make -k PRED=2hsdA PRED2=2h joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2h/2hsdA/struct-align/2hsdA.fssp-w0.5.mod', needed by `2hsdA/2hsdA-T0113-fssp-global.pw.a2m.gz'. gzip -f T0113.t2k.a2m /projects/compbio/bin/scripts/w0.5 T0113.t2k.a2m.gz T0113.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp -alignfile T0113.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 T0113.t2k.a2m.gz (1357 sequences, 261 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m. Dropping 39 (of 1357) duplicate sequences with differing IDs Dropping 541 (of 1357) sequences with > 80.0% id 777 sequences left after dropping 580 of 1357 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-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-alpha-16177/tmp.a2m (777 sequences, 261 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.mod T0113.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 2hsdA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t113' mkdir 2hsdA fixmode 2hsdA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/T0113-2hsdA-local.pw -i T0113.t2k-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0113.t2k-w0.5.mod T0113.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -180.115921 Database has 3 sequences with 767 residues. gzip -f 2hsdA/T0113-2hsdA-local.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99.a2m.gz /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-alpha-26135 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-alpha-26135/tmp -alignfile /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99.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/2h/2hsdA/nostruct-align/2hsdA.t99.a2m.gz (1574 sequences, 253 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-alpha-26135/tmp.a2m. Dropping 21 (of 1574) duplicate sequences with differing IDs Dropping 657 (of 1574) sequences with > 80.0% id 896 sequences left after dropping 678 of 1574 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-alpha-26135/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-alpha-26135/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-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-alpha-26135/tmp.a2m (896 sequences, 253 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-alpha-26135/tmp.mod /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 2hsdA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/2hsdA-T0113-local.pw -i /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26135/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -173.042618 Database has 3 sequences with 767 residues. gzip -f 2hsdA/2hsdA-T0113-local.pw.a2m make 2hsdA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/T0113-2hsdA-vit.pw \ -i T0113.t2k-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0113.t2k-w0.5.mod T0113.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -177.067932 Database has 3 sequences with 767 residues. gzip -f 2hsdA/T0113-2hsdA-vit.pw.a2m make 2hsdA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/2hsdA-T0113-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26135/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -169.417618 Database has 3 sequences with 767 residues. gzip -f 2hsdA/2hsdA-T0113-vit.pw.a2m make 2hsdA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/T0113-2hsdA-global.pw -i T0113.t2k-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0113.t2k-w0.5.mod T0113.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/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: -177.371353 Database has 3 sequences with 767 residues. gzip -f 2hsdA/T0113-2hsdA-global.pw.a2m make 2hsdA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/2hsdA-T0113-global.pw -i /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2h/2hsdA/nostruct-align/2hsdA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26135/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: -172.370346 Database has 3 sequences with 767 residues. gzip -f 2hsdA/2hsdA-T0113-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2hsdA/xxxx-2hsdA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=2hsdA PRED2=2h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2h/2hsdA/struct-align/2hsdA.fssp-w0.5.mod', needed by `2hsdA/2hsdA-T0113-fssp-global.pw.a2m.gz'. /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0113.t2k.2d.rdb T0113.t2k-2d.mod make 2hsdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/T0113-2hsdA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m T0113.t2k-2d.mod(1589): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 2hsdA Error in locating FIM delete in 2hsdA . Average NLL-Simple NULL score: -167.991776 Database has 3 sequences with 767 residues. gzip -f 2hsdA/T0113-2hsdA-2track-local.pw.a2m make[1]: *** No rule to make target ` ', needed by `joint'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=1hdcA PRED2=1h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1h/1hdcA/struct-align/1hdcA.fssp-w0.5.mod', needed by `1hdcA/1hdcA-T0113-fssp-global.pw.a2m.gz'. make 1hdcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `1hdcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 1hdcA/T0113-1hdcA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m T0113.t2k-2d.mod(1589): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1hdcA Error in locating FIM delete in 1hdcA . Average NLL-Simple NULL score: -165.462433 Database has 3 sequences with 767 residues. gzip -f 1hdcA/T0113-1hdcA-2track-local.pw.a2m make[1]: *** No rule to make target ` ', needed by `joint'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=2hsdA PRED2=2h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2h/2hsdA/struct-align/2hsdA.fssp-w0.5.mod', needed by `2hsdA/2hsdA-T0113-fssp-global.pw.a2m.gz'. make 2hsdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/T0113-2hsdA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m T0113.t2k-2d.mod(1589): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 2hsdA Error in locating FIM delete in 2hsdA . Average NLL-Simple NULL score: -167.991776 Database has 3 sequences with 767 residues. gzip -f 2hsdA/T0113-2hsdA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2hsdA/xxxx-2hsdA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=1hdcA PRED2=1h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1h/1hdcA/struct-align/1hdcA.fssp-w0.5.mod', needed by `1hdcA/1hdcA-T0113-fssp-global.pw.a2m.gz'. make 1hdcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `1hdcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 1hdcA/T0113-1hdcA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m T0113.t2k-2d.mod(1589): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1hdcA Error in locating FIM delete in 1hdcA . Average NLL-Simple NULL score: -165.462433 Database has 3 sequences with 767 residues. gzip -f 1hdcA/T0113-1hdcA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hdcA/xxxx-1hdcA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=2hsdA PRED2=2h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2h/2hsdA/struct-align/2hsdA.fssp-w0.5.mod', needed by `2hsdA/2hsdA-T0113-fssp-global.pw.a2m.gz'. make 2hsdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/T0113-2hsdA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m T0113.t2k-2d.mod(1589): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -167.991776 Database has 3 sequences with 767 residues. gzip -f 2hsdA/T0113-2hsdA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2hsdA/xxxx-2hsdA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=1hdcA PRED2=1h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1h/1hdcA/struct-align/1hdcA.fssp-w0.5.mod', needed by `1hdcA/1hdcA-T0113-fssp-global.pw.a2m.gz'. make 1hdcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `1hdcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 1hdcA/T0113-1hdcA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m T0113.t2k-2d.mod(1589): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -165.462433 Database has 3 sequences with 767 residues. gzip -f 1hdcA/T0113-1hdcA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hdcA/xxxx-1hdcA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=2hsdA PRED2=2h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2h/2hsdA/struct-align/2hsdA.fssp-w0.5.mod', needed by `2hsdA/2hsdA-T0113-fssp-global.pw.a2m.gz'. make 2hsdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/T0113-2hsdA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m T0113.t2k-2d.mod(1589): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -167.991776 Database has 3 sequences with 767 residues. gzip -f 2hsdA/T0113-2hsdA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2hsdA/xxxx-2hsdA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=1hdcA PRED2=1h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1h/1hdcA/struct-align/1hdcA.fssp-w0.5.mod', needed by `1hdcA/1hdcA-T0113-fssp-global.pw.a2m.gz'. make 1hdcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `1hdcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 1hdcA/T0113-1hdcA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m T0113.t2k-2d.mod(1589): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -165.462433 Database has 3 sequences with 767 residues. gzip -f 1hdcA/T0113-1hdcA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hdcA/xxxx-1hdcA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=2hsdA PRED2=2h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2h/2hsdA/struct-align/2hsdA.fssp-w0.5.mod', needed by `2hsdA/2hsdA-T0113-fssp-global.pw.a2m.gz'. make 2hsdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/T0113-2hsdA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.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. T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m T0113.t2k-2d.mod(1589): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 28.576498 Database has 3 sequences with 767 residues. gzip -f 2hsdA/T0113-2hsdA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2hsdA/xxxx-2hsdA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=1hdcA PRED2=1h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1h/1hdcA/struct-align/1hdcA.fssp-w0.5.mod', needed by `1hdcA/1hdcA-T0113-fssp-global.pw.a2m.gz'. make 1hdcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `1hdcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 1hdcA/T0113-1hdcA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.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. T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/tmp.a2m T0113.t2k-2d.mod(1589): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 48.091797 Database has 3 sequences with 767 residues. gzip -f 1hdcA/T0113-1hdcA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hdcA/xxxx-1hdcA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=2hsdA PRED2=2h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2h/2hsdA/struct-align/2hsdA.fssp-w0.5.mod', needed by `2hsdA/2hsdA-T0113-fssp-global.pw.a2m.gz'. make 2hsdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/T0113-2hsdA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.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 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/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. T0113.t2k-2d.mod(1595): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -181.099075 Database has 3 sequences with 767 residues. gzip -f 2hsdA/T0113-2hsdA-2track-local.pw.a2m make 2hsdA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2hsdA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2hsdA/T0113-2hsdA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.stride.seq,/projects/compbio/experiments/models.97/pdb/2h/2hsdA/info/2hsdA.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. T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/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. T0113.t2k-2d.mod(1595): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -179.364182 Database has 3 sequences with 767 residues. gzip -f 2hsdA/T0113-2hsdA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2hsdA/xxxx-2hsdA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=1hdcA PRED2=1h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1h/1hdcA/struct-align/1hdcA.fssp-w0.5.mod', needed by `1hdcA/1hdcA-T0113-fssp-global.pw.a2m.gz'. make 1hdcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `1hdcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 1hdcA/T0113-1hdcA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.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 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/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. T0113.t2k-2d.mod(1595): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -179.943405 Database has 3 sequences with 767 residues. gzip -f 1hdcA/T0113-1hdcA-2track-local.pw.a2m make 1hdcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `1hdcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 1hdcA/T0113-1hdcA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1h/1hdcA/info/1hdcA.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. T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/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. T0113.t2k-2d.mod(1595): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -178.208542 Database has 3 sequences with 767 residues. gzip -f 1hdcA/T0113-1hdcA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hdcA/xxxx-1hdcA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=2hsdA PRED2=2h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2h/2hsdA/struct-align/2hsdA.fssp-w0.5.mod', needed by `2hsdA/2hsdA-T0113-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2hsdA/xxxx-2hsdA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=1hdcA PRED2=1h joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1h/1hdcA/struct-align/1hdcA.fssp-w0.5.mod', needed by `1hdcA/1hdcA-T0113-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1hdcA/xxxx-1hdcA-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored) make -k PRED=2ae2A PRED2=2a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/2a/2ae2A/struct-align/2ae2A.fssp-w0.5.mod', needed by `2ae2A/2ae2A-T0113-fssp-global.pw.a2m.gz'. make 2ae2A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' mkdir 2ae2A fixmode 2ae2A make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2ae2A/T0113-2ae2A-local.pw -i T0113.t2k-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0113.t2k-w0.5.mod T0113.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/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: -176.001022 Database has 3 sequences with 780 residues. gzip -f 2ae2A/T0113-2ae2A-local.pw.a2m make 2ae2A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2ae2A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2ae2A/2ae2A-T0113-local.pw -i /projects/compbio/experiments/models.97/pdb/2a/2ae2A/nostruct-align/2ae2A.t99-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2a/2ae2A/nostruct-align/2ae2A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2a/2ae2A/nostruct-align/2ae2A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19797/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: -177.024368 Database has 3 sequences with 780 residues. gzip -f 2ae2A/2ae2A-T0113-local.pw.a2m make 2ae2A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2ae2A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2ae2A/T0113-2ae2A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride.seq,/projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.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 T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/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. T0113.t2k-2d.mod(1595): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -180.279984 Database has 3 sequences with 780 residues. gzip -f 2ae2A/T0113-2ae2A-2track-local.pw.a2m make 2ae2A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2ae2A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2ae2A/T0113-2ae2A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0113.t2k-w0.5.mod,T0113.t2k-2d.mod \ -db T0113.seq,T0113.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride.seq,/projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.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. T0113.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/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. T0113.t2k-2d.mod(1595): Reading track 1 model from MODEL -- Model from 2nd structure file T0113.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -178.989334 Database has 3 sequences with 780 residues. gzip -f 2ae2A/T0113-2ae2A-2track-global.pw.a2m make 2ae2A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2ae2A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2ae2A/T0113-2ae2A-vit.pw \ -i T0113.t2k-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0113.t2k-w0.5.mod T0113.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/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: -172.242691 Database has 3 sequences with 780 residues. gzip -f 2ae2A/T0113-2ae2A-vit.pw.a2m make 2ae2A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2ae2A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2ae2A/2ae2A-T0113-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/2a/2ae2A/nostruct-align/2ae2A.t99-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2a/2ae2A/nostruct-align/2ae2A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2a/2ae2A/nostruct-align/2ae2A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19797/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: -172.299026 Database has 3 sequences with 780 residues. gzip -f 2ae2A/2ae2A-T0113-vit.pw.a2m make 2ae2A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2ae2A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2ae2A/T0113-2ae2A-global.pw -i T0113.t2k-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0113.t2k-w0.5.mod T0113.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-16177/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: -173.079025 Database has 3 sequences with 780 residues. gzip -f 2ae2A/T0113-2ae2A-global.pw.a2m make 2ae2A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t113' make[2]: `2ae2A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' hmmscore 2ae2A/2ae2A-T0113-global.pw -i /projects/compbio/experiments/models.97/pdb/2a/2ae2A/nostruct-align/2ae2A.t99-w0.5.mod -db T0113.seq -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2ae2A/info/2ae2A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/2a/2ae2A/nostruct-align/2ae2A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/2a/2ae2A/nostruct-align/2ae2A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-19797/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: -175.491379 Database has 3 sequences with 780 residues. gzip -f 2ae2A/2ae2A-T0113-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2ae2A/xxxx-2ae2A-T0113-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t113' make: [joints] Error 2 (ignored)