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-local.pw -i /projects/compbio/experiments/models.97/pdb/1s/1snc/nostruct-align/1snc.t99-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 /projects/compbio/experiments/models.97/pdb/1s/1snc/nostruct-align/1snc.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1snc/nostruct-align/1snc.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31072/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -74.345833 Database has 3 sequences with 393 residues. gzip -f 1snc/1snc-T0091-local.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/1snc-T0091-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1s/1snc/nostruct-align/1snc.t99-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 /projects/compbio/experiments/models.97/pdb/1s/1snc/nostruct-align/1snc.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1snc/nostruct-align/1snc.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31072/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -70.989510 Database has 3 sequences with 393 residues. gzip -f 1snc/1snc-T0091-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/1snc-T0091-global.pw -i /projects/compbio/experiments/models.97/pdb/1s/1snc/nostruct-align/1snc.t99-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/nostruct-align/1snc.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1s/1snc/nostruct-align/1snc.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31072/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -65.216339 Database has 3 sequences with 393 residues. gzip -f 1snc/1snc-T0091-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-local.pw -i /projects/compbio/experiments/models.97/pdb/1n/1ng1/nostruct-align/1ng1.t99-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 /projects/compbio/experiments/models.97/pdb/1n/1ng1/nostruct-align/1ng1.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1ng1/nostruct-align/1ng1.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18008/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -156.388870 Database has 3 sequences with 697 residues. gzip -f 1ng1/1ng1-T0091-local.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 1ng1/1ng1-T0091-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1n/1ng1/nostruct-align/1ng1.t99-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 /projects/compbio/experiments/models.97/pdb/1n/1ng1/nostruct-align/1ng1.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1ng1/nostruct-align/1ng1.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18008/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -153.706833 Database has 3 sequences with 697 residues. gzip -f 1ng1/1ng1-T0091-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 1ng1/1ng1-T0091-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1ng1/nostruct-align/1ng1.t99-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/nostruct-align/1ng1.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1ng1/nostruct-align/1ng1.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-18008/tmp.a2m SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. Warning: First model node is not a FIM but null model probabilities are being taken from it anyway. Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -153.179718 Database has 3 sequences with 697 residues. gzip -f 1ng1/1ng1-T0091-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[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) make -k PRED=1snc PRED2=1s joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t91' /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0091.t2k.2d.rdb T0091.t2k-2d.mod 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-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.657501 Database has 3 sequences with 393 residues. gzip -f 1snc/T0091-1snc-2track-local.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/T0091-1ng1-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.120483 Database has 3 sequences with 697 residues. gzip -f 1ng1/T0091-1ng1-2track-local.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/T0091-1sesA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -46.037476 Database has 3 sequences with 951 residues. gzip -f 1sesA/T0091-1sesA-2track-local.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) 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/T0091-1snc-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.657501 Database has 3 sequences with 393 residues. gzip -f 1snc/T0091-1snc-2track-local.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/T0091-1ng1-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.120483 Database has 3 sequences with 697 residues. gzip -f 1ng1/T0091-1ng1-2track-local.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/T0091-1sesA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -46.037476 Database has 3 sequences with 951 residues. gzip -f 1sesA/T0091-1sesA-2track-local.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) 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/T0091-1snc-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.657501 Database has 3 sequences with 393 residues. gzip -f 1snc/T0091-1snc-2track-local.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/T0091-1ng1-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -43.120483 Database has 3 sequences with 697 residues. gzip -f 1ng1/T0091-1ng1-2track-local.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/T0091-1sesA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -46.037476 Database has 3 sequences with 951 residues. gzip -f 1sesA/T0091-1sesA-2track-local.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) 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/T0091-1snc-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.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. T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 807.327332 Database has 3 sequences with 393 residues. gzip -f 1snc/T0091-1snc-2track-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/T0091-1ng1-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.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. T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 4867.596191 Database has 3 sequences with 697 residues. gzip -f 1ng1/T0091-1ng1-2track-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/T0091-1sesA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.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. T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 8215.553711 Database has 3 sequences with 951 residues. gzip -f 1sesA/T0091-1sesA-2track-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) 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/T0091-1snc-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.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 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz 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. T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.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: -4283.187012 Database has 3 sequences with 393 residues. gzip -f 1snc/T0091-1snc-2track-local.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-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1snc/info/1snc.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. T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz 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. T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.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: -4275.109863 Database has 3 sequences with 393 residues. gzip -f 1snc/T0091-1snc-2track-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/T0091-1ng1-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.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 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz 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. T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.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: -4327.898926 Database has 3 sequences with 697 residues. gzip -f 1ng1/T0091-1ng1-2track-local.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/T0091-1ng1-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1ng1/info/1ng1.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. T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz 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. T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.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: -4304.634766 Database has 3 sequences with 697 residues. gzip -f 1ng1/T0091-1ng1-2track-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/T0091-1sesA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.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 T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz 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. T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.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: -4334.672852 Database has 3 sequences with 951 residues. gzip -f 1sesA/T0091-1sesA-2track-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-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0091.t2k-w0.5.mod,T0091.t2k-2d.mod \ -db T0091.seq,T0091.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1sesA/info/1sesA.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. T0091.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file T0091.t2k.a2m.gz 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. T0091.t2k-2d.mod(677): Reading track 1 model from MODEL -- Model from 2nd structure file T0091.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: -4287.300293 Database has 3 sequences with 951 residues. gzip -f 1sesA/T0091-1sesA-2track-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)