001
Skipped atom 670, because occupancy 0.25 <= existing 0.750001
Skipped atom 672, because occupancy 0.25 <= existing 0.750001
Skipped atom 674, because occupancy 0.25 <= existing 0.750001
Skipped atom 676, because occupancy 0.25 <= existing 0.750001
Skipped atom 678, because occupancy 0.25 <= existing 0.750001
Skipped atom 739, because occupancy 0.18 <= existing 0.820001
Skipped atom 741, because occupancy 0.18 <= existing 0.820001
Skipped atom 743, because occupancy 0.18 <= existing 0.820001
Skipped atom 745, because occupancy 0.18 <= existing 0.820001
Skipped atom 747, because occupancy 0.18 <= existing 0.820001
Skipped atom 749, because occupancy 0.18 <= existing 0.820001
Skipped atom 751, because occupancy 0.18 <= existing 0.820001
Skipped atom 753, because occupancy 0.18 <= existing 0.820001
Skipped atom 1618, because occupancy 0.16 <= existing 0.840001
Skipped atom 1620, because occupancy 0.16 <= existing 0.840001
Skipped atom 1622, because occupancy 0.16 <= existing 0.840001
Skipped atom 1624, because occupancy 0.16 <= existing 0.840001
Skipped atom 1626, because occupancy 0.16 <= existing 0.840001
Skipped atom 1628, because occupancy 0.16 <= existing 0.840001
Skipped atom 1659, because occupancy 0.26 <= existing 0.740001
Skipped atom 1661, because occupancy 0.26 <= existing 0.740001
Skipped atom 1663, because occupancy 0.26 <= existing 0.740001
Skipped atom 1665, because occupancy 0.26 <= existing 0.740001
Skipped atom 1667, because occupancy 0.26 <= existing 0.740001
Skipped atom 1669, because occupancy 0.26 <= existing 0.740001
Skipped atom 1762, because occupancy 0.42 <= existing 0.580001
Skipped atom 1764, because occupancy 0.42 <= existing 0.580001
Skipped atom 1766, because occupancy 0.42 <= existing 0.580001
Skipped atom 1768, because occupancy 0.42 <= existing 0.580001
Skipped atom 1770, because occupancy 0.42 <= existing 0.580001
Skipped atom 1772, because occupancy 0.42 <= existing 0.580001
Skipped atom 1774, because occupancy 0.42 <= existing 0.580001
Skipped atom 1776, because occupancy 0.42 <= existing 0.580001
Skipped atom 1778, because occupancy 0.42 <= existing 0.580001
Skipped atom 1780, because occupancy 0.42 <= existing 0.580001
Skipped atom 1782, because occupancy 0.42 <= existing 0.580001
Skipped atom 1875, because occupancy 0.4 <= existing 0.600001
Skipped atom 1877, because occupancy 0.4 <= existing 0.600001
Skipped atom 1879, because occupancy 0.4 <= existing 0.600001
Skipped atom 1881, because occupancy 0.4 <= existing 0.600001
Skipped atom 1883, because occupancy 0.4 <= existing 0.600001
Skipped atom 1885, because occupancy 0.4 <= existing 0.600001
Skipped atom 1887, because occupancy 0.4 <= existing 0.600001
Skipped atom 1889, because occupancy 0.4 <= existing 0.600001
Skipped atom 2034, because occupancy 0.49 <= existing 0.510001
Skipped atom 2036, because occupancy 0.49 <= existing 0.510001
Skipped atom 2038, because occupancy 0.49 <= existing 0.510001
Skipped atom 2040, because occupancy 0.49 <= existing 0.510001
Skipped atom 2042, because occupancy 0.49 <= existing 0.510001
Skipped atom 2044, because occupancy 0.49 <= existing 0.510001
Skipped atom 2046, because occupancy 0.49 <= existing 0.510001
Skipped atom 2048, because occupancy 0.49 <= existing 0.510001
Skipped atom 2050, because occupancy 0.49 <= existing 0.510001
Skipped atom 2264, because occupancy 0.29 <= existing 0.710001
Skipped atom 2266, because occupancy 0.29 <= existing 0.710001
Skipped atom 2268, because occupancy 0.29 <= existing 0.710001
Skipped atom 2270, because occupancy 0.29 <= existing 0.710001
Skipped atom 2272, because occupancy 0.29 <= existing 0.710001
Skipped atom 2274, because occupancy 0.29 <= existing 0.710001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3lck-orig.a2m
Writing a2m file: tmp/3lck-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32515


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32515/tmp -alignfile tmp/3lck-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3lck-orig.a2m (1 sequences, 271 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32515/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32515/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32515/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32515/tmp.a2m (1 sequences, 271 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32515/tmp.mod tmp/3lck-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-32515 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3lck-align.mod
tmp/3lck-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32515/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3lck-orig.a2m tmp/3lck-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3lck-align.mod
Running w0.5 tmp/3lck-orig.a2m tmp/3lck-align.mod
Running align2model tmp/3lck-align -i tmp/3lck-align.mod -db tmp/3lck-orig.a2m -db tmp/3lck-pdb.a2m
partial PDB gets fragment 126 through 135 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    4
THR    3    2
GLU    4   14
GLN    5   14
THR    6    2
LYS    8   28
ILE    9    2
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3lck.99.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3pcgA.208.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3pcgA.208.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3pcgA.208.2.a2m \
	-target T0124 -template 3pcgA \
	-out T0124-3pcgA.208.2 -outdir und
partial PDB gets fragment 16 through 25 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
LEU    2    3
GLN    3   14
GLN    4   13
GLU    5   11
VAL    7    1
GLU    9   15
TYR   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 3 rotamers of residue Y 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    1.46531
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3pcgA.208.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3pcgA.209.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3pcgA.209.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3pcgA.209.1.a2m \
	-target T0124 -template 3pcgA \
	-out T0124-3pcgA.209.1 -outdir und
partial PDB gets fragment 15 through 24 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    2
GLN    2   13
GLN    3   13
GLU    4   15
VAL    6    2
GLU    8   15
TYR    9    2
GLU   10   15
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    2.14631
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3pcgA.209.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3pcgA.210.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3pcgA.210.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3pcgA.210.3.a2m \
	-target T0124 -template 3pcgA \
	-out T0124-3pcgA.210.3 -outdir und
partial PDB gets fragment 14 through 23 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   15
GLN    2   10
GLU    3   13
VAL    5    3
GLU    7   11
TYR    8    2
GLU    9   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3pcgA.210.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3pcgA.210.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3pcgA.210.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3pcgA.210.5.a2m \
	-target T0124 -template 3pcgA \
	-out T0124-3pcgA.210.5 -outdir und
partial PDB gets fragment 12 through 22 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
13 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   14
GLN    2   12
GLU    3   15
GLU    7   15
TYR    8    3
GLU    9   11
GLU   10   15
LYS   11   26
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3pcgA.210.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3pcgA.212.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3pcgA.212.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3pcgA.212.0.a2m \
	-target T0124 -template 3pcgA \
	-out T0124-3pcgA.212.0 -outdir und
partial PDB gets fragment 12 through 21 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   15
VAL    3    3
GLU    5   13
TYR    6    3
GLU    7   15
GLU    8   13
LYS    9   25
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     2    6     30.0000
Cluster     1 =   2   6
2 clashing residues after turn 
Residue clashes:
2-6
cluster 1 has 2 members and 5.000e+01 combinations:
 6  2 
Energy     30.0000
Searching cluster 2
Combinations for 2 members in cluster 1 OK: 5.000e+01 - Sending to search
12.913852 < 30.000000: keeping 
0.000000 < 13.510925: keeping 
Solved cluster 1: residual clashing  0.76
Still clashes at these sidechain pairs:
Residual clashes =    4.74728
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3pcgA.212.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3pcgA.213.0.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3pcgA.213.0.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3pcgA.213.0.a2m \
	-target T0124 -template 3pcgA \
	-out T0124-3pcgA.213.0 -outdir und
partial PDB gets fragment 11 through 20 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    2    3
GLU    4   15
GLU    6   12
GLU    7   13
LYS    8   30
LEU    9    3
LYS   10   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3pcgA.213.0 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3pcgA.214.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3pcgA.214.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3pcgA.214.1.a2m \
	-target T0124 -template 3pcgA \
	-out T0124-3pcgA.214.1 -outdir und
partial PDB gets fragment 10 through 19 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    3
GLU    3   15
TYR    4    3
GLU    5   15
GLU    6   12
LYS    7   27
LEU    8    3
LYS    9   30
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     4    8     21.5336
Cluster     1 =   4   8
2 clashing residues after turn 
Residue clashes:
4-8
cluster 1 has 2 members and 1.100e+02 combinations:
 8  4 
Energy     21.5336
Searching cluster 4
Combinations for 2 members in cluster 1 OK: 1.100e+02 - Sending to search
15.178003 < 21.533638: keeping 
0.000000 < 15.775077: keeping 
Solved cluster 1: residual clashing  0.76
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3pcgA.214.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3pcgA.215.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3pcgA.215.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3pcgA.215.4.a2m \
	-target T0124 -template 3pcgA \
	-out T0124-3pcgA.215.4 -outdir und
partial PDB gets fragment 9 through 18 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    2   16
TYR    3    3
GLU    4   15
GLU    5   14
LYS    6   28
LEU    7    2
LYS    8   27
THR    9    2
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    9     21.5336
Cluster     1 =   5   9
2 clashing residues after turn 
Residue clashes:
5-9
cluster 1 has 2 members and 1.100e+02 combinations:
 9  5 
Energy     21.5336
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 1.100e+02 - Sending to search
15.178003 < 21.533638: keeping 
0.000000 < 15.775077: keeping 
Solved cluster 1: residual clashing  0.76
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3pcgA.215.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3pcgA.216.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3pcgA.216.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3pcgA.216.5.a2m \
	-target T0124 -template 3pcgA \
	-out T0124-3pcgA.216.5 -outdir und
partial PDB gets fragment 8 through 17 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   14
TYR    2    3
GLU    3   16
GLU    4   15
LYS    5   30
LEU    6    2
LYS    7   28
THR    8    1
LEU    9    3
THR   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =   10.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3pcgA.216.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-3tss.93.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-3tss.93.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-3tss.93.5.a2m \
	-target T0124 -template 3tss \
	-out T0124-3tss.93.5 -outdir und
Skipped atom 1010, because occupancy 0.5 <= existing 0.500001
Skipped atom 1012, because occupancy 0.5 <= existing 0.500001
Skipped atom 1014, because occupancy 0.5 <= existing 0.500001
Skipped atom 1016, because occupancy 0.5 <= existing 0.500001
Skipped atom 1018, because occupancy 0.5 <= existing 0.500001
Skipped atom 1020, because occupancy 0.5 <= existing 0.500001
Skipped atom 1022, because occupancy 0.5 <= existing 0.500001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/3tss-orig.a2m
Writing a2m file: tmp/3tss-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14296


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14296/tmp -alignfile tmp/3tss-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/3tss-orig.a2m (1 sequences, 194 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14296/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14296/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14296/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14296/tmp.a2m (1 sequences, 194 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14296/tmp.mod tmp/3tss-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14296 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/3tss-align.mod
tmp/3tss-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14296/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/3tss-orig.a2m tmp/3tss-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/3tss-align.mod
Running w0.5 tmp/3tss-orig.a2m tmp/3tss-align.mod
Running align2model tmp/3tss-align -i tmp/3tss-align.mod -db tmp/3tss-orig.a2m -db tmp/3tss-pdb.a2m
partial PDB gets fragment 59 through 68 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ARG    1   27
ARG    2   30
ARG    3   26
GLU    5   16
GLN    6   13
HIS    7    3
THR    9    3
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-3tss.93.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-4eugA.8.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-4eugA.8.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-4eugA.8.1.a2m \
	-target T0124 -template 4eugA \
	-out T0124-4eugA.8.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/4eugA-orig.a2m
Writing a2m file: tmp/4eugA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13812


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13812/tmp -alignfile tmp/4eugA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/4eugA-orig.a2m (1 sequences, 229 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13812/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13812/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13812/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13812/tmp.a2m (1 sequences, 229 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13812/tmp.mod tmp/4eugA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-13812 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/4eugA-align.mod
tmp/4eugA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13812/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/4eugA-orig.a2m tmp/4eugA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/4eugA-align.mod
Running w0.5 tmp/4eugA-orig.a2m tmp/4eugA-align.mod
Running align2model tmp/4eugA-align -i tmp/4eugA-align.mod -db tmp/4eugA-orig.a2m -db tmp/4eugA-pdb.a2m
partial PDB gets fragment 213 through 222 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
PRO    1    2
GLU    2   12
PRO    3    2
GLN    4   12
THR    5    3
SER    7    3
LEU    8    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-4eugA.8.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-4eugA.9.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-4eugA.9.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-4eugA.9.2.a2m \
	-target T0124 -template 4eugA \
	-out T0124-4eugA.9.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/4eugA-orig.a2m
Writing a2m file: tmp/4eugA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9143


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9143/tmp -alignfile tmp/4eugA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/4eugA-orig.a2m (1 sequences, 229 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9143/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9143/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9143/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9143/tmp.a2m (1 sequences, 229 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9143/tmp.mod tmp/4eugA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9143 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/4eugA-align.mod
tmp/4eugA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9143/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/4eugA-orig.a2m tmp/4eugA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/4eugA-align.mod
Running w0.5 tmp/4eugA-orig.a2m tmp/4eugA-align.mod
Running align2model tmp/4eugA-align -i tmp/4eugA-align.mod -db tmp/4eugA-orig.a2m -db tmp/4eugA-pdb.a2m
partial PDB gets fragment 212 through 221 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLU    1   16
PRO    2    2
GLN    3   11
THR    4    1
SER    6    3
LEU    7    3
GLU    9   15
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-4eugA.9.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-4tsvA.81.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-4tsvA.81.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-4tsvA.81.2.a2m \
	-target T0124 -template 4tsvA \
	-out T0124-4tsvA.81.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/4tsvA-orig.a2m
Writing a2m file: tmp/4tsvA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21428


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21428/tmp -alignfile tmp/4tsvA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/4tsvA-orig.a2m (1 sequences, 150 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21428/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21428/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21428/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21428/tmp.a2m (1 sequences, 150 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21428/tmp.mod tmp/4tsvA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21428 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/4tsvA-align.mod
tmp/4tsvA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21428/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/4tsvA-orig.a2m tmp/4tsvA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/4tsvA-align.mod
Running w0.5 tmp/4tsvA-orig.a2m tmp/4tsvA-align.mod
Running align2model tmp/4tsvA-align -i tmp/4tsvA-align.mod -db tmp/4tsvA-orig.a2m -db tmp/4tsvA-pdb.a2m
partial PDB gets fragment 89 through 98 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
ILE    2    3
HIS    3    3
LEU    4    3
GLU    7   12
TYR    8    2
HIS    9    3
ASP   10    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-4tsvA.81.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-4ubpB.82.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-4ubpB.82.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-4ubpB.82.5.a2m \
	-target T0124 -template 4ubpB \
	-out T0124-4ubpB.82.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/4ubpB-orig.a2m
Writing a2m file: tmp/4ubpB-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5631


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5631/tmp -alignfile tmp/4ubpB-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/4ubpB-orig.a2m (1 sequences, 126 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5631/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5631/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5631/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5631/tmp.a2m (1 sequences, 126 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5631/tmp.mod tmp/4ubpB-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5631 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/4ubpB-align.mod
tmp/4ubpB-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5631/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/4ubpB-orig.a2m tmp/4ubpB-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/4ubpB-align.mod
Running w0.5 tmp/4ubpB-orig.a2m tmp/4ubpB-align.mod
Running align2model tmp/4ubpB-align -i tmp/4ubpB-align.mod -db tmp/4ubpB-orig.a2m -db tmp/4ubpB-pdb.a2m
partial PDB gets fragment 79 through 88 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
ILE    1    5
HIS    2    3
LEU    3    3
GLU    5   14
TYR    7    3
HIS    8    3
ASP    9    5
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-4ubpB.82.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-4ubpB.83.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-4ubpB.83.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-4ubpB.83.2.a2m \
	-target T0124 -template 4ubpB \
	-out T0124-4ubpB.83.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/4ubpB-orig.a2m
Writing a2m file: tmp/4ubpB-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21907


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21907/tmp -alignfile tmp/4ubpB-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/4ubpB-orig.a2m (1 sequences, 126 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21907/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21907/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21907/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21907/tmp.a2m (1 sequences, 126 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21907/tmp.mod tmp/4ubpB-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21907 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/4ubpB-align.mod
tmp/4ubpB-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21907/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/4ubpB-orig.a2m tmp/4ubpB-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/4ubpB-align.mod
Running w0.5 tmp/4ubpB-orig.a2m tmp/4ubpB-align.mod
Running align2model tmp/4ubpB-align -i tmp/4ubpB-align.mod -db tmp/4ubpB-orig.a2m -db tmp/4ubpB-pdb.a2m
partial PDB gets fragment 78 through 87 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
HIS    1    3
LEU    2    3
GLU    5   15
TYR    6    2
HIS    7    4
ASP    8    6
ILE   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-4ubpB.83.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-4ubpB.84.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-4ubpB.84.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-4ubpB.84.2.a2m \
	-target T0124 -template 4ubpB \
	-out T0124-4ubpB.84.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/4ubpB-orig.a2m
Writing a2m file: tmp/4ubpB-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7424


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7424/tmp -alignfile tmp/4ubpB-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/4ubpB-orig.a2m (1 sequences, 126 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7424/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7424/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7424/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7424/tmp.a2m (1 sequences, 126 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7424/tmp.mod tmp/4ubpB-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7424 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/4ubpB-align.mod
tmp/4ubpB-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7424/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/4ubpB-orig.a2m tmp/4ubpB-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/4ubpB-align.mod
Running w0.5 tmp/4ubpB-orig.a2m tmp/4ubpB-align.mod
Running align2model tmp/4ubpB-align -i tmp/4ubpB-align.mod -db tmp/4ubpB-orig.a2m -db tmp/4ubpB-pdb.a2m
partial PDB gets fragment 77 through 86 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    4   16
TYR    5    3
HIS    6    3
ASP    7    6
ILE    9    4
ARG   10   25
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-4ubpB.84.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-5csmA.21.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-5csmA.21.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-5csmA.21.5.a2m \
	-target T0124 -template 5csmA \
	-out T0124-5csmA.21.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/5csmA-orig.a2m
Writing a2m file: tmp/5csmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-10092


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-10092/tmp -alignfile tmp/5csmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/5csmA-orig.a2m (1 sequences, 256 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-10092/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10092/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10092/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10092/tmp.a2m (1 sequences, 256 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10092/tmp.mod tmp/5csmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10092 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/5csmA-align.mod
tmp/5csmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10092/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/5csmA-orig.a2m tmp/5csmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/5csmA-align.mod
Running w0.5 tmp/5csmA-orig.a2m tmp/5csmA-align.mod
Running align2model tmp/5csmA-align -i tmp/5csmA-align.mod -db tmp/5csmA-orig.a2m -db tmp/5csmA-pdb.a2m
partial PDB gets fragment 228 through 237 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
MET    1   10
LYS    2   24
LEU    3    3
PHE    4    2
LEU    5    3
LYS    6   26
LEU    7    3
LEU    8    3
LYS   10   23
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     5    9     16.9433
Cluster     1 =   5   9
2 clashing residues after turn 
Residue clashes:
5-9
cluster 1 has 2 members and 4.000e+00 combinations:
 5  9 
Energy     16.9433
Searching cluster 5
Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search
0.000000 < 16.943268: keeping 
Solved cluster 1: residual clashing  0.42
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-5csmA.21.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-5csmA.29.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-5csmA.29.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-5csmA.29.3.a2m \
	-target T0124 -template 5csmA \
	-out T0124-5csmA.29.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/5csmA-orig.a2m
Writing a2m file: tmp/5csmA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14179


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14179/tmp -alignfile tmp/5csmA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/5csmA-orig.a2m (1 sequences, 256 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14179/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14179/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14179/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14179/tmp.a2m (1 sequences, 256 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14179/tmp.mod tmp/5csmA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14179 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/5csmA-align.mod
tmp/5csmA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14179/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/5csmA-orig.a2m tmp/5csmA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/5csmA-align.mod
Running w0.5 tmp/5csmA-orig.a2m tmp/5csmA-align.mod
Running align2model tmp/5csmA-align -i tmp/5csmA-align.mod -db tmp/5csmA-orig.a2m -db tmp/5csmA-pdb.a2m
partial PDB gets fragment 222 through 231 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   26
LYS    2   26
GLN    3   12
GLU    4   12
LYS    5   24
GLU    6   12
LEU    7    3
LYS    8   24
GLU    9   12
LEU   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-5csmA.29.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-5ukdA.115.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-5ukdA.115.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-5ukdA.115.5.a2m \
	-target T0124 -template 5ukdA \
	-out T0124-5ukdA.115.5 -outdir und
partial PDB gets fragment 58 through 67 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   11
ILE    2    5
GLU    4    8
LEU    5    3
LYS    6   24
LEU    8    3
LYS    9   30
GLU   10   13
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-5ukdA.115.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-6gsvA.5.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-6gsvA.5.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-6gsvA.5.3.a2m \
	-target T0124 -template 6gsvA \
	-out T0124-6gsvA.5.3 -outdir und
partial PDB gets fragment 207 through 216 extending start
Debugging on !
Reading sequence file
Reading input structure 
11 residues read 
Measuring phi and psi 
Getting chi values
THR    1    1
GLN    2   13
LEU    3    3
PRO    4    2
GLU    5   16
PRO    6    2
GLN    7   15
THR    8    2
SER   10    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 1 rotamers of residue T 2 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     6    7     17.4308
Cluster     1 =   6   7
2 clashing residues after turn 
Residue clashes:
6-7
cluster 1 has 2 members and 2.000e+00 combinations:
 6  7 
Energy     21.3215
Searching cluster 6
Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search
Solved cluster 1: residual clashing 21.32
Still clashes at these sidechain pairs:
ires=    6 irot=   15 jres=    7 jrot=    1      17.4308
Residual clashes =   17.43080
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-6gsvA.5.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-6gsvA.6.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-6gsvA.6.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-6gsvA.6.3.a2m \
	-target T0124 -template 6gsvA \
	-out T0124-6gsvA.6.3 -outdir und
partial PDB gets fragment 206 through 215 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
12 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   12
LEU    2    2
PRO    3    2
GLU    4   15
PRO    5    2
GLN    6   15
THR    7    1
LEU   10    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 15 rotamers of residue Q 7 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue L 11 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
keepclash     3    7     76.2462
Cluster     1 =   3   7
2 clashing residues after turn 
Residue clashes:
3-7
cluster 1 has 2 members and 3.000e+01 combinations:
 7  3 
Energy    126.5030
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 3.000e+01 - Sending to search
53.293301 < 126.502991: keeping 
9.748075 < 106.457184: keeping 
3.257874 < 19.862549: keeping 
Solved cluster 1: residual clashing 16.28
Still clashes at these sidechain pairs:
Residual clashes =   12.82321
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-6gsvA.6.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-7odcA.0.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-7odcA.0.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-7odcA.0.3.a2m \
	-target T0124 -template 7odcA \
	-out T0124-7odcA.0.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/7odcA-orig.a2m
Writing a2m file: tmp/7odcA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-31571


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-31571/tmp -alignfile tmp/7odcA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/7odcA-orig.a2m (1 sequences, 424 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-31571/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-31571/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-31571/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31571/tmp.a2m (1 sequences, 424 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-31571/tmp.mod tmp/7odcA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-31571 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/7odcA-align.mod
tmp/7odcA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-31571/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/7odcA-orig.a2m tmp/7odcA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/7odcA-align.mod
Running w0.5 tmp/7odcA-orig.a2m tmp/7odcA-align.mod
Running align2model tmp/7odcA-align -i tmp/7odcA-align.mod -db tmp/7odcA-orig.a2m -db tmp/7odcA-pdb.a2m
partial PDB gets fragment 382 through 386 extending start
Debugging on !
Reading sequence file
Reading input structure 
6 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
MET    2   10
LYS    3   24
GLU    4   12
VAL    5    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-7odcA.0.3 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-7odcA.2.5.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-7odcA.2.5.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-7odcA.2.5.a2m \
	-target T0124 -template 7odcA \
	-out T0124-7odcA.2.5 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/7odcA-orig.a2m
Writing a2m file: tmp/7odcA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15388


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15388/tmp -alignfile tmp/7odcA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/7odcA-orig.a2m (1 sequences, 424 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15388/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15388/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15388/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15388/tmp.a2m (1 sequences, 424 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15388/tmp.mod tmp/7odcA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15388 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/7odcA-align.mod
tmp/7odcA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15388/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/7odcA-orig.a2m tmp/7odcA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/7odcA-align.mod
Running w0.5 tmp/7odcA-orig.a2m tmp/7odcA-align.mod
Running align2model tmp/7odcA-align -i tmp/7odcA-align.mod -db tmp/7odcA-orig.a2m -db tmp/7odcA-pdb.a2m
partial PDB gets fragment 382 through 386 extending start
Debugging on !
Reading sequence file
Reading input structure 
6 residues read 
Measuring phi and psi 
Getting chi values
LYS    1   24
GLU    2   12
VAL    3    1
THR    4    1
GLN    5   14
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-7odcA.2.5 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-7odcA.4.2.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-7odcA.4.2.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-7odcA.4.2.a2m \
	-target T0124 -template 7odcA \
	-out T0124-7odcA.4.2 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/7odcA-orig.a2m
Writing a2m file: tmp/7odcA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18672


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18672/tmp -alignfile tmp/7odcA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/7odcA-orig.a2m (1 sequences, 424 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18672/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18672/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18672/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18672/tmp.a2m (1 sequences, 424 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18672/tmp.mod tmp/7odcA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18672 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/7odcA-align.mod
tmp/7odcA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18672/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/7odcA-orig.a2m tmp/7odcA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/7odcA-align.mod
Running w0.5 tmp/7odcA-orig.a2m tmp/7odcA-align.mod
Running align2model tmp/7odcA-align -i tmp/7odcA-align.mod -db tmp/7odcA-orig.a2m -db tmp/7odcA-pdb.a2m
partial PDB gets fragment 382 through 386 extending start
Debugging on !
Reading sequence file
Reading input structure 
6 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    1
THR    2    1
GLN    3   11
LEU    4    3
PRO    5    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-7odcA.4.2 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-7odcA.4.4.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-7odcA.4.4.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-7odcA.4.4.a2m \
	-target T0124 -template 7odcA \
	-out T0124-7odcA.4.4 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/7odcA-orig.a2m
Writing a2m file: tmp/7odcA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14716


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14716/tmp -alignfile tmp/7odcA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/7odcA-orig.a2m (1 sequences, 424 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14716/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14716/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14716/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14716/tmp.a2m (1 sequences, 424 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14716/tmp.mod tmp/7odcA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14716 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/7odcA-align.mod
tmp/7odcA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14716/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/7odcA-orig.a2m tmp/7odcA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/7odcA-align.mod
Running w0.5 tmp/7odcA-orig.a2m tmp/7odcA-align.mod
Running align2model tmp/7odcA-align -i tmp/7odcA-align.mod -db tmp/7odcA-orig.a2m -db tmp/7odcA-pdb.a2m
partial PDB gets fragment 380 through 386 extending start
Debugging on !
Reading sequence file
Reading input structure 
8 residues read 
Measuring phi and psi 
Getting chi values
VAL    1    2
THR    2    2
GLN    3   11
LEU    4    3
PRO    5    2
GLU    6   12
PRO    7    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 8 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-7odcA.4.4 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-7odcA.6.1.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-7odcA.6.1.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-7odcA.6.1.a2m \
	-target T0124 -template 7odcA \
	-out T0124-7odcA.6.1 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/7odcA-orig.a2m
Writing a2m file: tmp/7odcA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30973


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30973/tmp -alignfile tmp/7odcA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/7odcA-orig.a2m (1 sequences, 424 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30973/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30973/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30973/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30973/tmp.a2m (1 sequences, 424 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30973/tmp.mod tmp/7odcA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30973 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/7odcA-align.mod
tmp/7odcA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30973/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/7odcA-orig.a2m tmp/7odcA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/7odcA-align.mod
Running w0.5 tmp/7odcA-orig.a2m tmp/7odcA-align.mod
Running align2model tmp/7odcA-align -i tmp/7odcA-align.mod -db tmp/7odcA-orig.a2m -db tmp/7odcA-pdb.a2m
partial PDB gets fragment 380 through 386 extending start
Debugging on !
Reading sequence file
Reading input structure 
8 residues read 
Measuring phi and psi 
Getting chi values
GLN    1   13
LEU    2    3
PRO    3    2
GLU    4   12
PRO    5    2
GLN    6   12
THR    7    2
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 4 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
All 2 rotamers of residue P 6 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-7odcA.6.1 done
gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
gmake[1]: [und/T0124-7odcA.7.3.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
gmake[1]: [und/T0124-7odcA.7.3.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m fragments/T0124-7odcA.7.3.a2m \
	-target T0124 -template 7odcA \
	-out T0124-7odcA.7.3 -outdir und
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/7odcA-orig.a2m
Writing a2m file: tmp/7odcA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9523


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9523/tmp -alignfile tmp/7odcA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/7odcA-orig.a2m (1 sequences, 424 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9523/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9523/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9523/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9523/tmp.a2m (1 sequences, 424 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9523/tmp.mod tmp/7odcA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9523 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/7odcA-align.mod
tmp/7odcA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9523/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/7odcA-orig.a2m tmp/7odcA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/7odcA-align.mod
Running w0.5 tmp/7odcA-orig.a2m tmp/7odcA-align.mod
Running align2model tmp/7odcA-align -i tmp/7odcA-align.mod -db tmp/7odcA-orig.a2m -db tmp/7odcA-pdb.a2m
partial PDB gets fragment 379 through 386 extending start
Debugging on !
Reading sequence file
Reading input structure 
9 residues read 
Measuring phi and psi 
Getting chi values
LEU    1    3
GLU    3   13
PRO    4    2
THR    6    2
SER    8    3
Building many copies of each residue
Checking backbone and frame clashes 
Finding the lowest 
Also, print out the first version, pre-bump
All 2 rotamers of residue P 5 conflict with the backbone.
This may be a problem with the backbone,or a subtle problem with the 
rotamers. Please be aware of this, and examine it.
Finding disulfide bonds.
Found 0 disulfide bonds.
Residue clashes:
0 clashing residues after turn 
Residue clashes:
Still clashes at these sidechain pairs:
Residual clashes =    0.00000
Printing 
gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'
T0124-7odcA.7.3 done