make -k PRED=1cxlA PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1cxlA/struct-align/1cxlA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1cxlA/struct-align/1cxlA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10621 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10621/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1cxlA/struct-align/1cxlA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1c/1cxlA/struct-align/1cxlA.fssp.a2m.gz (101 sequences, 686 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10621/tmp.a2m. Dropping 17 (of 101) duplicate sequences with differing IDs Dropping 14 (of 101) sequences with > 80.0% id 70 sequences left after dropping 31 of 101 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10621/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10621/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10621/tmp.a2m (70 sequences, 686 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10621/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1cxlA/struct-align/1cxlA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1cxlA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1cxlA fixmode 1cxlA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/1cxlA-T0107-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cxlA/struct-align/1cxlA.fssp-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cxlA/struct-align/1cxlA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cxlA/struct-align/1cxlA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10621/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -345.670319 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/1cxlA-T0107-fssp-global.pw.a2m /projects/compbio/bin/scripts/w0.5 T0107.t2k.a2m.gz T0107.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp -alignfile T0107.t2k.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file T0107.t2k.a2m.gz (29 sequences, 188 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m. Dropping 3 (of 29) duplicate sequences with differing IDs Dropping 12 (of 29) sequences with > 80.0% id 14 sequences left after dropping 15 of 29 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m (14 sequences, 188 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.mod T0107.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1cxlA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/T0107-1cxlA-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -70.062645 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/T0107-1cxlA-local.pw.a2m make 1cxlA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/1cxlA-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cxlA/nostruct-align/1cxlA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cxlA/nostruct-align/1cxlA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cxlA/nostruct-align/1cxlA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2159/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -360.876373 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/1cxlA-T0107-local.pw.a2m make 1cxlA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/T0107-1cxlA-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -64.709648 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/T0107-1cxlA-vit.pw.a2m make 1cxlA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/1cxlA-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1cxlA/nostruct-align/1cxlA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cxlA/nostruct-align/1cxlA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cxlA/nostruct-align/1cxlA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2159/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -356.481323 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/1cxlA-T0107-vit.pw.a2m make 1cxlA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/T0107-1cxlA-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 21.095856 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/T0107-1cxlA-global.pw.a2m make 1cxlA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/1cxlA-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cxlA/nostruct-align/1cxlA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cxlA/nostruct-align/1cxlA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cxlA/nostruct-align/1cxlA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2159/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -350.822418 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/1cxlA-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cxlA/xxxx-1cxlA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1taxA PRED2=1t joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1t/1taxA/struct-align/1taxA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1t/1taxA/struct-align/1taxA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11079 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11079/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1t/1taxA/struct-align/1taxA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1t/1taxA/struct-align/1taxA.fssp.a2m.gz (99 sequences, 302 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11079/tmp.a2m. Dropping 13 (of 99) duplicate sequences with differing IDs Dropping 4 (of 99) sequences with > 80.0% id 82 sequences left after dropping 17 of 99 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11079/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11079/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11079/tmp.a2m (82 sequences, 302 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11079/tmp.mod /projects/compbio/experiments/models.97/pdb/1t/1taxA/struct-align/1taxA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1taxA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1taxA fixmode 1taxA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/1taxA-T0107-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1taxA/struct-align/1taxA.fssp-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1taxA/struct-align/1taxA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1taxA/struct-align/1taxA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11079/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -109.005333 Database has 3 sequences with 792 residues. gzip -f 1taxA/1taxA-T0107-fssp-global.pw.a2m make 1taxA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/T0107-1taxA-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -69.686951 Database has 3 sequences with 792 residues. gzip -f 1taxA/T0107-1taxA-local.pw.a2m make 1taxA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/1taxA-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1taxA/nostruct-align/1taxA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1taxA/nostruct-align/1taxA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1taxA/nostruct-align/1taxA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13132/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -200.283249 Database has 3 sequences with 792 residues. gzip -f 1taxA/1taxA-T0107-local.pw.a2m make 1taxA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/T0107-1taxA-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -64.123955 Database has 3 sequences with 792 residues. gzip -f 1taxA/T0107-1taxA-vit.pw.a2m make 1taxA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/1taxA-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1t/1taxA/nostruct-align/1taxA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1taxA/nostruct-align/1taxA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1taxA/nostruct-align/1taxA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13132/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -196.439590 Database has 3 sequences with 792 residues. gzip -f 1taxA/1taxA-T0107-vit.pw.a2m make 1taxA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/T0107-1taxA-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -37.004040 Database has 3 sequences with 792 residues. gzip -f 1taxA/T0107-1taxA-global.pw.a2m make 1taxA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/1taxA-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1taxA/nostruct-align/1taxA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1taxA/nostruct-align/1taxA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1taxA/nostruct-align/1taxA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-13132/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -194.980713 Database has 3 sequences with 792 residues. gzip -f 1taxA/1taxA-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1taxA/xxxx-1taxA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cfr PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1cfr/struct-align/1cfr.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1cfr/struct-align/1cfr.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7137 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7137/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1c/1cfr/struct-align/1cfr.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1c/1cfr/struct-align/1cfr.fssp.a2m.gz (1 sequences, 283 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7137/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7137/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7137/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7137/tmp.a2m (1 sequences, 283 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7137/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1cfr/struct-align/1cfr.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1cfr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1cfr fixmode 1cfr make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/1cfr-T0107-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cfr/struct-align/1cfr.fssp-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cfr/struct-align/1cfr.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cfr/struct-align/1cfr.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7137/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -291.483673 Database has 3 sequences with 756 residues. gzip -f 1cfr/1cfr-T0107-fssp-global.pw.a2m make 1cfr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/T0107-1cfr-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -73.477257 Database has 3 sequences with 756 residues. gzip -f 1cfr/T0107-1cfr-local.pw.a2m make 1cfr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/1cfr-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cfr/nostruct-align/1cfr.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cfr/nostruct-align/1cfr.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cfr/nostruct-align/1cfr.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12336/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -298.841583 Database has 3 sequences with 756 residues. gzip -f 1cfr/1cfr-T0107-local.pw.a2m make 1cfr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/T0107-1cfr-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -66.063591 Database has 3 sequences with 756 residues. gzip -f 1cfr/T0107-1cfr-vit.pw.a2m make 1cfr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/1cfr-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1c/1cfr/nostruct-align/1cfr.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cfr/nostruct-align/1cfr.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cfr/nostruct-align/1cfr.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12336/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -295.821259 Database has 3 sequences with 756 residues. gzip -f 1cfr/1cfr-T0107-vit.pw.a2m make 1cfr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/T0107-1cfr-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -48.681366 Database has 3 sequences with 756 residues. gzip -f 1cfr/T0107-1cfr-global.pw.a2m make 1cfr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/1cfr-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cfr/nostruct-align/1cfr.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1cfr/nostruct-align/1cfr.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1c/1cfr/nostruct-align/1cfr.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12336/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -292.411377 Database has 3 sequences with 756 residues. gzip -f 1cfr/1cfr-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cfr/xxxx-1cfr-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1vpsA PRED2=1v joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1v/1vpsA/struct-align/1vpsA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1v/1vpsA/struct-align/1vpsA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-16230 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-16230/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1v/1vpsA/struct-align/1vpsA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1v/1vpsA/struct-align/1vpsA.fssp.a2m.gz (34 sequences, 285 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-16230/tmp.a2m. Dropping 20 (of 34) duplicate sequences with differing IDs Dropping 11 (of 34) sequences with > 80.0% id 3 sequences left after dropping 31 of 34 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-16230/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-16230/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-16230/tmp.a2m (3 sequences, 285 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-16230/tmp.mod /projects/compbio/experiments/models.97/pdb/1v/1vpsA/struct-align/1vpsA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1vpsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1vpsA fixmode 1vpsA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/1vpsA-T0107-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1v/1vpsA/struct-align/1vpsA.fssp-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1v/1vpsA/struct-align/1vpsA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1v/1vpsA/struct-align/1vpsA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-16230/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -243.346695 Database has 3 sequences with 762 residues. gzip -f 1vpsA/1vpsA-T0107-fssp-global.pw.a2m make 1vpsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/T0107-1vpsA-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -69.645607 Database has 3 sequences with 762 residues. gzip -f 1vpsA/T0107-1vpsA-local.pw.a2m make 1vpsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/1vpsA-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1v/1vpsA/nostruct-align/1vpsA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1v/1vpsA/nostruct-align/1vpsA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1v/1vpsA/nostruct-align/1vpsA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20747/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -238.800598 Database has 3 sequences with 762 residues. gzip -f 1vpsA/1vpsA-T0107-local.pw.a2m make 1vpsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/T0107-1vpsA-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -64.675262 Database has 3 sequences with 762 residues. gzip -f 1vpsA/T0107-1vpsA-vit.pw.a2m make 1vpsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/1vpsA-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1v/1vpsA/nostruct-align/1vpsA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1v/1vpsA/nostruct-align/1vpsA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1v/1vpsA/nostruct-align/1vpsA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20747/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -234.906921 Database has 3 sequences with 762 residues. gzip -f 1vpsA/1vpsA-T0107-vit.pw.a2m make 1vpsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/T0107-1vpsA-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.378693 Database has 3 sequences with 762 residues. gzip -f 1vpsA/T0107-1vpsA-global.pw.a2m make 1vpsA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/1vpsA-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1v/1vpsA/nostruct-align/1vpsA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1v/1vpsA/nostruct-align/1vpsA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1v/1vpsA/nostruct-align/1vpsA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20747/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -234.505692 Database has 3 sequences with 762 residues. gzip -f 1vpsA/1vpsA-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1vpsA/xxxx-1vpsA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1aszB PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1aszB/struct-align/1aszB.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1aszB/struct-align/1aszB.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2337 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2337/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1aszB/struct-align/1aszB.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1a/1aszB/struct-align/1aszB.fssp.a2m.gz (19 sequences, 490 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2337/tmp.a2m. Dropping 3 (of 19) duplicate sequences with differing IDs 16 sequences left after dropping 3 of 19 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2337/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2337/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2337/tmp.a2m (16 sequences, 490 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2337/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1aszB/struct-align/1aszB.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1aszB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1aszB fixmode 1aszB make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/1aszB-T0107-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aszB/struct-align/1aszB.fssp-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aszB/struct-align/1aszB.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1aszB/struct-align/1aszB.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-2337/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -309.337036 Database has 3 sequences with 1168 residues. gzip -f 1aszB/1aszB-T0107-fssp-global.pw.a2m make 1aszB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/T0107-1aszB-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -69.026917 Database has 3 sequences with 1168 residues. gzip -f 1aszB/T0107-1aszB-local.pw.a2m make 1aszB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/1aszB-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aszB/nostruct-align/1aszB.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aszB/nostruct-align/1aszB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1aszB/nostruct-align/1aszB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9904/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -259.672241 Database has 3 sequences with 1168 residues. gzip -f 1aszB/1aszB-T0107-local.pw.a2m make 1aszB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/T0107-1aszB-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -64.069916 Database has 3 sequences with 1168 residues. gzip -f 1aszB/T0107-1aszB-vit.pw.a2m make 1aszB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/1aszB-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1aszB/nostruct-align/1aszB.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aszB/nostruct-align/1aszB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1aszB/nostruct-align/1aszB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9904/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -255.413528 Database has 3 sequences with 1168 residues. gzip -f 1aszB/1aszB-T0107-vit.pw.a2m make 1aszB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/T0107-1aszB-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -11.092702 Database has 3 sequences with 1168 residues. gzip -f 1aszB/T0107-1aszB-global.pw.a2m make 1aszB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/1aszB-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1aszB/nostruct-align/1aszB.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1aszB/nostruct-align/1aszB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1aszB/nostruct-align/1aszB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-9904/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -247.097046 Database has 3 sequences with 1168 residues. gzip -f 1aszB/1aszB-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aszB/xxxx-1aszB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1asyA PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1asyA/struct-align/1asyA.fssp-w0.5.mod', needed by `1asyA/1asyA-T0107-fssp-global.pw.a2m.gz'. make 1asyA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1asyA fixmode 1asyA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/T0107-1asyA-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -69.026917 Database has 3 sequences with 1168 residues. gzip -f 1asyA/T0107-1asyA-local.pw.a2m make 1asyA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/1asyA-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1asyA/nostruct-align/1asyA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1asyA/nostruct-align/1asyA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1asyA/nostruct-align/1asyA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-32595/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -259.637299 Database has 3 sequences with 1168 residues. gzip -f 1asyA/1asyA-T0107-local.pw.a2m make 1asyA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/T0107-1asyA-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -64.069916 Database has 3 sequences with 1168 residues. gzip -f 1asyA/T0107-1asyA-vit.pw.a2m make 1asyA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/1asyA-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1asyA/nostruct-align/1asyA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1asyA/nostruct-align/1asyA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1asyA/nostruct-align/1asyA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-32595/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -255.376953 Database has 3 sequences with 1168 residues. gzip -f 1asyA/1asyA-T0107-vit.pw.a2m make 1asyA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/T0107-1asyA-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -11.092702 Database has 3 sequences with 1168 residues. gzip -f 1asyA/T0107-1asyA-global.pw.a2m make 1asyA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/1asyA-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1asyA/nostruct-align/1asyA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1asyA/nostruct-align/1asyA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1asyA/nostruct-align/1asyA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-32595/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -247.117432 Database has 3 sequences with 1168 residues. gzip -f 1asyA/1asyA-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1asyA/xxxx-1asyA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1b8aA PRED2=1b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1b8aA/struct-align/1b8aA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1b8aA/struct-align/1b8aA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10006 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10006/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1b/1b8aA/struct-align/1b8aA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1b/1b8aA/struct-align/1b8aA.fssp.a2m.gz (21 sequences, 438 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10006/tmp.a2m. Dropping 4 (of 21) duplicate sequences with differing IDs 17 sequences left after dropping 4 of 21 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10006/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10006/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10006/tmp.a2m (17 sequences, 438 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10006/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1b8aA/struct-align/1b8aA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1b8aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1b8aA fixmode 1b8aA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/1b8aA-T0107-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b8aA/struct-align/1b8aA.fssp-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1b8aA/struct-align/1b8aA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1b8aA/struct-align/1b8aA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10006/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -268.976074 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/1b8aA-T0107-fssp-global.pw.a2m make 1b8aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/T0107-1b8aA-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -69.021706 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/T0107-1b8aA-local.pw.a2m make 1b8aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/1b8aA-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b8aA/nostruct-align/1b8aA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1b8aA/nostruct-align/1b8aA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1b8aA/nostruct-align/1b8aA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18890/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -258.653046 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/1b8aA-T0107-local.pw.a2m make 1b8aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/T0107-1b8aA-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -64.113373 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/T0107-1b8aA-vit.pw.a2m make 1b8aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/1b8aA-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1b8aA/nostruct-align/1b8aA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1b8aA/nostruct-align/1b8aA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1b8aA/nostruct-align/1b8aA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18890/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -255.221069 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/1b8aA-T0107-vit.pw.a2m make 1b8aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/T0107-1b8aA-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -20.466074 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/T0107-1b8aA-global.pw.a2m make 1b8aA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/1b8aA-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b8aA/nostruct-align/1b8aA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1b8aA/nostruct-align/1b8aA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1b/1b8aA/nostruct-align/1b8aA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18890/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -248.240051 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/1b8aA-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b8aA/xxxx-1b8aA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1eerB PRED2=1e joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1e/1eerB/struct-align/1eerB.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1e/1eerB/struct-align/1eerB.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11560 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11560/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1e/1eerB/struct-align/1eerB.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1e/1eerB/struct-align/1eerB.fssp.a2m.gz (27 sequences, 213 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11560/tmp.a2m. Dropping 2 (of 27) duplicate sequences with differing IDs Dropping 7 (of 27) sequences with > 80.0% id 18 sequences left after dropping 9 of 27 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11560/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11560/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11560/tmp.a2m (18 sequences, 213 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11560/tmp.mod /projects/compbio/experiments/models.97/pdb/1e/1eerB/struct-align/1eerB.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1eerB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1eerB fixmode 1eerB make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/1eerB-T0107-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1eerB/struct-align/1eerB.fssp-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1eerB/struct-align/1eerB.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1eerB/struct-align/1eerB.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11560/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -123.408699 Database has 3 sequences with 628 residues. gzip -f 1eerB/1eerB-T0107-fssp-global.pw.a2m make 1eerB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/T0107-1eerB-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -69.062828 Database has 3 sequences with 628 residues. gzip -f 1eerB/T0107-1eerB-local.pw.a2m make 1eerB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/1eerB-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1eerB/nostruct-align/1eerB.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1eerB/nostruct-align/1eerB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1eerB/nostruct-align/1eerB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19401/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -90.011482 Database has 3 sequences with 628 residues. gzip -f 1eerB/1eerB-T0107-local.pw.a2m make 1eerB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/T0107-1eerB-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -63.690155 Database has 3 sequences with 628 residues. gzip -f 1eerB/T0107-1eerB-vit.pw.a2m make 1eerB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/1eerB-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1e/1eerB/nostruct-align/1eerB.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1eerB/nostruct-align/1eerB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1eerB/nostruct-align/1eerB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19401/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -86.233803 Database has 3 sequences with 628 residues. gzip -f 1eerB/1eerB-T0107-vit.pw.a2m make 1eerB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/T0107-1eerB-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -49.985729 Database has 3 sequences with 628 residues. gzip -f 1eerB/T0107-1eerB-global.pw.a2m make 1eerB make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/1eerB-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1eerB/nostruct-align/1eerB.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1e/1eerB/nostruct-align/1eerB.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1e/1eerB/nostruct-align/1eerB.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19401/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -86.661713 Database has 3 sequences with 628 residues. gzip -f 1eerB/1eerB-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eerB/xxxx-1eerB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1lylA PRED2=1l joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1l/1lylA/struct-align/1lylA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1l/1lylA/struct-align/1lylA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-975 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-975/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1l/1lylA/struct-align/1lylA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1l/1lylA/struct-align/1lylA.fssp.a2m.gz (16 sequences, 482 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-975/tmp.a2m. Dropping 1 (of 16) duplicate sequences with differing IDs Dropping 1 (of 16) sequences with > 80.0% id 14 sequences left after dropping 2 of 16 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-975/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-975/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-975/tmp.a2m (14 sequences, 482 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-975/tmp.mod /projects/compbio/experiments/models.97/pdb/1l/1lylA/struct-align/1lylA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1lylA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1lylA fixmode 1lylA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/1lylA-T0107-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lylA/struct-align/1lylA.fssp-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lylA/struct-align/1lylA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1l/1lylA/struct-align/1lylA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-975/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -302.964386 Database has 3 sequences with 1174 residues. gzip -f 1lylA/1lylA-T0107-fssp-global.pw.a2m make 1lylA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/T0107-1lylA-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -71.297386 Database has 3 sequences with 1174 residues. gzip -f 1lylA/T0107-1lylA-local.pw.a2m make 1lylA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/1lylA-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lylA/nostruct-align/1lylA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lylA/nostruct-align/1lylA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1l/1lylA/nostruct-align/1lylA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-10638/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -281.077087 Database has 3 sequences with 1174 residues. gzip -f 1lylA/1lylA-T0107-local.pw.a2m make 1lylA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/T0107-1lylA-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -66.099419 Database has 3 sequences with 1174 residues. gzip -f 1lylA/T0107-1lylA-vit.pw.a2m make 1lylA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/1lylA-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1l/1lylA/nostruct-align/1lylA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lylA/nostruct-align/1lylA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1l/1lylA/nostruct-align/1lylA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-10638/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -276.269745 Database has 3 sequences with 1174 residues. gzip -f 1lylA/1lylA-T0107-vit.pw.a2m make 1lylA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/T0107-1lylA-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -10.408742 Database has 3 sequences with 1174 residues. gzip -f 1lylA/T0107-1lylA-global.pw.a2m make 1lylA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/1lylA-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1l/1lylA/nostruct-align/1lylA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1l/1lylA/nostruct-align/1lylA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1l/1lylA/nostruct-align/1lylA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-10638/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -268.309052 Database has 3 sequences with 1174 residues. gzip -f 1lylA/1lylA-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lylA/xxxx-1lylA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1fnhA PRED2=1f joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1f/1fnhA/struct-align/1fnhA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1f/1fnhA/struct-align/1fnhA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-15232 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-15232/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1f/1fnhA/struct-align/1fnhA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1f/1fnhA/struct-align/1fnhA.fssp.a2m.gz (19 sequences, 269 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-15232/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-15232/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-15232/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-15232/tmp.a2m (19 sequences, 269 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-15232/tmp.mod /projects/compbio/experiments/models.97/pdb/1f/1fnhA/struct-align/1fnhA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1fnhA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1fnhA fixmode 1fnhA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/1fnhA-T0107-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1f/1fnhA/struct-align/1fnhA.fssp-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1f/1fnhA/struct-align/1fnhA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1f/1fnhA/struct-align/1fnhA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-15232/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -151.132706 Database has 3 sequences with 728 residues. gzip -f 1fnhA/1fnhA-T0107-fssp-global.pw.a2m make 1fnhA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/T0107-1fnhA-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -68.696289 Database has 3 sequences with 728 residues. gzip -f 1fnhA/T0107-1fnhA-local.pw.a2m make 1fnhA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/1fnhA-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1f/1fnhA/nostruct-align/1fnhA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1f/1fnhA/nostruct-align/1fnhA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1f/1fnhA/nostruct-align/1fnhA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18871/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -123.233948 Database has 3 sequences with 728 residues. gzip -f 1fnhA/1fnhA-T0107-local.pw.a2m make 1fnhA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/T0107-1fnhA-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -63.813953 Database has 3 sequences with 728 residues. gzip -f 1fnhA/T0107-1fnhA-vit.pw.a2m make 1fnhA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/1fnhA-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1f/1fnhA/nostruct-align/1fnhA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1f/1fnhA/nostruct-align/1fnhA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1f/1fnhA/nostruct-align/1fnhA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18871/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -119.107948 Database has 3 sequences with 728 residues. gzip -f 1fnhA/1fnhA-T0107-vit.pw.a2m make 1fnhA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/T0107-1fnhA-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -38.980030 Database has 3 sequences with 728 residues. gzip -f 1fnhA/T0107-1fnhA-global.pw.a2m make 1fnhA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/1fnhA-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1f/1fnhA/nostruct-align/1fnhA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1f/1fnhA/nostruct-align/1fnhA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1f/1fnhA/nostruct-align/1fnhA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18871/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -121.220055 Database has 3 sequences with 728 residues. gzip -f 1fnhA/1fnhA-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fnhA/xxxx-1fnhA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cxlA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0107.t2k.2d.rdb T0107.t2k-2d.mod make 1cxlA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/T0107-1cxlA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1cxlA Error in locating FIM delete in 1cxlA . Average NLL-Simple NULL score: -55.632324 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/T0107-1cxlA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cxlA/xxxx-1cxlA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1taxA PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1taxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/T0107-1taxA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1taxA Error in locating FIM delete in 1taxA . Average NLL-Simple NULL score: -55.554279 Database has 3 sequences with 792 residues. gzip -f 1taxA/T0107-1taxA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1taxA/xxxx-1taxA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cfr PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1cfr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/T0107-1cfr-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1cfr Error in locating FIM delete in 1cfr . Average NLL-Simple NULL score: -55.819233 Database has 3 sequences with 756 residues. gzip -f 1cfr/T0107-1cfr-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cfr/xxxx-1cfr-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1vpsA PRED2=1v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1vpsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/T0107-1vpsA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1vpsA Error in locating FIM delete in 1vpsA . Average NLL-Simple NULL score: -53.926899 Database has 3 sequences with 762 residues. gzip -f 1vpsA/T0107-1vpsA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1vpsA/xxxx-1vpsA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1aszB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1aszB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/T0107-1aszB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1aszB Error in locating FIM delete in 1aszB . Average NLL-Simple NULL score: -56.255939 Database has 3 sequences with 1168 residues. gzip -f 1aszB/T0107-1aszB-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aszB/xxxx-1aszB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1asyA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1asyA/struct-align/1asyA.fssp-w0.5.mod', needed by `1asyA/1asyA-T0107-fssp-global.pw.a2m.gz'. make 1asyA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/T0107-1asyA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1asyA Error in locating FIM delete in 1asyA . Average NLL-Simple NULL score: -55.826580 Database has 3 sequences with 1168 residues. gzip -f 1asyA/T0107-1asyA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1asyA/xxxx-1asyA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1b8aA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1b8aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/T0107-1b8aA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1b8aA Error in locating FIM delete in 1b8aA . Average NLL-Simple NULL score: -55.830402 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/T0107-1b8aA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b8aA/xxxx-1b8aA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1eerB PRED2=1e joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1eerB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/T0107-1eerB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1eerB Error in locating FIM delete in 1eerB . Average NLL-Simple NULL score: -54.944611 Database has 3 sequences with 628 residues. gzip -f 1eerB/T0107-1eerB-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eerB/xxxx-1eerB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1lylA PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1lylA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/T0107-1lylA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1lylA Error in locating FIM delete in 1lylA . Average NLL-Simple NULL score: -55.794720 Database has 3 sequences with 1174 residues. gzip -f 1lylA/T0107-1lylA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lylA/xxxx-1lylA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1fnhA PRED2=1f joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1fnhA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/T0107-1fnhA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1fnhA Error in locating FIM delete in 1fnhA . Average NLL-Simple NULL score: -54.191608 Database has 3 sequences with 728 residues. gzip -f 1fnhA/T0107-1fnhA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fnhA/xxxx-1fnhA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cxlA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1cxlA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/T0107-1cxlA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.632324 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/T0107-1cxlA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cxlA/xxxx-1cxlA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1taxA PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1taxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/T0107-1taxA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.554279 Database has 3 sequences with 792 residues. gzip -f 1taxA/T0107-1taxA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1taxA/xxxx-1taxA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cfr PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1cfr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/T0107-1cfr-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.819233 Database has 3 sequences with 756 residues. gzip -f 1cfr/T0107-1cfr-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cfr/xxxx-1cfr-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1vpsA PRED2=1v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1vpsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/T0107-1vpsA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.926899 Database has 3 sequences with 762 residues. gzip -f 1vpsA/T0107-1vpsA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1vpsA/xxxx-1vpsA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1aszB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1aszB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/T0107-1aszB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.255939 Database has 3 sequences with 1168 residues. gzip -f 1aszB/T0107-1aszB-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aszB/xxxx-1aszB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1asyA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1asyA/struct-align/1asyA.fssp-w0.5.mod', needed by `1asyA/1asyA-T0107-fssp-global.pw.a2m.gz'. make 1asyA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/T0107-1asyA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.826580 Database has 3 sequences with 1168 residues. gzip -f 1asyA/T0107-1asyA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1asyA/xxxx-1asyA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1b8aA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1b8aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/T0107-1b8aA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.830402 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/T0107-1b8aA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b8aA/xxxx-1b8aA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1eerB PRED2=1e joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1eerB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/T0107-1eerB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -54.944611 Database has 3 sequences with 628 residues. gzip -f 1eerB/T0107-1eerB-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eerB/xxxx-1eerB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1lylA PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1lylA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/T0107-1lylA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.794720 Database has 3 sequences with 1174 residues. gzip -f 1lylA/T0107-1lylA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lylA/xxxx-1lylA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1fnhA PRED2=1f joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1fnhA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/T0107-1fnhA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -54.191608 Database has 3 sequences with 728 residues. gzip -f 1fnhA/T0107-1fnhA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fnhA/xxxx-1fnhA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cxlA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1cxlA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/T0107-1cxlA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.632324 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/T0107-1cxlA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cxlA/xxxx-1cxlA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1taxA PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1taxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/T0107-1taxA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.554279 Database has 3 sequences with 792 residues. gzip -f 1taxA/T0107-1taxA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1taxA/xxxx-1taxA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cfr PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1cfr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/T0107-1cfr-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.819233 Database has 3 sequences with 756 residues. gzip -f 1cfr/T0107-1cfr-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cfr/xxxx-1cfr-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1vpsA PRED2=1v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1vpsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/T0107-1vpsA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.926899 Database has 3 sequences with 762 residues. gzip -f 1vpsA/T0107-1vpsA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1vpsA/xxxx-1vpsA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1aszB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1aszB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/T0107-1aszB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.255939 Database has 3 sequences with 1168 residues. gzip -f 1aszB/T0107-1aszB-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aszB/xxxx-1aszB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1asyA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1asyA/struct-align/1asyA.fssp-w0.5.mod', needed by `1asyA/1asyA-T0107-fssp-global.pw.a2m.gz'. make 1asyA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/T0107-1asyA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.826580 Database has 3 sequences with 1168 residues. gzip -f 1asyA/T0107-1asyA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1asyA/xxxx-1asyA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1b8aA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1b8aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/T0107-1b8aA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.830402 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/T0107-1b8aA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b8aA/xxxx-1b8aA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1eerB PRED2=1e joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1eerB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/T0107-1eerB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -54.944611 Database has 3 sequences with 628 residues. gzip -f 1eerB/T0107-1eerB-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eerB/xxxx-1eerB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1lylA PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1lylA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/T0107-1lylA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.794720 Database has 3 sequences with 1174 residues. gzip -f 1lylA/T0107-1lylA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lylA/xxxx-1lylA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1fnhA PRED2=1f joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1fnhA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/T0107-1fnhA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -54.191608 Database has 3 sequences with 728 residues. gzip -f 1fnhA/T0107-1fnhA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fnhA/xxxx-1fnhA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cxlA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1cxlA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/T0107-1cxlA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 13128.643555 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/T0107-1cxlA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cxlA/xxxx-1cxlA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1taxA PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1taxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/T0107-1taxA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 2962.221680 Database has 3 sequences with 792 residues. gzip -f 1taxA/T0107-1taxA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1taxA/xxxx-1taxA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cfr PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1cfr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/T0107-1cfr-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 2565.813721 Database has 3 sequences with 756 residues. gzip -f 1cfr/T0107-1cfr-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cfr/xxxx-1cfr-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1vpsA PRED2=1v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1vpsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/T0107-1vpsA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 2539.993408 Database has 3 sequences with 762 residues. gzip -f 1vpsA/T0107-1vpsA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1vpsA/xxxx-1vpsA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1aszB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1aszB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/T0107-1aszB-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 7906.126465 Database has 3 sequences with 1168 residues. gzip -f 1aszB/T0107-1aszB-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aszB/xxxx-1aszB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1asyA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1asyA/struct-align/1asyA.fssp-w0.5.mod', needed by `1asyA/1asyA-T0107-fssp-global.pw.a2m.gz'. make 1asyA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/T0107-1asyA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 7907.178223 Database has 3 sequences with 1168 residues. gzip -f 1asyA/T0107-1asyA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1asyA/xxxx-1asyA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1b8aA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1b8aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/T0107-1b8aA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 6540.876953 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/T0107-1b8aA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b8aA/xxxx-1b8aA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1eerB PRED2=1e joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1eerB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/T0107-1eerB-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 636.338196 Database has 3 sequences with 628 residues. gzip -f 1eerB/T0107-1eerB-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eerB/xxxx-1eerB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1lylA PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1lylA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/T0107-1lylA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 7690.217285 Database has 3 sequences with 1174 residues. gzip -f 1lylA/T0107-1lylA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lylA/xxxx-1lylA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1fnhA PRED2=1f joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1fnhA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/T0107-1fnhA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 2121.482666 Database has 3 sequences with 728 residues. gzip -f 1fnhA/T0107-1fnhA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fnhA/xxxx-1fnhA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cxlA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1cxlA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/T0107-1cxlA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7466.712891 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/T0107-1cxlA-2track-local.pw.a2m make 1cxlA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cxlA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cxlA/T0107-1cxlA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cxlA/info/1cxlA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7378.439453 Database has 3 sequences with 1560 residues. gzip -f 1cxlA/T0107-1cxlA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cxlA/xxxx-1cxlA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1taxA PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1taxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/T0107-1taxA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7421.972168 Database has 3 sequences with 792 residues. gzip -f 1taxA/T0107-1taxA-2track-local.pw.a2m make 1taxA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1taxA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1taxA/T0107-1taxA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1taxA/info/1taxA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7415.528809 Database has 3 sequences with 792 residues. gzip -f 1taxA/T0107-1taxA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1taxA/xxxx-1taxA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cfr PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1cfr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/T0107-1cfr-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7403.771973 Database has 3 sequences with 756 residues. gzip -f 1cfr/T0107-1cfr-2track-local.pw.a2m make 1cfr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1cfr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1cfr/T0107-1cfr-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cfr/info/1cfr.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7398.794434 Database has 3 sequences with 756 residues. gzip -f 1cfr/T0107-1cfr-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cfr/xxxx-1cfr-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1vpsA PRED2=1v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1vpsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/T0107-1vpsA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7465.096191 Database has 3 sequences with 762 residues. gzip -f 1vpsA/T0107-1vpsA-2track-local.pw.a2m make 1vpsA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1vpsA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1vpsA/T0107-1vpsA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.seq,/projects/compbio/experiments/models.97/pdb/1v/1vpsA/info/1vpsA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7455.290527 Database has 3 sequences with 762 residues. gzip -f 1vpsA/T0107-1vpsA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1vpsA/xxxx-1vpsA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1aszB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1aszB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/T0107-1aszB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7456.342285 Database has 3 sequences with 1168 residues. gzip -f 1aszB/T0107-1aszB-2track-local.pw.a2m make 1aszB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1aszB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1aszB/T0107-1aszB-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1aszB/info/1aszB.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7420.991699 Database has 3 sequences with 1168 residues. gzip -f 1aszB/T0107-1aszB-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aszB/xxxx-1aszB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1asyA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1asyA/struct-align/1asyA.fssp-w0.5.mod', needed by `1asyA/1asyA-T0107-fssp-global.pw.a2m.gz'. make 1asyA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/T0107-1asyA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7454.373047 Database has 3 sequences with 1168 residues. gzip -f 1asyA/T0107-1asyA-2track-local.pw.a2m make 1asyA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1asyA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1asyA/T0107-1asyA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1asyA/info/1asyA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7419.032715 Database has 3 sequences with 1168 residues. gzip -f 1asyA/T0107-1asyA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1asyA/xxxx-1asyA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1b8aA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1b8aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/T0107-1b8aA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7440.184082 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/T0107-1b8aA-2track-local.pw.a2m make 1b8aA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1b8aA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1b8aA/T0107-1b8aA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8aA/info/1b8aA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7416.324707 Database has 3 sequences with 1064 residues. gzip -f 1b8aA/T0107-1b8aA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b8aA/xxxx-1b8aA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1eerB PRED2=1e joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1eerB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/T0107-1eerB-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7460.134766 Database has 3 sequences with 628 residues. gzip -f 1eerB/T0107-1eerB-2track-local.pw.a2m make 1eerB make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1eerB' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1eerB/T0107-1eerB-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1eerB/info/1eerB.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7456.382324 Database has 3 sequences with 628 residues. gzip -f 1eerB/T0107-1eerB-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eerB/xxxx-1eerB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1lylA PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1lylA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/T0107-1lylA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7447.760254 Database has 3 sequences with 1174 residues. gzip -f 1lylA/T0107-1lylA-2track-local.pw.a2m make 1lylA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1lylA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1lylA/T0107-1lylA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.seq,/projects/compbio/experiments/models.97/pdb/1l/1lylA/info/1lylA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7407.286621 Database has 3 sequences with 1174 residues. gzip -f 1lylA/T0107-1lylA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lylA/xxxx-1lylA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1fnhA PRED2=1f joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make 1fnhA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/T0107-1fnhA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7474.460449 Database has 3 sequences with 728 residues. gzip -f 1fnhA/T0107-1fnhA-2track-local.pw.a2m make 1fnhA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[2]: `1fnhA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' hmmscore 1fnhA/T0107-1fnhA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.seq,/projects/compbio/experiments/models.97/pdb/1f/1fnhA/info/1fnhA.stride.2d \ -fim_method_score 5 -insert_method_score 5 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. T0107.t2k-2d.mod(1151): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb FIM_method 5 (the generic node) not available in model. Tables not modified. Insert_method 5 (the generic node) not available in model. Tables not modified. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -7463.312500 Database has 3 sequences with 728 residues. gzip -f 1fnhA/T0107-1fnhA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fnhA/xxxx-1fnhA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cxlA PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cxlA/xxxx-1cxlA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1taxA PRED2=1t joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1taxA/xxxx-1taxA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cfr PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cfr/xxxx-1cfr-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1vpsA PRED2=1v joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1vpsA/xxxx-1vpsA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1aszB PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aszB/xxxx-1aszB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1asyA PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1asyA/struct-align/1asyA.fssp-w0.5.mod', needed by `1asyA/1asyA-T0107-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1asyA/xxxx-1asyA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1b8aA PRED2=1b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b8aA/xxxx-1b8aA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1eerB PRED2=1e joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eerB/xxxx-1eerB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1lylA PRED2=1l joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lylA/xxxx-1lylA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1fnhA PRED2=1f joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fnhA/xxxx-1fnhA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1nkr PRED2=1n joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nkr/xxxx-1nkr-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1pvc3 PRED2=1p joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1p/1pvc3/struct-align/1pvc3.fssp-w0.5.mod', needed by `1pvc3/1pvc3-T0107-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1pvc3/xxxx-1pvc3-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1axkA PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make 1axkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' mkdir 1axkA fixmode 1axkA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1axkA/1axkA-T0107-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1axkA/struct-align/1axkA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-27149/tmp.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -273.790680 Database has 3 sequences with 975 residues. gzip -f 1axkA/1axkA-T0107-fssp-global.pw.a2m make 1axkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1axkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1axkA/T0107-1axkA-local.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -70.339203 Database has 3 sequences with 975 residues. gzip -f 1axkA/T0107-1axkA-local.pw.a2m make 1axkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1axkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1axkA/1axkA-T0107-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26573/tmp.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -248.604233 Database has 3 sequences with 975 residues. gzip -f 1axkA/1axkA-T0107-local.pw.a2m make 1axkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1axkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1axkA/T0107-1axkA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1157): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.509815 Database has 3 sequences with 975 residues. gzip -f 1axkA/T0107-1axkA-2track-local.pw.a2m make 1axkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1axkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1axkA/T0107-1axkA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0107.t2k-w0.5.mod,T0107.t2k-2d.mod \ -db T0107.seq,T0107.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0107.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m T0107.t2k-2d.mod(1157): Reading track 1 model from MODEL -- Model from 2nd structure file T0107.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 19.069651 Database has 3 sequences with 975 residues. gzip -f 1axkA/T0107-1axkA-2track-global.pw.a2m make 1axkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1axkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1axkA/T0107-1axkA-vit.pw \ -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -65.425201 Database has 3 sequences with 975 residues. gzip -f 1axkA/T0107-1axkA-vit.pw.a2m make 1axkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1axkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1axkA/1axkA-T0107-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26573/tmp.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -245.032532 Database has 3 sequences with 975 residues. gzip -f 1axkA/1axkA-T0107-vit.pw.a2m make 1axkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1axkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1axkA/T0107-1axkA-global.pw -i T0107.t2k-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0107.t2k-w0.5.mod T0107.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6410/tmp.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -27.969412 Database has 3 sequences with 975 residues. gzip -f 1axkA/T0107-1axkA-global.pw.a2m make 1axkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t107' make[2]: `1axkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' hmmscore 1axkA/1axkA-T0107-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod -db T0107.seq -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1axkA/info/1axkA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1axkA/nostruct-align/1axkA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26573/tmp.a2m SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -245.461731 Database has 3 sequences with 975 residues. gzip -f 1axkA/1axkA-T0107-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cxlA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cxlA/xxxx-1cxlA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1taxA PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1taxA/xxxx-1taxA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1cfr PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1cfr/xxxx-1cfr-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1vpsA PRED2=1v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1vpsA/xxxx-1vpsA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1aszB PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1aszB/xxxx-1aszB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1asyA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1a/1asyA/struct-align/1asyA.fssp-w0.5.mod', needed by `1asyA/1asyA-T0107-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1asyA/xxxx-1asyA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1b8aA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b8aA/xxxx-1b8aA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1eerB PRED2=1e joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eerB/xxxx-1eerB-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1lylA PRED2=1l joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1lylA/xxxx-1lylA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1fnhA PRED2=1f joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1fnhA/xxxx-1fnhA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1nkr PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nkr/xxxx-1nkr-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1pvc3 PRED2=1p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1p/1pvc3/struct-align/1pvc3.fssp-w0.5.mod', needed by `1pvc3/1pvc3-T0107-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1pvc3/xxxx-1pvc3-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=1axkA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1axkA/xxxx-1axkA-T0107-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' make: [joints] Error 2 (ignored) make -k PRED=2nlrA PRED2=2n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2n/2nlrA/struct-align/2nlrA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/2n/2nlrA/struct-align/2nlrA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22599 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22599/tmp -alignfile /projects/compbio/experiments/models.97/pdb/2n/2nlrA/struct-align/2nlrA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/2n/2nlrA/struct-align/2nlrA.fssp.a2m.gz (3 sequences, 222 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22599/tmp.a2m. Dropping 1 (of 3) sequences with > 80.0% id 2 sequences left after dropping 1 of 3 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22599/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22599/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22599/tmp.a2m (2 sequences, 222 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22599/tmp.mod /projects/compbio/experiments/models.97/pdb/2n/2nlrA/struct-align/2nlrA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-22599 80.0% id 1 sequences left after dropping 21 of 22 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-moo-30825/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-moo-30825/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-moo-30825/tmp.a2m (1 sequences, 225 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-moo-30825/tmp.mod /projects/compbio/experiments/models.97/pdb/1e/1ema/struct-align/1ema.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-moo-30825