make: Nothing to be done for `joints'.
make -k PRED=1a4mA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2868


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2868/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp.a2m.gz (63 sequences, 349 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2868/tmp.a2m.
Dropping 8 (of 63) duplicate sequences with differing IDs
Dropping 5 (of 63) sequences with > 80.0% id
50 sequences left after dropping 13 of 63 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2868/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2868/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2868/tmp.a2m (50 sequences, 349 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2868/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2868 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1a4mA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
mkdir 1a4mA
fixmode 1a4mA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1a4mA/1a4mA-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2868/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -43.272018
Database has 2 sequences with 454 residues.
gzip -f 1a4mA/1a4mA-T0097-fssp-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 T0097.t2k.a2m.gz T0097.t2k-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4723


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp -alignfile T0097.t2k.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file T0097.t2k.a2m.gz (13 sequences, 105 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m.
Dropping 1 (of 13) duplicate sequences with differing IDs
Dropping 2 (of 13) sequences with > 80.0% id
10 sequences left after dropping 3 of 13 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m (10 sequences, 105 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.mod T0097.t2k-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4723 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1a4mA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1a4mA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1a4mA/T0097-1a4mA-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -54.896469
Database has 2 sequences with 454 residues.
gzip -f 1a4mA/T0097-1a4mA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a4mA/nostruct-align/1a4mA.t2k-w0.5.mod', needed by `1a4mA/1a4mA-T0097-local.pw.a2m.gz'.
make 1a4mA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1a4mA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1a4mA/T0097-1a4mA-vit.pw \
	 -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.429962
Database has 2 sequences with 454 residues.
gzip -f 1a4mA/T0097-1a4mA-vit.pw.a2m
make 1a4mA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1a4mA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1a4mA/T0097-1a4mA-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -110.265076
Database has 2 sequences with 454 residues.
gzip -f 1a4mA/T0097-1a4mA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a4mA/xxxx-1a4mA-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1aj8A PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-8481


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-8481/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp.a2m.gz (4 sequences, 371 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-8481/tmp.a2m.
Dropping 1 (of 4) sequences with > 80.0% id
3 sequences left after dropping 1 of 4 sequences.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-8481/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-8481/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8481/tmp.a2m (3 sequences, 371 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-8481/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-8481 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1aj8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
mkdir 1aj8A
fixmode 1aj8A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1aj8A/1aj8A-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8481/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -214.522522
Database has 2 sequences with 476 residues.
gzip -f 1aj8A/1aj8A-T0097-fssp-global.pw.a2m
make 1aj8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1aj8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1aj8A/T0097-1aj8A-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -55.582932
Database has 2 sequences with 476 residues.
gzip -f 1aj8A/T0097-1aj8A-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1aj8A/nostruct-align/1aj8A.t2k-w0.5.mod', needed by `1aj8A/1aj8A-T0097-local.pw.a2m.gz'.
make 1aj8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1aj8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1aj8A/T0097-1aj8A-vit.pw \
	 -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.239899
Database has 2 sequences with 476 residues.
gzip -f 1aj8A/T0097-1aj8A-vit.pw.a2m
make 1aj8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1aj8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1aj8A/T0097-1aj8A-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -114.754578
Database has 2 sequences with 476 residues.
gzip -f 1aj8A/T0097-1aj8A-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aj8A/xxxx-1aj8A-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1c1gA PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14345


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14345/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp.a2m.gz (20 sequences, 284 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14345/tmp.a2m.
No sequences have been droppd.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14345/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14345/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14345/tmp.a2m (20 sequences, 284 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14345/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-14345 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1c1gA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
mkdir 1c1gA
fixmode 1c1gA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gA/1c1gA-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14345/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -189.553543
Database has 2 sequences with 389 residues.
gzip -f 1c1gA/1c1gA-T0097-fssp-global.pw.a2m
make 1c1gA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gA/T0097-1c1gA-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -55.527542
Database has 2 sequences with 389 residues.
gzip -f 1c1gA/T0097-1c1gA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1c1gA/nostruct-align/1c1gA.t2k-w0.5.mod', needed by `1c1gA/1c1gA-T0097-local.pw.a2m.gz'.
make 1c1gA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gA/T0097-1c1gA-vit.pw \
	 -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.205536
Database has 2 sequences with 389 residues.
gzip -f 1c1gA/T0097-1c1gA-vit.pw.a2m
make 1c1gA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gA/T0097-1c1gA-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -111.427551
Database has 2 sequences with 389 residues.
gzip -f 1c1gA/T0097-1c1gA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c1gA/xxxx-1c1gA-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1c1gB PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-5793


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-5793/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp.a2m.gz (13 sequences, 284 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-5793/tmp.a2m.
No sequences have been droppd.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-5793/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-5793/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5793/tmp.a2m (13 sequences, 284 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-5793/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-5793 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1c1gB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
mkdir 1c1gB
fixmode 1c1gB
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gB/1c1gB-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5793/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -214.261047
Database has 2 sequences with 389 residues.
gzip -f 1c1gB/1c1gB-T0097-fssp-global.pw.a2m
make 1c1gB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gB/T0097-1c1gB-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -55.527542
Database has 2 sequences with 389 residues.
gzip -f 1c1gB/T0097-1c1gB-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1c1gB/nostruct-align/1c1gB.t2k-w0.5.mod', needed by `1c1gB/1c1gB-T0097-local.pw.a2m.gz'.
make 1c1gB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gB/T0097-1c1gB-vit.pw \
	 -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.205536
Database has 2 sequences with 389 residues.
gzip -f 1c1gB/T0097-1c1gB-vit.pw.a2m
make 1c1gB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gB/T0097-1c1gB-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -111.427551
Database has 2 sequences with 389 residues.
gzip -f 1c1gB/T0097-1c1gB-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c1gB/xxxx-1c1gB-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1c1gC PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-4599


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-4599/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp.a2m.gz (2 sequences, 284 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-4599/tmp.a2m.
No sequences have been droppd.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-4599/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-4599/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4599/tmp.a2m (2 sequences, 284 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-4599/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-4599 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1c1gC
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
mkdir 1c1gC
fixmode 1c1gC
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gC/1c1gC-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4599/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -263.957031
Database has 2 sequences with 389 residues.
gzip -f 1c1gC/1c1gC-T0097-fssp-global.pw.a2m
make 1c1gC
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gC' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gC/T0097-1c1gC-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -55.527542
Database has 2 sequences with 389 residues.
gzip -f 1c1gC/T0097-1c1gC-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1c1gC/nostruct-align/1c1gC.t2k-w0.5.mod', needed by `1c1gC/1c1gC-T0097-local.pw.a2m.gz'.
make 1c1gC
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gC' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gC/T0097-1c1gC-vit.pw \
	 -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.205536
Database has 2 sequences with 389 residues.
gzip -f 1c1gC/T0097-1c1gC-vit.pw.a2m
make 1c1gC
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gC' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gC/T0097-1c1gC-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -111.427551
Database has 2 sequences with 389 residues.
gzip -f 1c1gC/T0097-1c1gC-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c1gC/xxxx-1c1gC-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1c1gD PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.conf

@@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-15410


@@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-15410/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp.a2m.gz \
    		-a protein -percent_id 0.8
SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50
Reading alignment file /projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp.a2m.gz (5 sequences, 284 columns) as A2M alignment.
Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-15410/tmp.a2m.
No sequences have been droppd.


@@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15410/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15410/tmp.a2m \
		-insert /projects/compbio/lib/fssp-trained.regularizer \
		-ins_jump_conf 1 \
		-match_jump_conf 1 \
		-del_jump_conf 1 \
		-prior_library /projects/compbio/lib/recode3.20comp \
		-binary_output 1  -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10
Reading parameter file /projects/compbio/lib/fssp-trained.regularizer
/projects/compbio/lib/fssp-trained.regularizer(1):  Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP
SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13
Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15410/tmp.a2m (5 sequences, 284 columns) as A2M alignment.


@@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15410/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp-w0.5.mod


@@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15410 </dev/null
Reading /projects/compbio/bin/scripts/sam-t99.confmake 1c1gD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
mkdir 1c1gD
fixmode 1c1gD
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gD/1c1gD-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15410/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -247.914551
Database has 2 sequences with 389 residues.
gzip -f 1c1gD/1c1gD-T0097-fssp-global.pw.a2m
make 1c1gD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gD/T0097-1c1gD-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride-mixed.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -55.527542
Database has 2 sequences with 389 residues.
gzip -f 1c1gD/T0097-1c1gD-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1c1gD/nostruct-align/1c1gD.t2k-w0.5.mod', needed by `1c1gD/1c1gD-T0097-local.pw.a2m.gz'.
make 1c1gD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gD/T0097-1c1gD-vit.pw \
	 -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride-mixed.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -51.205536
Database has 2 sequences with 389 residues.
gzip -f 1c1gD/T0097-1c1gD-vit.pw.a2m
make 1c1gD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gD/T0097-1c1gD-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride-mixed.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -111.427551
Database has 2 sequences with 389 residues.
gzip -f 1c1gD/T0097-1c1gD-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c1gD/xxxx-1c1gD-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1a4mA PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1a4mA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1a4mA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1a4mA/1a4mA-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1a4mA/struct-align/1a4mA.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-2868/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -71.558357
Database has 3 sequences with 803 residues.
gzip -f 1a4mA/1a4mA-T0097-fssp-global.pw.a2m
make 1a4mA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1a4mA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1a4mA/T0097-1a4mA-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -41.583607
Database has 3 sequences with 803 residues.
gzip -f 1a4mA/T0097-1a4mA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1a4mA/nostruct-align/1a4mA.t2k-w0.5.mod', needed by `1a4mA/1a4mA-T0097-local.pw.a2m.gz'.
make 1a4mA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1a4mA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1a4mA/T0097-1a4mA-vit.pw \
	-i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -37.319599
Database has 3 sequences with 803 residues.
gzip -f 1a4mA/T0097-1a4mA-vit.pw.a2m
make 1a4mA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1a4mA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1a4mA/T0097-1a4mA-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1a4mA/info/1a4mA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -99.539429
Database has 3 sequences with 803 residues.
gzip -f 1a4mA/T0097-1a4mA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a4mA/xxxx-1a4mA-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1aj8A PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1aj8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1aj8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1aj8A/1aj8A-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1aj8A/struct-align/1aj8A.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-8481/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -297.148346
Database has 3 sequences with 847 residues.
gzip -f 1aj8A/1aj8A-T0097-fssp-global.pw.a2m
make 1aj8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1aj8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1aj8A/T0097-1aj8A-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -42.498890
Database has 3 sequences with 847 residues.
gzip -f 1aj8A/T0097-1aj8A-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1aj8A/nostruct-align/1aj8A.t2k-w0.5.mod', needed by `1aj8A/1aj8A-T0097-local.pw.a2m.gz'.
make 1aj8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1aj8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1aj8A/T0097-1aj8A-vit.pw \
	-i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -37.066181
Database has 3 sequences with 847 residues.
gzip -f 1aj8A/T0097-1aj8A-vit.pw.a2m
make 1aj8A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1aj8A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1aj8A/T0097-1aj8A-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1aj8A/info/1aj8A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -105.525429
Database has 3 sequences with 847 residues.
gzip -f 1aj8A/T0097-1aj8A-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aj8A/xxxx-1aj8A-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1c1gA PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1c1gA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gA/1c1gA-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c1gA/struct-align/1c1gA.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14345/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -236.611038
Database has 3 sequences with 673 residues.
gzip -f 1c1gA/1c1gA-T0097-fssp-global.pw.a2m
make 1c1gA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gA/T0097-1c1gA-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -42.425037
Database has 3 sequences with 673 residues.
gzip -f 1c1gA/T0097-1c1gA-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1c1gA/nostruct-align/1c1gA.t2k-w0.5.mod', needed by `1c1gA/1c1gA-T0097-local.pw.a2m.gz'.
make 1c1gA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gA/T0097-1c1gA-vit.pw \
	-i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -37.020367
Database has 3 sequences with 673 residues.
gzip -f 1c1gA/T0097-1c1gA-vit.pw.a2m
make 1c1gA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gA/T0097-1c1gA-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gA/info/1c1gA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -101.089394
Database has 3 sequences with 673 residues.
gzip -f 1c1gA/T0097-1c1gA-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c1gA/xxxx-1c1gA-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1c1gB PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1c1gB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gB/1c1gB-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c1gB/struct-align/1c1gB.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-5793/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -271.068054
Database has 3 sequences with 673 residues.
gzip -f 1c1gB/1c1gB-T0097-fssp-global.pw.a2m
make 1c1gB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gB/T0097-1c1gB-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -42.425037
Database has 3 sequences with 673 residues.
gzip -f 1c1gB/T0097-1c1gB-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1c1gB/nostruct-align/1c1gB.t2k-w0.5.mod', needed by `1c1gB/1c1gB-T0097-local.pw.a2m.gz'.
make 1c1gB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gB/T0097-1c1gB-vit.pw \
	-i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -37.020367
Database has 3 sequences with 673 residues.
gzip -f 1c1gB/T0097-1c1gB-vit.pw.a2m
make 1c1gB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gB/T0097-1c1gB-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gB/info/1c1gB.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -101.089394
Database has 3 sequences with 673 residues.
gzip -f 1c1gB/T0097-1c1gB-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c1gB/xxxx-1c1gB-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1c1gC PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1c1gC
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gC' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gC/1c1gC-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c1gC/struct-align/1c1gC.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4599/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -337.948700
Database has 3 sequences with 673 residues.
gzip -f 1c1gC/1c1gC-T0097-fssp-global.pw.a2m
make 1c1gC
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gC' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gC/T0097-1c1gC-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -42.425037
Database has 3 sequences with 673 residues.
gzip -f 1c1gC/T0097-1c1gC-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1c1gC/nostruct-align/1c1gC.t2k-w0.5.mod', needed by `1c1gC/1c1gC-T0097-local.pw.a2m.gz'.
make 1c1gC
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gC' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gC/T0097-1c1gC-vit.pw \
	-i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -37.020367
Database has 3 sequences with 673 residues.
gzip -f 1c1gC/T0097-1c1gC-vit.pw.a2m
make 1c1gC
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gC' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gC/T0097-1c1gC-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gC/info/1c1gC.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -101.089394
Database has 3 sequences with 673 residues.
gzip -f 1c1gC/T0097-1c1gC-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c1gC/xxxx-1c1gC-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)
make -k PRED=1c1gD PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make 1c1gD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gD/1c1gD-T0097-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1c1gD/struct-align/1c1gD.fssp-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15410/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -315.800049
Database has 3 sequences with 673 residues.
gzip -f 1c1gD/1c1gD-T0097-fssp-global.pw.a2m
make 1c1gD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gD/T0097-1c1gD-local.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -42.425037
Database has 3 sequences with 673 residues.
gzip -f 1c1gD/T0097-1c1gD-local.pw.a2m
make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1c/1c1gD/nostruct-align/1c1gD.t2k-w0.5.mod', needed by `1c1gD/1c1gD-T0097-local.pw.a2m.gz'.
make 1c1gD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gD/T0097-1c1gD-vit.pw \
	-i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -37.020367
Database has 3 sequences with 673 residues.
gzip -f 1c1gD/T0097-1c1gD-vit.pw.a2m
make 1c1gD
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97'
make[2]: `1c1gD' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
hmmscore 1c1gD/T0097-1c1gD-global.pw -i T0097.t2k-w0.5.mod -db T0097.seq -db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1c1gD/info/1c1gD.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file T0097.t2k-w0.5.mod
T0097.t2k-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-4723/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -101.089394
Database has 3 sequences with 673 residues.
gzip -f 1c1gD/T0097-1c1gD-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1c1gD/xxxx-1c1gD-T0097-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t97'
make: [joints] Error 2 (ignored)