make -k 1cxlA.indexes \
	1taxA.indexes \
	1cfr.indexes \
	1vpsA.indexes \
	1aszB.indexes \
	1asyA.idexes \
	1b8aA.indexes \
	1eerB.indexes \
	1lylA.indexes \
	1fnhA.indexes \
	1nkr.indexes \
	1pvc3.indexes \
	1axkA.indexes \
	2nlrA.indexes \
	1ema.indexes \
	1a0tP.indexes
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1cxlA-local.index und/1cxlA-T0107-local.index \
	und/1cxlA-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/T0107-1cxlA-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/T0107-1cxlA-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1cxlA/T0107-1cxlA-local.pw.a2m.gz \
	-target T0107 -template 1cxlA \
	-out T0107-1cxlA-local -outdir und
Sequence named 1cxlA has all gap columns.
It will be included anyway.
Sequence named 1cxlA has all gap columns.
It will be included anyway.
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[2]: `und/1cxlA-T0107-local.index' is up to date.
make[2]: `und/1cxlA-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1taxA-local.index und/1taxA-T0107-local.index \
	und/1taxA-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
make[2]: `und/T0107-1taxA-local.index' is up to date.
make[2]: `und/1taxA-T0107-local.index' is up to date.
make[2]: `und/1taxA-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1cfr-local.index und/1cfr-T0107-local.index \
	und/1cfr-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
make[2]: `und/T0107-1cfr-local.index' is up to date.
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/1cfr-T0107-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/1cfr-T0107-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1cfr/1cfr-T0107-local.pw.a2m.gz \
	-target T0107 -template 1cfr \
	-out 1cfr-T0107-local -outdir und
Sequence named T0107 has all gap columns.
It will be included anyway.
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1cfr-orig.a2m
Writing a2m file: tmp/1cfr-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-9688


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-9688/tmp -alignfile tmp/1cfr-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1cfr-orig.a2m (1 sequences, 285 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-9688/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-9688/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-9688/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9688/tmp.a2m (1 sequences, 285 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-9688/tmp.mod tmp/1cfr-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-9688 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cfr-align.mod
tmp/1cfr-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-9688/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1cfr-orig.a2m tmp/1cfr-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1cfr-align.mod
Running w0.5 tmp/1cfr-orig.a2m tmp/1cfr-align.mod
Running align2model tmp/1cfr-align -i tmp/1cfr-align.mod -db tmp/1cfr-orig.a2m -db tmp/1cfr-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[2]: `und/1cfr-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1vpsA-local.index und/1vpsA-T0107-local.index \
	und/1vpsA-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/T0107-1vpsA-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/T0107-1vpsA-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1vpsA/T0107-1vpsA-local.pw.a2m.gz \
	-target T0107 -template 1vpsA \
	-out T0107-1vpsA-local -outdir und
Sequence named 1vpsA has all gap columns.
It will be included anyway.
Sequence named 1vpsA has all gap columns.
It will be included anyway.
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1vpsA-orig.a2m
Writing a2m file: tmp/1vpsA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-6090


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-6090/tmp -alignfile tmp/1vpsA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1vpsA-orig.a2m (1 sequences, 289 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-6090/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-6090/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-6090/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6090/tmp.a2m (1 sequences, 289 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-6090/tmp.mod tmp/1vpsA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-6090 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1vpsA-align.mod
tmp/1vpsA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-6090/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1vpsA-orig.a2m tmp/1vpsA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1vpsA-align.mod
Running w0.5 tmp/1vpsA-orig.a2m tmp/1vpsA-align.mod
Running align2model tmp/1vpsA-align -i tmp/1vpsA-align.mod -db tmp/1vpsA-orig.a2m -db tmp/1vpsA-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[2]: `und/1vpsA-T0107-local.index' is up to date.
make[2]: `und/1vpsA-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1aszB-local.index und/1aszB-T0107-local.index \
	und/1aszB-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/T0107-1aszB-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/T0107-1aszB-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1aszB/T0107-1aszB-local.pw.a2m.gz \
	-target T0107 -template 1aszB \
	-out T0107-1aszB-local -outdir und
Sequence named 1aszB has all gap columns.
It will be included anyway.
Sequence named 1aszB has all gap columns.
It will be included anyway.
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[2]: `und/1aszB-T0107-local.index' is up to date.
make[2]: `und/1aszB-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make[1]: *** No rule to make target `1asyA.idexes'.
make -k und/T0107-1b8aA-local.index und/1b8aA-T0107-local.index \
	und/1b8aA-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/T0107-1b8aA-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/T0107-1b8aA-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1b8aA/T0107-1b8aA-local.pw.a2m.gz \
	-target T0107 -template 1b8aA \
	-out T0107-1b8aA-local -outdir und
Sequence named 1b8aA has all gap columns.
It will be included anyway.
Sequence named 1b8aA has all gap columns.
It will be included anyway.
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[2]: `und/1b8aA-T0107-local.index' is up to date.
make[2]: `und/1b8aA-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1eerB-local.index und/1eerB-T0107-local.index \
	und/1eerB-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/T0107-1eerB-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/T0107-1eerB-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1eerB/T0107-1eerB-local.pw.a2m.gz \
	-target T0107 -template 1eerB \
	-out T0107-1eerB-local -outdir und
Sequence named 1eerB has all gap columns.
It will be included anyway.
Sequence named 1eerB has all gap columns.
It will be included anyway.
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1eerB-orig.a2m
Writing a2m file: tmp/1eerB-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18479


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18479/tmp -alignfile tmp/1eerB-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1eerB-orig.a2m (1 sequences, 227 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18479/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18479/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18479/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18479/tmp.a2m (1 sequences, 227 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18479/tmp.mod tmp/1eerB-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18479 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1eerB-align.mod
tmp/1eerB-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18479/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1eerB-orig.a2m tmp/1eerB-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1eerB-align.mod
Running w0.5 tmp/1eerB-orig.a2m tmp/1eerB-align.mod
Running align2model tmp/1eerB-align -i tmp/1eerB-align.mod -db tmp/1eerB-orig.a2m -db tmp/1eerB-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[2]: `und/1eerB-T0107-local.index' is up to date.
make[2]: `und/1eerB-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1lylA-local.index und/1lylA-T0107-local.index \
	und/1lylA-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
make[2]: `und/T0107-1lylA-local.index' is up to date.
make[2]: `und/1lylA-T0107-local.index' is up to date.
make[2]: `und/1lylA-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1fnhA-local.index und/1fnhA-T0107-local.index \
	und/1fnhA-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/T0107-1fnhA-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/T0107-1fnhA-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1fnhA/T0107-1fnhA-local.pw.a2m.gz \
	-target T0107 -template 1fnhA \
	-out T0107-1fnhA-local -outdir und
Sequence named 1fnhA has all gap columns.
It will be included anyway.
Sequence named 1fnhA has all gap columns.
It will be included anyway.
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1fnhA-orig.a2m
Writing a2m file: tmp/1fnhA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3692


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3692/tmp -alignfile tmp/1fnhA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1fnhA-orig.a2m (1 sequences, 271 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3692/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3692/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3692/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3692/tmp.a2m (1 sequences, 271 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3692/tmp.mod tmp/1fnhA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-3692 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1fnhA-align.mod
tmp/1fnhA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3692/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1fnhA-orig.a2m tmp/1fnhA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1fnhA-align.mod
Running w0.5 tmp/1fnhA-orig.a2m tmp/1fnhA-align.mod
Running align2model tmp/1fnhA-align -i tmp/1fnhA-align.mod -db tmp/1fnhA-orig.a2m -db tmp/1fnhA-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[2]: `und/1fnhA-T0107-local.index' is up to date.
make[2]: `und/1fnhA-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1nkr-local.index und/1nkr-T0107-local.index \
	und/1nkr-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/T0107-1nkr-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/T0107-1nkr-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1nkr/T0107-1nkr-local.pw.a2m.gz \
	-target T0107 -template 1nkr \
	-out T0107-1nkr-local -outdir und
Sequence named 1nkr has all gap columns.
It will be included anyway.
Sequence named 1nkr has all gap columns.
It will be included anyway.
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1nkr-orig.a2m
Writing a2m file: tmp/1nkr-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7991


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7991/tmp -alignfile tmp/1nkr-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1nkr-orig.a2m (1 sequences, 201 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7991/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7991/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7991/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7991/tmp.a2m (1 sequences, 201 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7991/tmp.mod tmp/1nkr-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-7991 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1nkr-align.mod
tmp/1nkr-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7991/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1nkr-orig.a2m tmp/1nkr-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1nkr-align.mod
Running w0.5 tmp/1nkr-orig.a2m tmp/1nkr-align.mod
Running align2model tmp/1nkr-align -i tmp/1nkr-align.mod -db tmp/1nkr-orig.a2m -db tmp/1nkr-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[2]: `und/1nkr-T0107-local.index' is up to date.
make[2]: `und/1nkr-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1pvc3-local.index und/1pvc3-T0107-local.index \
	und/1pvc3-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/T0107-1pvc3-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/T0107-1pvc3-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1pvc3/T0107-1pvc3-local.pw.a2m.gz \
	-target T0107 -template 1pvc3 \
	-out T0107-1pvc3-local -outdir und
Sequence named 1pvc3 has all gap columns.
It will be included anyway.
Sequence named 1pvc3 has all gap columns.
It will be included anyway.
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/1pvc3-orig.a2m
Writing a2m file: tmp/1pvc3-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-17630


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-17630/tmp -alignfile tmp/1pvc3-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/1pvc3-orig.a2m (1 sequences, 238 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-17630/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-17630/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-17630/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17630/tmp.a2m (1 sequences, 238 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-17630/tmp.mod tmp/1pvc3-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-17630 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pvc3-align.mod
tmp/1pvc3-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-17630/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/1pvc3-orig.a2m tmp/1pvc3-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/1pvc3-align.mod
Running w0.5 tmp/1pvc3-orig.a2m tmp/1pvc3-align.mod
Running align2model tmp/1pvc3-align -i tmp/1pvc3-align.mod -db tmp/1pvc3-orig.a2m -db tmp/1pvc3-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[2]: `und/1pvc3-T0107-local.index' is up to date.
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/1pvc3-T0107-fssp-global.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/1pvc3-T0107-fssp-global.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1pvc3/1pvc3-T0107-fssp-global.pw.a2m.gz \
	-target T0107 -template 1pvc3 \
	-out 1pvc3-T0107-fssp-global -outdir und
Couldn't open file 1pvc3/1pvc3-T0107-fssp-global.pw.a2m.gz or 1pvc3/1pvc3-T0107-fssp-global.pw.a2m.gz.gz for input
Can't open A2M file 1pvc3/1pvc3-T0107-fssp-global.pw.a2m.gz for input
/projects/kestrel/users/karplus/burial/slicer/slicer: Error while reading the input a2m file.
/projects/kestrel/users/karplus/burial/slicer/slicer: ERROR read_input_alignment failed.
make[2]: *** [und/1pvc3-T0107-fssp-global.index] Error 1
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make[1]: *** [1pvc3.indexes] Error 2
make -k und/T0107-1axkA-local.index und/1axkA-T0107-local.index \
	und/1axkA-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
make[2]: `und/T0107-1axkA-local.index' is up to date.
make[2]: `und/1axkA-T0107-local.index' is up to date.
make[2]: `und/1axkA-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-2nlrA-local.index und/2nlrA-T0107-local.index \
	und/2nlrA-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
make[2]: `und/T0107-2nlrA-local.index' is up to date.
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/2nlrA-T0107-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/2nlrA-T0107-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 2nlrA/2nlrA-T0107-local.pw.a2m.gz \
	-target T0107 -template 2nlrA \
	-out 2nlrA-T0107-local -outdir und
Sequence named T0107 has all gap columns.
It will be included anyway.
Skipped atom 171, because occupancy 0.31 <= existing 0.690001
Skipped atom 175, because occupancy 0.31 <= existing 0.690001
Skipped atom 177, because occupancy 0.31 <= existing 0.690001
Skipped atom 179, because occupancy 0.31 <= existing 0.690001
Skipped atom 214, because occupancy 0.47 <= existing 0.530001
Skipped atom 218, because occupancy 0.47 <= existing 0.530001
Skipped atom 220, because occupancy 0.47 <= existing 0.530001
Skipped atom 222, because occupancy 0.47 <= existing 0.530001
Skipped atom 224, because occupancy 0.47 <= existing 0.530001
Skipped atom 226, because occupancy 0.47 <= existing 0.530001
Skipped atom 611, because occupancy 0.32 <= existing 0.420001
Skipped atom 612, because occupancy 0.26 <= existing 0.420001
Skipped atom 616, because occupancy 0.32 <= existing 0.420001
Skipped atom 617, because occupancy 0.26 <= existing 0.420001
Skipped atom 619, because occupancy 0.32 <= existing 0.420001
Skipped atom 620, because occupancy 0.26 <= existing 0.420001
Skipped atom 622, because occupancy 0.32 <= existing 0.420001
Skipped atom 623, because occupancy 0.26 <= existing 0.420001
Skipped atom 625, because occupancy 0.32 <= existing 0.420001
Skipped atom 626, because occupancy 0.26 <= existing 0.420001
Skipped atom 628, because occupancy 0.32 <= existing 0.420001
Skipped atom 629, because occupancy 0.26 <= existing 0.420001
Skipped atom 631, because occupancy 0.32 <= existing 0.420001
Skipped atom 632, because occupancy 0.26 <= existing 0.420001
Skipped atom 634, because occupancy 0.32 <= existing 0.420001
Skipped atom 635, because occupancy 0.26 <= existing 0.420001
Skipped atom 681, because occupancy 0.38 <= existing 0.620001
Skipped atom 683, because occupancy 0.38 <= existing 0.620001
Skipped atom 685, because occupancy 0.38 <= existing 0.620001
Skipped atom 687, because occupancy 0.38 <= existing 0.620001
Skipped atom 689, because occupancy 0.38 <= existing 0.620001
Skipped atom 734, because occupancy 0.5 <= existing 0.500001
Skipped atom 736, because occupancy 0.5 <= existing 0.500001
Skipped atom 738, because occupancy 0.5 <= existing 0.500001
Skipped atom 740, because occupancy 0.5 <= existing 0.500001
Skipped atom 742, because occupancy 0.5 <= existing 0.500001
Skipped atom 744, because occupancy 0.5 <= existing 0.500001
Skipped atom 756, because occupancy 0.5 <= existing 0.500001
Skipped atom 796, because occupancy 0.18 <= existing 0.820001
Skipped atom 798, because occupancy 0.18 <= existing 0.820001
Skipped atom 800, because occupancy 0.18 <= existing 0.820001
Skipped atom 802, because occupancy 0.18 <= existing 0.820001
Skipped atom 804, because occupancy 0.18 <= existing 0.820001
Skipped atom 806, because occupancy 0.18 <= existing 0.820001
Skipped atom 808, because occupancy 0.18 <= existing 0.820001
Skipped atom 810, because occupancy 0.18 <= existing 0.820001
Skipped atom 1122, because occupancy 0.38 <= existing 0.620001
Skipped atom 1124, because occupancy 0.38 <= existing 0.620001
Skipped atom 1126, because occupancy 0.38 <= existing 0.620001
Skipped atom 1128, because occupancy 0.38 <= existing 0.620001
Skipped atom 1130, because occupancy 0.38 <= existing 0.620001
Skipped atom 1132, because occupancy 0.38 <= existing 0.620001
Skipped atom 1134, because occupancy 0.38 <= existing 0.620001
Skipped atom 1136, because occupancy 0.38 <= existing 0.620001
Skipped atom 1165, because occupancy 0.3 <= existing 0.700001
Skipped atom 1167, because occupancy 0.3 <= existing 0.700001
Skipped atom 1171, because occupancy 0.3 <= existing 0.700001
Skipped atom 1173, because occupancy 0.3 <= existing 0.700001
Skipped atom 1175, because occupancy 0.3 <= existing 0.700001
Skipped atom 1349, because occupancy 0.5 <= existing 0.510001
Skipped atom 1353, because occupancy 0.5 <= existing 0.510001
Skipped atom 1355, because occupancy 0.5 <= existing 0.510001
Skipped atom 1444, because occupancy 0.5 <= existing 0.500001
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 1476, because occupancy 0.5 <= existing 0.500001
Skipped atom 1478, because occupancy 0.5 <= existing 0.500001
Skipped atom 1480, because occupancy 0.5 <= existing 0.500001
Skipped atom 1482, because occupancy 0.5 <= existing 0.500001
Skipped atom 1484, because occupancy 0.5 <= existing 0.500001
Skipped atom 1486, because occupancy 0.5 <= existing 0.500001
Skipped atom 1488, because occupancy 0.5 <= existing 0.500001
Skipped atom 1490, because occupancy 0.5 <= existing 0.500001
Skipped atom 1492, because occupancy 0.5 <= existing 0.500001
Skipped atom 1494, because occupancy 0.5 <= existing 0.500001
Skipped atom 1496, because occupancy 0.5 <= existing 0.500001
Skipped atom 1498, because occupancy 0.5 <= existing 0.500001
Skipped atom 1500, because occupancy 0.5 <= existing 0.500001
Skipped atom 1502, because occupancy 0.5 <= existing 0.500001
Skipped atom 1504, because occupancy 0.5 <= existing 0.500001
Skipped atom 1506, because occupancy 0.5 <= existing 0.500001
Skipped atom 1508, because occupancy 0.5 <= existing 0.500001
Skipped atom 1520, because occupancy 0.5 <= existing 0.500001
Skipped atom 1522, because occupancy 0.5 <= existing 0.500001
Skipped atom 1841, because occupancy 0.34 <= existing 0.660001
Skipped atom 1843, because occupancy 0.34 <= existing 0.660001
Skipped atom 1845, because occupancy 0.34 <= existing 0.660001
Skipped atom 1847, because occupancy 0.34 <= existing 0.660001
Skipped atom 1849, because occupancy 0.34 <= existing 0.660001
Skipped atom 1879, because occupancy 0.34 <= existing 0.440001
Skipped atom 1880, because occupancy 0.22 <= existing 0.440001
Skipped atom 1882, because occupancy 0.34 <= existing 0.440001
Skipped atom 1883, because occupancy 0.22 <= existing 0.440001
Skipped atom 1885, because occupancy 0.34 <= existing 0.440001
Skipped atom 1886, because occupancy 0.22 <= existing 0.440001
Skipped atom 1888, because occupancy 0.34 <= existing 0.440001
Skipped atom 1889, because occupancy 0.22 <= existing 0.440001
Skipped atom 1891, because occupancy 0.34 <= existing 0.440001
Skipped atom 1892, because occupancy 0.22 <= existing 0.440001
Skipped atom 1894, because occupancy 0.34 <= existing 0.440001
Skipped atom 1895, because occupancy 0.22 <= existing 0.440001
Skipped atom 1897, because occupancy 0.34 <= existing 0.440001
Skipped atom 1898, because occupancy 0.22 <= existing 0.440001
Skipped atom 1900, because occupancy 0.34 <= existing 0.440001
Skipped atom 1901, because occupancy 0.22 <= existing 0.440001
Skipped atom 1903, because occupancy 0.34 <= existing 0.440001
Skipped atom 1904, because occupancy 0.22 <= existing 0.440001
Skipped atom 2029, because occupancy 0.39 <= existing 0.610001
Skipped atom 2033, because occupancy 0.39 <= existing 0.610001
Skipped atom 2035, because occupancy 0.39 <= existing 0.610001
Skipped atom 2037, because occupancy 0.39 <= existing 0.610001
Skipped atom 2039, because occupancy 0.39 <= existing 0.610001
Skipped atom 2041, because occupancy 0.39 <= existing 0.610001
Skipped atom 2043, because occupancy 0.39 <= existing 0.610001
Skipped atom 2045, because occupancy 0.39 <= existing 0.610001
Skipped atom 2159, because occupancy 0.36 <= existing 0.640001
Skipped atom 2161, because occupancy 0.36 <= existing 0.640001
Skipped atom 2163, because occupancy 0.36 <= existing 0.640001
Skipped atom 2165, because occupancy 0.36 <= existing 0.640001
Skipped atom 2167, because occupancy 0.36 <= existing 0.640001
Skipped atom 2169, because occupancy 0.36 <= existing 0.640001
Skipped atom 2171, because occupancy 0.36 <= existing 0.640001
Skipped atom 2173, because occupancy 0.36 <= existing 0.640001
Skipped atom 2236, because occupancy 0.25 <= existing 0.750001
Skipped atom 2238, because occupancy 0.25 <= existing 0.750001
Skipped atom 2240, because occupancy 0.25 <= existing 0.750001
Skipped atom 2242, because occupancy 0.25 <= existing 0.750001
Skipped atom 2244, because occupancy 0.25 <= existing 0.750001
Skipped atom 2246, because occupancy 0.25 <= existing 0.750001
Skipped atom 2248, because occupancy 0.25 <= existing 0.750001
Skipped atom 2474, because occupancy 0.27 <= existing 0.730001
Skipped atom 2476, because occupancy 0.27 <= existing 0.730001
Skipped atom 2478, because occupancy 0.27 <= existing 0.730001
Skipped atom 2480, because occupancy 0.27 <= existing 0.730001
Skipped atom 2482, because occupancy 0.27 <= existing 0.730001
Skipped atom 2484, because occupancy 0.27 <= existing 0.730001
Skipped atom 2511, because occupancy 0.34 <= existing 0.670001
Skipped atom 2515, because occupancy 0.34 <= existing 0.670001
Skipped atom 2517, because occupancy 0.34 <= existing 0.670001
Skipped atom 2519, because occupancy 0.34 <= existing 0.670001
Skipped atom 2521, because occupancy 0.34 <= existing 0.670001
Skipped atom 2676, because occupancy 0.29 <= existing 0.710001
Skipped atom 2678, because occupancy 0.29 <= existing 0.710001
Skipped atom 2680, because occupancy 0.29 <= existing 0.710001
Skipped atom 2682, because occupancy 0.29 <= existing 0.710001
Skipped atom 2684, because occupancy 0.29 <= existing 0.710001
Skipped atom 2686, because occupancy 0.29 <= existing 0.710001
Skipped atom 2733, because occupancy 0.4 <= existing 0.610001
Skipped atom 2735, because occupancy 0.4 <= existing 0.610001
Skipped atom 2794, because occupancy 0.37 <= existing 0.630001
Skipped atom 2798, because occupancy 0.37 <= existing 0.630001
Skipped atom 2800, because occupancy 0.37 <= existing 0.630001
Skipped atom 2802, because occupancy 0.37 <= existing 0.630001
Skipped atom 2804, because occupancy 0.37 <= existing 0.630001
Skipped atom 2872, because occupancy 0.34 <= existing 0.660001
Skipped atom 2876, because occupancy 0.34 <= existing 0.660001
Skipped atom 2878, because occupancy 0.34 <= existing 0.660001
Skipped atom 2880, because occupancy 0.34 <= existing 0.660001
Skipped atom 2882, because occupancy 0.34 <= existing 0.660001
Skipped atom 2884, because occupancy 0.34 <= existing 0.660001
Skipped atom 2886, because occupancy 0.34 <= existing 0.660001
Skipped atom 2888, because occupancy 0.34 <= existing 0.660001
Skipped atom 2966, because occupancy 0.29 <= existing 0.710001
Skipped atom 2970, because occupancy 0.29 <= existing 0.710001
Skipped atom 2972, because occupancy 0.29 <= existing 0.710001
Skipped atom 2974, because occupancy 0.29 <= existing 0.710001
Skipped atom 2976, because occupancy 0.29 <= existing 0.710001
Skipped atom 2978, because occupancy 0.29 <= existing 0.710001
Skipped atom 2980, because occupancy 0.29 <= existing 0.710001
Skipped atom 2982, because occupancy 0.29 <= existing 0.710001
Skipped atom 2998, because occupancy 0.34 <= existing 0.660001
Skipped atom 3000, because occupancy 0.34 <= existing 0.660001
Skipped atom 3002, because occupancy 0.34 <= existing 0.660001
Skipped atom 3004, because occupancy 0.34 <= existing 0.660001
Skipped atom 3006, because occupancy 0.34 <= existing 0.660001
Skipped atom 3008, because occupancy 0.34 <= existing 0.660001
Skipped atom 3010, because occupancy 0.34 <= existing 0.660001
Skipped atom 3012, because occupancy 0.34 <= existing 0.660001
Skipped atom 3300, because occupancy 0.34 <= existing 0.650001
Skipped atom 3304, because occupancy 0.34 <= existing 0.650001
Skipped atom 3306, because occupancy 0.34 <= existing 0.650001
Skipped atom 3308, because occupancy 0.34 <= existing 0.650001
Skipped atom 3310, because occupancy 0.34 <= existing 0.650001
Skipped atom 3312, because occupancy 0.34 <= existing 0.650001
Skipped atom 3449, because occupancy 0.11 <= existing 0.890001
Skipped atom 3451, because occupancy 0.11 <= existing 0.890001
Skipped atom 3453, because occupancy 0.11 <= existing 0.890001
Skipped atom 3455, because occupancy 0.11 <= existing 0.890001
Skipped atom 3457, because occupancy 0.11 <= existing 0.890001
Skipped atom 3459, because occupancy 0.11 <= existing 0.890001
Skipped atom 3516, because occupancy 0.28 <= existing 0.720001
Skipped atom 3518, because occupancy 0.28 <= existing 0.720001
Skipped atom 3520, because occupancy 0.28 <= existing 0.720001
Skipped atom 3522, because occupancy 0.28 <= existing 0.720001
Skipped atom 3524, because occupancy 0.28 <= existing 0.720001
PDB sequence and aligned sequence are not exact.
Writing a2m file: tmp/2nlrA-orig.a2m
Writing a2m file: tmp/2nlrA-pdb.a2m
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18322


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18322/tmp -alignfile tmp/2nlrA-orig.a2m \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59
Reading alignment file tmp/2nlrA-orig.a2m (1 sequences, 234 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18322/tmp.a2m.
No sequences have been dropped.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18322/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18322/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18322/tmp.a2m (1 sequences, 234 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18322/tmp.mod tmp/2nlrA-align.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18322 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/2nlrA-align.mod
tmp/2nlrA-align.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18322/tmp.a2m
SAM: align2model v3.2 (July 31, 2000) compiled 07/31/00_14:08:20
Sequence Files:  tmp/2nlrA-orig.a2m tmp/2nlrA-pdb.a2m
 Model FIM_method_score geometric mean of match probabilities (6).
% Single Track Model:  tmp/2nlrA-align.mod
Running w0.5 tmp/2nlrA-orig.a2m tmp/2nlrA-align.mod
Running align2model tmp/2nlrA-align -i tmp/2nlrA-align.mod -db tmp/2nlrA-orig.a2m -db tmp/2nlrA-pdb.a2m
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
make[2]: `und/2nlrA-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1ema-local.index und/1ema-T0107-local.index \
	und/1ema-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
make[2]: `und/T0107-1ema-local.index' is up to date.
make[2]: `und/1ema-T0107-local.index' is up to date.
make[2]: `und/1ema-T0107-fssp-global.index' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make -k und/T0107-1a0tP-local.index und/1a0tP-T0107-local.index \
	und/1a0tP-T0107-fssp-global.index
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107'
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/T0107-1a0tP-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/T0107-1a0tP-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1a0tP/T0107-1a0tP-local.pw.a2m.gz \
	-target T0107 -template 1a0tP \
	-out T0107-1a0tP-local -outdir und
Sequence named 1a0tP has all gap columns.
It will be included anyway.
Sequence named 1a0tP has all gap columns.
It will be included anyway.
/projects/kestrel/users/karplus/burial/slicer/slicer: no segments found
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/1a0tP-T0107-local.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/1a0tP-T0107-local.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1a0tP/1a0tP-T0107-local.pw.a2m.gz \
	-target T0107 -template 1a0tP \
	-out 1a0tP-T0107-local -outdir und
partial PDB gets fragment 73 through 83 extending start extending end
partial PDB gets fragment 216 through 225 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
25 residues read 
Measuring phi and psi 
Getting chi values
ASN    1    4
LYS    2   28
ASP    3    5
ASN    4    5
SER    5    2
PRO    7    2
GLU    9   12
GLN   10   13
ASP   11    4
SER   14    2
GLU   16   14
ILE   17    4
PHE   18    3
ILE   19    2
ASP   20    6
GLU   21   14
ASN   22    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   10     31.4972
Cluster     1 =   3  10
2 clashing residues after turn 
Residue clashes:
3-10
cluster 1 has 2 members and 7.700e+01 combinations:
 10  3 
Energy     39.5342
Searching cluster 3
Combinations for 2 members in cluster 1 OK: 7.700e+01 - Sending to search
7.634816 < 39.534222: keeping 
5.423293 < 13.999188: keeping 
4.388660 < 9.637838: keeping 
3.217643 < 8.750723: keeping 
0.000000 < 8.511392: keeping 
Solved cluster 1: residual clashing  3.67
Still clashes at these sidechain pairs:
ires=    7 irot=    1 jres=   10 jrot=    7      12.0580
Residual clashes =   19.38258
Printing 
mkdir tmp
mkdir: cannot create tmp.
tmp: File exists
make[2]: [und/1a0tP-T0107-fssp-global.index] Error 2 (ignored)
mkdir und
mkdir: cannot create und.
und: File exists
make[2]: [und/1a0tP-T0107-fssp-global.index] Error 2 (ignored)
/projects/kestrel/users/karplus/burial/slicer/slicer \
	-a2m 1a0tP/1a0tP-T0107-fssp-global.pw.a2m.gz \
	-target T0107 -template 1a0tP \
	-out 1a0tP-T0107-fssp-global -outdir und
partial PDB gets fragment 0 through 7 extending end
partial PDB gets fragment 35 through 55 extending start extending end
partial PDB gets fragment 57 through 58 extending start extending end
partial PDB gets fragment 61 through 75 extending start extending end
partial PDB gets fragment 118 through 118 extending start extending end
partial PDB gets fragment 133 through 142 extending start extending end
partial PDB gets fragment 167 through 196 extending start extending end
partial PDB gets fragment 214 through 225 extending start extending end
partial PDB gets fragment 236 through 245 extending start extending end
partial PDB gets fragment 283 through 314 extending start extending end
partial PDB gets fragment 349 through 366 extending start extending end
Debugging on !
Reading sequence file
Reading input structure 
180 residues read 
Measuring phi and psi 
Getting chi values
VAL    0    2
THR    2    2
LYS    4   26
TYR    5    2
THR    7    3
GLU   11   15
ASP   13    5
GLU   14   12
ILE   15    4
TRP   16    3
THR   18    2
THR   19    1
GLU   20   14
GLU   21   12
ILE   22    3
GLU   23   16
ARG   24   27
LYS   25   27
VAL   27    1
MET   29   11
SER   33    2
ASP   37    5
LYS   38   29
ASN   39    5
THR   41    2
ARG   45   25
LEU   47    2
TRP   48    6
ASP   49    3
GLU   50   14
ASN   51    5
LEU   54    3
ILE   57    3
VAL   58    1
LYS   59   31
ASP   60    6
PRO   61    2
VAL   62    3
LEU   63    4
ASN   64    4
LYS   65   31
ASP   66    6
ASN   69    4
PRO   72    2
TRP   73    6
GLU   74   13
GLN   75   12
ASP   76    6
SER   77    3
VAL   78    1
GLU   79   16
ILE   80    3
PHE   81    3
ILE   82    4
ASP   83    5
GLU   84   14
ASN   85    3
ASN   86    5
HIS   87    3
LYS   88   29
THR   89    2
TYR   91    2
TYR   92    3
GLU   93   12
ASP   94    7
ASP   95    3
ASP   96    3
GLN   98    7
ARG  101   25
VAL  102    1
ASN  103    5
TYR  104    3
MET  105   13
ASN  106    6
GLU  107   14
GLN  108   12
THR  109    3
PHE  110    3
THR  112    2
SER  117    3
PRO  118    2
ARG  120   28
PHE  121    3
LYS  122   32
THR  123    3
TYR  129    3
ILE  130    5
VAL  131    2
GLU  132   15
ILE  135    3
TRP  137    5
LYS  138   25
THR  139    2
ILE  140    4
LYS  141   28
PRO  142    2
THR  143    1
PRO  144    2
ASN  145    4
THR  146    3
VAL  147    2
ILE  148    3
ILE  152    2
GLN  153   12
VAL  154    2
ASN  155    5
ASP  156    3
ASN  158    4
GLN  161   13
ARG  162   32
VAL  163    1
ILE  165    5
ILE  166    4
SER  167    3
TRP  168    3
SER  169    2
ASP  170    5
PRO  171    2
THR  172    2
ASN  173    5
ASN  174    5
SER  175    2
TRP  176    4
ARG  177   27
ASP  178    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 73 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 93 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 104 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 T 144 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 W 169 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    21   52     12.6204
keepclash    49   51     23.4217
keepclash    72   73     11.2651
keepclash    74   97     37.5791
keepclash    80   82    105.2383
keepclash    80   93    182.6167
keepclash    82   93    111.4907
keepclash    95  104     21.0140
keepclash   111  113     15.7579
keepclash   133  149     19.9215
keepclash   142  143     12.7558
keepclash   151  153     29.1360
keepclash   169  173     20.0967
keepclash   172  178     21.2833
turnclash     21    6   23    0     27.5591
turnclash     21    9   50    0     36.0575
Cluster     1 =  21  23  50  52
Cluster     2 =  49  51
Cluster     3 =  72  73
Cluster     4 =  74  97
Cluster     5 =  80  82  93  95 104
Cluster     6 = 111 113
Cluster     7 = 133 149
Cluster     8 = 142 143
Cluster     9 = 151 153
Cluster    10 = 169 173
Cluster    11 = 172 178
27 clashing residues after turn 
Residue clashes:
21-52
21-23
21-50
49-51
72-73
74-97
80-82
80-93
82-93
93-95
95-104
111-113
133-149
142-143
151-153
169-173
172-178
23-50
cluster 1 has 4 members and 2.700e+02 combinations:
 23  50  52  21 
Energy     18.7494
Searching cluster 21
Combinations for 4 members in cluster 1 OK: 2.700e+02 - Sending to search
15.120675 < 18.749439: keeping 
7.954826 < 16.775936: keeping 
7.690449 < 10.256342: keeping 
6.129048 < 9.934170: keeping 
0.000000 < 7.947854: keeping 
0.000000 < 5.158955: keeping 
Solved cluster 1: residual clashing  4.68
cluster 2 has 2 members and 4.200e+01 combinations:
 49  51 
Energy     24.1976
Searching cluster 49
Combinations for 2 members in cluster 2 OK: 4.200e+01 - Sending to search
0.000000 < 24.197567: keeping 
Solved cluster 2: residual clashing  1.28
cluster 3 has 2 members and 0.000e+00 combinations:
 72  73 
Energy     48.6538
Searching cluster 72
Combinations for 2 members in cluster 3 OK: 0.000e+00 - Sending to search
Solved cluster 3: residual clashing 48.65
cluster 4 has 2 members and 2.000e+00 combinations:
 74  97 
Energy     38.2605
Searching cluster 74
Combinations for 2 members in cluster 4 OK: 2.000e+00 - Sending to search
25.507858 < 38.260471: keeping 
Solved cluster 4: residual clashing 28.53
cluster 5 has 5 members and 1.890e+03 combinations:
 93  104  82  95  80 
Energy    491.8824
Searching cluster 80
Combinations for 5 members in cluster 5 OK: 1.890e+03 - Sending to search
242.575256 < 491.882416: keeping 
230.421173 < 315.031250: keeping 
164.381790 < 303.009247: keeping 
154.319214 < 237.475922: keeping 
92.549194 < 227.479218: keeping 
78.860184 < 162.782379: keeping 
42.891068 < 149.225464: keeping 
32.828484 < 113.762390: keeping 
21.275753 < 103.765678: keeping 
Solved cluster 5: residual clashing 98.38
cluster 6 has 2 members and 6.000e+00 combinations:
 113  111 
Energy     15.7579
Searching cluster 111
Combinations for 2 members in cluster 6 OK: 6.000e+00 - Sending to search
0.000000 < 15.757898: keeping 
Solved cluster 6: residual clashing  0.01
cluster 7 has 2 members and 2.600e+01 combinations:
 149  133 
Energy     20.6489
Searching cluster 133
Combinations for 2 members in cluster 7 OK: 2.600e+01 - Sending to search
0.000000 < 20.648912: keeping 
Solved cluster 7: residual clashing  1.41
cluster 8 has 2 members and 5.600e+01 combinations:
 143  142 
Energy     12.7558
Searching cluster 142
Combinations for 2 members in cluster 8 OK: 5.600e+01 - Sending to search
0.000000 < 12.755798: keeping 
Solved cluster 8: residual clashing  0.76
cluster 9 has 2 members and 0.000e+00 combinations:
 151  153 
Energy     29.1360
Searching cluster 151
Combinations for 2 members in cluster 9 OK: 0.000e+00 - Sending to search
24.616133 < 29.136009: keeping 
Solved cluster 9: residual clashing 25.91
cluster 10 has 2 members and 6.000e+00 combinations:
 169  173 
Energy    175.4837
Searching cluster 169
Combinations for 2 members in cluster 10 OK: 6.000e+00 - Sending to search
28.598251 < 175.483734: keeping 
Solved cluster 10: residual clashing 40.79
cluster 11 has 2 members and 1.000e+01 combinations:
 172  178 
Energy     22.8720
Searching cluster 172
Combinations for 2 members in cluster 11 OK: 1.000e+01 - Sending to search
19.181959 < 22.871990: keeping 
8.623346 < 20.979836: keeping 
7.400794 < 10.647414: keeping 
Solved cluster 11: residual clashing  9.63
Still clashes at these sidechain pairs:
ires=   72 irot=    1 jres=   73 jrot=    1      11.2651
ires=   74 irot=    3 jres=   97 jrot=    2      25.5079
ires=   80 irot=   15 jres=   93 jrot=    3      10.3243
ires=   93 irot=    3 jres=  106 jrot=    1      10.0082
ires=   95 irot=    2 jres=  104 jrot=    1      10.9515
ires=  151 irot=    1 jres=  153 jrot=    2      24.6161
ires=  169 irot=    2 jres=  173 jrot=    1      28.5983
Residual clashes =  186.02646
Printing 
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107'
make: *** [indexes] Error 2