make -k PRED=1snc PRED2=1s joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp-w0.5.mod Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp.a2m.gz (41 sequences, 135 columns) as A2M alignment. make 1snc make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' mkdir 1snc fixmode 1snc make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1snc/1snc-T0091-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -163.016022 Database has 2 sequences with 258 residues. gzip -f 1snc/1snc-T0091-fssp-global.pw.a2m /projects/compbio/experiments/models.97/scripts/w0.5 T0091.t2k.a2m.gz T0091.t2k-w0.5.mod Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file T0091.t2k.a2m.gz (30 sequences, 109 columns) as A2M alignment. make 1snc make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1snc' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1snc/T0091-1snc-local.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -69.313362 Database has 2 sequences with 258 residues. gzip -f 1snc/T0091-1snc-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1snc/nostruct-align/1snc.t2k-w0.5.mod', needed by `1snc/1snc-T0091-local.pw.a2m.gz'. make 1snc make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1snc' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1snc/T0091-1snc-vit.pw \ -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -66.888870 Database has 2 sequences with 258 residues. gzip -f 1snc/T0091-1snc-vit.pw.a2m make 1snc make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1snc' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1snc/T0091-1snc-global.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -111.647034 Database has 2 sequences with 258 residues. gzip -f 1snc/T0091-1snc-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1snc/xxxx-1snc-T0091-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' make: [joints] Error 2 (ignored) make -k PRED=1ng1 PRED2=1n joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' /projects/compbio/experiments/models.97/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp-w0.5.mod Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp.a2m.gz (22 sequences, 294 columns) as A2M alignment. make 1ng1 make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' mkdir 1ng1 fixmode 1ng1 make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1ng1/1ng1-T0091-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -281.929535 Database has 2 sequences with 403 residues. gzip -f 1ng1/1ng1-T0091-fssp-global.pw.a2m make 1ng1 make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1ng1' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1ng1/T0091-1ng1-local.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -66.378548 Database has 2 sequences with 403 residues. gzip -f 1ng1/T0091-1ng1-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1n/1ng1/nostruct-align/1ng1.t2k-w0.5.mod', needed by `1ng1/1ng1-T0091-local.pw.a2m.gz'. make 1ng1 make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1ng1' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1ng1/T0091-1ng1-vit.pw \ -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -62.637039 Database has 2 sequences with 403 residues. gzip -f 1ng1/T0091-1ng1-vit.pw.a2m make 1ng1 make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1ng1' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1ng1/T0091-1ng1-global.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -126.363525 Database has 2 sequences with 403 residues. gzip -f 1ng1/T0091-1ng1-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ng1/xxxx-1ng1-T0091-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' make: [joints] Error 2 (ignored) make -k PRED=1sesA PRED2=1s joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' mkdir 1sesA fixmode 1sesA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/1sesA-T0091-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -287.610046 Database has 2 sequences with 530 residues. gzip -f 1sesA/1sesA-T0091-fssp-global.pw.a2m make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/T0091-1sesA-local.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -67.887581 Database has 2 sequences with 530 residues. gzip -f 1sesA/T0091-1sesA-local.pw.a2m make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/1sesA-T0091-local.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -186.699081 Database has 2 sequences with 530 residues. gzip -f 1sesA/1sesA-T0091-local.pw.a2m make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/T0091-1sesA-vit.pw \ -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -63.645584 Database has 2 sequences with 530 residues. gzip -f 1sesA/T0091-1sesA-vit.pw.a2m make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/1sesA-T0091-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -183.224091 Database has 2 sequences with 530 residues. gzip -f 1sesA/1sesA-T0091-vit.pw.a2m make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/T0091-1sesA-global.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -140.259033 Database has 2 sequences with 530 residues. gzip -f 1sesA/T0091-1sesA-global.pw.a2m make 1sesA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/1sesA-T0091-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -279.968536 Database has 2 sequences with 530 residues. gzip -f 1sesA/1sesA-T0091-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sesA/xxxx-1sesA-T0091-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t91' make: [joints] Error 2 (ignored) make -k PRED=1snc PRED2=1s joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make 1snc make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1snc' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1snc/1snc-T0091-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1snc/struct-align/1snc.fssp.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -202.653687 Database has 3 sequences with 393 residues. gzip -f 1snc/1snc-T0091-fssp-global.pw.a2m make 1snc make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1snc' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1snc/T0091-1snc-local.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -51.675491 Database has 3 sequences with 393 residues. gzip -f 1snc/T0091-1snc-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1s/1snc/nostruct-align/1snc.t2k-w0.5.mod', needed by `1snc/1snc-T0091-local.pw.a2m.gz'. make 1snc make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1snc' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1snc/T0091-1snc-vit.pw \ -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -48.827496 Database has 3 sequences with 393 residues. gzip -f 1snc/T0091-1snc-vit.pw.a2m make 1snc make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1snc' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1snc/T0091-1snc-global.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -90.567024 Database has 3 sequences with 393 residues. gzip -f 1snc/T0091-1snc-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1snc/xxxx-1snc-T0091-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' make: [joints] Error 2 (ignored) make -k PRED=1ng1 PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make 1ng1 make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1ng1' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1ng1/1ng1-T0091-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1n/1ng1/struct-align/1ng1.fssp.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -363.939056 Database has 3 sequences with 697 residues. gzip -f 1ng1/1ng1-T0091-fssp-global.pw.a2m make 1ng1 make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1ng1' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1ng1/T0091-1ng1-local.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.735844 Database has 3 sequences with 697 residues. gzip -f 1ng1/T0091-1ng1-local.pw.a2m make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1n/1ng1/nostruct-align/1ng1.t2k-w0.5.mod', needed by `1ng1/1ng1-T0091-local.pw.a2m.gz'. make 1ng1 make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1ng1' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1ng1/T0091-1ng1-vit.pw \ -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.125500 Database has 3 sequences with 697 residues. gzip -f 1ng1/T0091-1ng1-vit.pw.a2m make 1ng1 make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1ng1' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1ng1/T0091-1ng1-global.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -111.287025 Database has 3 sequences with 697 residues. gzip -f 1ng1/T0091-1ng1-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ng1/xxxx-1ng1-T0091-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' make: [joints] Error 2 (ignored) make -k PRED=1sesA PRED2=1s joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/1sesA-T0091-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/struct-align/1sesA.fssp.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -387.514069 Database has 3 sequences with 951 residues. gzip -f 1sesA/1sesA-T0091-fssp-global.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/T0091-1sesA-local.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -49.747890 Database has 3 sequences with 951 residues. gzip -f 1sesA/T0091-1sesA-local.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/1sesA-T0091-local.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -244.477539 Database has 3 sequences with 951 residues. gzip -f 1sesA/1sesA-T0091-local.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/T0091-1sesA-vit.pw \ -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -44.470226 Database has 3 sequences with 951 residues. gzip -f 1sesA/T0091-1sesA-vit.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/1sesA-T0091-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -241.696899 Database has 3 sequences with 951 residues. gzip -f 1sesA/1sesA-T0091-vit.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/T0091-1sesA-global.pw -i T0091.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0091.t2k-w0.5.mod T0091.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file T0091.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -129.814377 Database has 3 sequences with 951 residues. gzip -f 1sesA/T0091-1sesA-global.pw.a2m make 1sesA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t91' make[2]: `1sesA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' hmmscore 1sesA/1sesA-T0091-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod -db T0091.seq -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/experiments/models.97/pdb/1s/1sesA/nostruct-align/1sesA.t2k.a2m.gz SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -367.185059 Database has 3 sequences with 951 residues. gzip -f 1sesA/1sesA-T0091-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1sesA/xxxx-1sesA-T0091-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t91' make: [joints] Error 2 (ignored)