make -k PRED=1efcA PRED2=1e joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make 1efcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' mkdir 1efcA fixmode 1efcA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1efcA/T0095-1efcA-local.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1efcA/T0095-1efcA-local.pw.a2m make 1efcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1efcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1efcA/1efcA-T0095-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1efcA/nostruct-align/1efcA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1efcA/1efcA-T0095-local.pw.a2m make 1efcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1efcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1efcA/T0095-1efcA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1efcA/T0095-1efcA-2track-local.pw.a2m make 1efcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1efcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1efcA/T0095-1efcA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1efcA/T0095-1efcA-2track-global.pw.a2m make 1efcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1efcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1efcA/T0095-1efcA-vit.pw \ -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1efcA/T0095-1efcA-vit.pw.a2m make 1efcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1efcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1efcA/1efcA-T0095-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1e/1efcA/nostruct-align/1efcA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1efcA/1efcA-T0095-vit.pw.a2m make 1efcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1efcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1efcA/T0095-1efcA-global.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1efcA/T0095-1efcA-global.pw.a2m make 1efcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1efcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1efcA/1efcA-T0095-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1efcA/nostruct-align/1efcA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1efcA/1efcA-T0095-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1e/1efcA/struct-align/1efcA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1e/1efcA/struct-align/1efcA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1efcA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1efcA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1efcA/1efcA-T0095-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1efcA/struct-align/1efcA.fssp-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1efcA/info/1efcA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1efcA/1efcA-T0095-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' make -k PRED=1bjwA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make 1bjwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' mkdir 1bjwA fixmode 1bjwA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1bjwA/T0095-1bjwA-local.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bjwA/T0095-1bjwA-local.pw.a2m make 1bjwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1bjwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1bjwA/1bjwA-T0095-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bjwA/nostruct-align/1bjwA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bjwA/1bjwA-T0095-local.pw.a2m make 1bjwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1bjwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1bjwA/T0095-1bjwA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bjwA/T0095-1bjwA-2track-local.pw.a2m make 1bjwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1bjwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1bjwA/T0095-1bjwA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bjwA/T0095-1bjwA-2track-global.pw.a2m make 1bjwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1bjwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1bjwA/T0095-1bjwA-vit.pw \ -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bjwA/T0095-1bjwA-vit.pw.a2m make 1bjwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1bjwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1bjwA/1bjwA-T0095-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1bjwA/nostruct-align/1bjwA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bjwA/1bjwA-T0095-vit.pw.a2m make 1bjwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1bjwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1bjwA/T0095-1bjwA-global.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bjwA/T0095-1bjwA-global.pw.a2m make 1bjwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1bjwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1bjwA/1bjwA-T0095-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bjwA/nostruct-align/1bjwA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bjwA/1bjwA-T0095-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1bjwA/struct-align/1bjwA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1bjwA/struct-align/1bjwA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1bjwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1bjwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1bjwA/1bjwA-T0095-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bjwA/struct-align/1bjwA.fssp-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1bjwA/info/1bjwA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1bjwA/1bjwA-T0095-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' make -k PRED=1d2fA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make 1d2fA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' mkdir 1d2fA fixmode 1d2fA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1d2fA/T0095-1d2fA-local.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1d2fA/T0095-1d2fA-local.pw.a2m make 1d2fA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1d2fA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1d2fA/1d2fA-T0095-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d2fA/nostruct-align/1d2fA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1d2fA/1d2fA-T0095-local.pw.a2m make 1d2fA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1d2fA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1d2fA/T0095-1d2fA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1d2fA/T0095-1d2fA-2track-local.pw.a2m make 1d2fA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1d2fA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1d2fA/T0095-1d2fA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1d2fA/T0095-1d2fA-2track-global.pw.a2m make 1d2fA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1d2fA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1d2fA/T0095-1d2fA-vit.pw \ -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1d2fA/T0095-1d2fA-vit.pw.a2m make 1d2fA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1d2fA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1d2fA/1d2fA-T0095-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1d/1d2fA/nostruct-align/1d2fA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1d2fA/1d2fA-T0095-vit.pw.a2m make 1d2fA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1d2fA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1d2fA/T0095-1d2fA-global.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1d2fA/T0095-1d2fA-global.pw.a2m make 1d2fA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1d2fA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1d2fA/1d2fA-T0095-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d2fA/nostruct-align/1d2fA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1d2fA/1d2fA-T0095-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1d/1d2fA/struct-align/1d2fA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1d/1d2fA/struct-align/1d2fA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1d2fA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1d2fA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1d2fA/1d2fA-T0095-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1d2fA/struct-align/1d2fA.fssp-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2fA/info/1d2fA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1d2fA/1d2fA-T0095-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' make -k PRED=1b8gA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make 1b8gA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' mkdir 1b8gA fixmode 1b8gA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1b8gA/T0095-1b8gA-local.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1b8gA/T0095-1b8gA-local.pw.a2m make 1b8gA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1b8gA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1b8gA/1b8gA-T0095-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b8gA/nostruct-align/1b8gA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1b8gA/1b8gA-T0095-local.pw.a2m make 1b8gA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1b8gA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1b8gA/T0095-1b8gA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1b8gA/T0095-1b8gA-2track-local.pw.a2m make 1b8gA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1b8gA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1b8gA/T0095-1b8gA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1b8gA/T0095-1b8gA-2track-global.pw.a2m make 1b8gA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1b8gA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1b8gA/T0095-1b8gA-vit.pw \ -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1b8gA/T0095-1b8gA-vit.pw.a2m make 1b8gA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1b8gA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1b8gA/1b8gA-T0095-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1b/1b8gA/nostruct-align/1b8gA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1b8gA/1b8gA-T0095-vit.pw.a2m make 1b8gA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1b8gA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1b8gA/T0095-1b8gA-global.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1b8gA/T0095-1b8gA-global.pw.a2m make 1b8gA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1b8gA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1b8gA/1b8gA-T0095-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b8gA/nostruct-align/1b8gA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1b8gA/1b8gA-T0095-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1b8gA/struct-align/1b8gA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1b8gA/struct-align/1b8gA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1b8gA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1b8gA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1b8gA/1b8gA-T0095-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b8gA/struct-align/1b8gA.fssp-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1b8gA/info/1b8gA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1b8gA/1b8gA-T0095-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' make -k PRED=1dovA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make 1dovA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' mkdir 1dovA fixmode 1dovA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1dovA/T0095-1dovA-local.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1dovA/T0095-1dovA-local.pw.a2m make 1dovA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1dovA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1dovA/1dovA-T0095-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dovA/nostruct-align/1dovA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1dovA/1dovA-T0095-local.pw.a2m make 1dovA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1dovA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1dovA/T0095-1dovA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1dovA/T0095-1dovA-2track-local.pw.a2m make 1dovA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1dovA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1dovA/T0095-1dovA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1dovA/T0095-1dovA-2track-global.pw.a2m make 1dovA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1dovA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1dovA/T0095-1dovA-vit.pw \ -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1dovA/T0095-1dovA-vit.pw.a2m make 1dovA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1dovA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1dovA/1dovA-T0095-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1d/1dovA/nostruct-align/1dovA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1dovA/1dovA-T0095-vit.pw.a2m make 1dovA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1dovA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1dovA/T0095-1dovA-global.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1dovA/T0095-1dovA-global.pw.a2m make 1dovA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1dovA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1dovA/1dovA-T0095-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dovA/nostruct-align/1dovA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dovA/info/1dovA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1dovA/1dovA-T0095-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' make -k PRED=2a0b PRED2=2a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make 2a0b make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' mkdir 2a0b fixmode 2a0b make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 2a0b/T0095-2a0b-local.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2a0b/T0095-2a0b-local.pw.a2m make 2a0b make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `2a0b' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 2a0b/2a0b-T0095-local.pw -i /projects/compbio/experiments/models.97/pdb/2a/2a0b/nostruct-align/2a0b.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2a0b/2a0b-T0095-local.pw.a2m make 2a0b make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `2a0b' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 2a0b/T0095-2a0b-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.seq,/projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2a0b/T0095-2a0b-2track-local.pw.a2m make 2a0b make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `2a0b' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 2a0b/T0095-2a0b-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.seq,/projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2a0b/T0095-2a0b-2track-global.pw.a2m make 2a0b make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `2a0b' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 2a0b/T0095-2a0b-vit.pw \ -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2a0b/T0095-2a0b-vit.pw.a2m make 2a0b make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `2a0b' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 2a0b/2a0b-T0095-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/2a/2a0b/nostruct-align/2a0b.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2a0b/2a0b-T0095-vit.pw.a2m make 2a0b make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `2a0b' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 2a0b/T0095-2a0b-global.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2a0b/T0095-2a0b-global.pw.a2m make 2a0b make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `2a0b' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 2a0b/2a0b-T0095-global.pw -i /projects/compbio/experiments/models.97/pdb/2a/2a0b/nostruct-align/2a0b.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2a0b/2a0b-T0095-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/2a/2a0b/struct-align/2a0b.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/2a/2a0b/struct-align/2a0b.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 2a0b make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `2a0b' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 2a0b/2a0b-T0095-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/2a/2a0b/struct-align/2a0b.fssp-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/2a/2a0b/info/2a0b.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 2a0b/2a0b-T0095-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' make -k PRED=6prcM PRED2=6p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make 6prcM make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' mkdir 6prcM fixmode 6prcM make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 6prcM/T0095-6prcM-local.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 6prcM/T0095-6prcM-local.pw.a2m make 6prcM make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `6prcM' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 6prcM/6prcM-T0095-local.pw -i /projects/compbio/experiments/models.97/pdb/6p/6prcM/nostruct-align/6prcM.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 6prcM/6prcM-T0095-local.pw.a2m make 6prcM make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `6prcM' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 6prcM/T0095-6prcM-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.seq,/projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 6prcM/T0095-6prcM-2track-local.pw.a2m make 6prcM make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `6prcM' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 6prcM/T0095-6prcM-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.seq,/projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 6prcM/T0095-6prcM-2track-global.pw.a2m make 6prcM make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `6prcM' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 6prcM/T0095-6prcM-vit.pw \ -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 6prcM/T0095-6prcM-vit.pw.a2m make 6prcM make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `6prcM' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 6prcM/6prcM-T0095-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/6p/6prcM/nostruct-align/6prcM.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 6prcM/6prcM-T0095-vit.pw.a2m make 6prcM make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `6prcM' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 6prcM/T0095-6prcM-global.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 6prcM/T0095-6prcM-global.pw.a2m make 6prcM make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `6prcM' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 6prcM/6prcM-T0095-global.pw -i /projects/compbio/experiments/models.97/pdb/6p/6prcM/nostruct-align/6prcM.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 6prcM/6prcM-T0095-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/6p/6prcM/struct-align/6prcM.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/6p/6prcM/struct-align/6prcM.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 6prcM make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `6prcM' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 6prcM/6prcM-T0095-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/6p/6prcM/struct-align/6prcM.fssp-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/6p/6prcM/info/6prcM.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 6prcM/6prcM-T0095-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' make -k PRED=1eyvA PRED2=1e joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make 1eyvA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' mkdir 1eyvA fixmode 1eyvA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1eyvA/T0095-1eyvA-local.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eyvA/T0095-1eyvA-local.pw.a2m make 1eyvA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1eyvA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1eyvA/1eyvA-T0095-local.pw -i /projects/compbio/experiments/models.97/pdb/1e/1eyvA/nostruct-align/1eyvA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eyvA/1eyvA-T0095-local.pw.a2m make 1eyvA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1eyvA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1eyvA/T0095-1eyvA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eyvA/T0095-1eyvA-2track-local.pw.a2m make 1eyvA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1eyvA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1eyvA/T0095-1eyvA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride.seq,/projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eyvA/T0095-1eyvA-2track-global.pw.a2m make 1eyvA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1eyvA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1eyvA/T0095-1eyvA-vit.pw \ -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eyvA/T0095-1eyvA-vit.pw.a2m make 1eyvA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1eyvA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1eyvA/1eyvA-T0095-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1e/1eyvA/nostruct-align/1eyvA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eyvA/1eyvA-T0095-vit.pw.a2m make 1eyvA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1eyvA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1eyvA/T0095-1eyvA-global.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eyvA/T0095-1eyvA-global.pw.a2m make 1eyvA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1eyvA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1eyvA/1eyvA-T0095-global.pw -i /projects/compbio/experiments/models.97/pdb/1e/1eyvA/nostruct-align/1eyvA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1e/1eyvA/info/1eyvA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1eyvA/1eyvA-T0095-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' make -k PRED=1abwA PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make 1abwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' mkdir 1abwA fixmode 1abwA make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1abwA/T0095-1abwA-local.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1abwA/T0095-1abwA-local.pw.a2m make 1abwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1abwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1abwA/1abwA-T0095-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1abwA/nostruct-align/1abwA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1abwA/1abwA-T0095-local.pw.a2m make 1abwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1abwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1abwA/T0095-1abwA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1abwA/T0095-1abwA-2track-local.pw.a2m make 1abwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1abwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1abwA/T0095-1abwA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1abwA/T0095-1abwA-2track-global.pw.a2m make 1abwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1abwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1abwA/T0095-1abwA-vit.pw \ -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1abwA/T0095-1abwA-vit.pw.a2m make 1abwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1abwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1abwA/1abwA-T0095-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1abwA/nostruct-align/1abwA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1abwA/1abwA-T0095-vit.pw.a2m make 1abwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1abwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1abwA/T0095-1abwA-global.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1abwA/T0095-1abwA-global.pw.a2m make 1abwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1abwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1abwA/1abwA-T0095-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1abwA/nostruct-align/1abwA.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1abwA/1abwA-T0095-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1abwA/struct-align/1abwA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1abwA/struct-align/1abwA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1abwA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t95' make[2]: `1abwA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 1abwA/1abwA-T0095-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1abwA/struct-align/1abwA.fssp-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1abwA/info/1abwA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 gzip -f 1abwA/1abwA-T0095-fssp-global.pw.a2m make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t95' make -k PRED=1efcA PRED2=1e joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1efcA/xxxx-1efcA-T0095-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' make: [joints] Error 2 (ignored) make -k PRED=1bjwA PRED2=1b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bjwA/xxxx-1bjwA-T0095-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' make: [joints] Error 2 (ignored) make -k PRED=1d2fA PRED2=1d joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d2fA/xxxx-1d2fA-T0095-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' make: [joints] Error 2 (ignored) make -k PRED=1b8gA PRED2=1b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1b8gA/xxxx-1b8gA-T0095-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' make: [joints] Error 2 (ignored) make -k PRED=1dovA PRED2=1d joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1d/1dovA/struct-align/1dovA.fssp-w0.5.mod', needed by `1dovA/1dovA-T0095-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dovA/xxxx-1dovA-T0095-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' make: [joints] Error 2 (ignored) make -k PRED=2a0b PRED2=2a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `2a0b/xxxx-2a0b-T0095-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' make: [joints] Error 2 (ignored) make -k PRED=6prcM PRED2=6p joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `6prcM/xxxx-6prcM-T0095-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' make: [joints] Error 2 (ignored) make -k PRED=1eyvA PRED2=1e joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1e/1eyvA/struct-align/1eyvA.fssp-w0.5.mod', needed by `1eyvA/1eyvA-T0095-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1eyvA/xxxx-1eyvA-T0095-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' make: [joints] Error 2 (ignored) make -k PRED=1abwA PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1abwA/xxxx-1abwA-T0095-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' make: [joints] Error 2 (ignored) echo 1.110 1.110 make -k PRED=3bct PRED2=3b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make 3bct make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' mkdir 3bct fixmode 3bct make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 3bct/T0095-3bct-local.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0095.t2k-w0.5.mod T0095.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6120/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -88.478111 Database has 3 sequences with 1159 residues. gzip -f 3bct/T0095-3bct-local.pw.a2m make 3bct make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[2]: `3bct' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 3bct/3bct-T0095-local.pw -i /projects/compbio/experiments/models.97/pdb/3b/3bct/nostruct-align/3bct.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/3b/3bct/nostruct-align/3bct.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/3b/3bct/nostruct-align/3bct.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25595/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -218.062790 Database has 3 sequences with 1159 residues. gzip -f 3bct/3bct-T0095-local.pw.a2m make 3bct make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[2]: `3bct' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 3bct/T0095-3bct-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride.seq,/projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 T0095.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6120/tmp.a2m T0095.t2k-2d.mod(1493): Reading track 1 model from MODEL -- Model from 2nd structure file T0095.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -107.408928 Database has 3 sequences with 1159 residues. gzip -f 3bct/T0095-3bct-2track-local.pw.a2m make 3bct make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[2]: `3bct' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 3bct/T0095-3bct-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0095.t2k-w0.5.mod,T0095.t2k-2d.mod \ -db T0095.seq,T0095.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride.seq,/projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 You are performing full sequence database search. Experience has shown that fully local scoring is usually the best choice. Use '-SW 2' to enable. T0095.t2k-w0.5.mod(21): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6120/tmp.a2m T0095.t2k-2d.mod(1493): Reading track 1 model from MODEL -- Model from 2nd structure file T0095.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -78.843155 Database has 3 sequences with 1159 residues. gzip -f 3bct/T0095-3bct-2track-global.pw.a2m make 3bct make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[2]: `3bct' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 3bct/T0095-3bct-vit.pw \ -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0095.t2k-w0.5.mod T0095.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6120/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -84.255424 Database has 3 sequences with 1159 residues. gzip -f 3bct/T0095-3bct-vit.pw.a2m make 3bct make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[2]: `3bct' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 3bct/3bct-T0095-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/3b/3bct/nostruct-align/3bct.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/3b/3bct/nostruct-align/3bct.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/3b/3bct/nostruct-align/3bct.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25595/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -213.573105 Database has 3 sequences with 1159 residues. gzip -f 3bct/3bct-T0095-vit.pw.a2m make 3bct make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[2]: `3bct' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 3bct/T0095-3bct-global.pw -i T0095.t2k-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0095.t2k-w0.5.mod T0095.t2k-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6120/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 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: -51.615326 Database has 3 sequences with 1159 residues. gzip -f 3bct/T0095-3bct-global.pw.a2m make 3bct make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t95' make[2]: `3bct' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t95' /projects/compbio/bin/alpha.new/hmmscore 3bct/3bct-T0095-global.pw -i /projects/compbio/experiments/models.97/pdb/3b/3bct/nostruct-align/3bct.t99-w0.5.mod -db T0095.seq -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3b/3bct/info/3bct.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/3b/3bct/nostruct-align/3bct.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/3b/3bct/nostruct-align/3bct.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-25595/tmp.a2m SAM: /projects/compbio/bin/alpha.new/hmmscore v3.2 (July 31, 2000) compiled 08/11/00_16:27:39 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: -213.447998 Database has 3 sequences with 1159 residues. gzip -f 3bct/3bct-T0095-global.pw.a2m /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/3b/3bct/struct-align/3bct.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/3b/3bct/struct-align/3bct.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8429 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8429/tmp -alignfile /projects/compbio/experiments/models.97/pdb/3b/3bct/struct-align/3bct.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/3b/3bct/struct-align/3bct.fssp.a2m.gz (9 sequences, 457 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8429/tmp.a2m. Dropping 1 (of 9) sequences with > 80.0% id 8 sequences left after dropping 1 of 9 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8429/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8429/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8429/tmp.a2m (8 sequences, 457 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8429/tmp.mod /projects/compbio/experiments/models.97/pdb/3b/3bct/struct-align/3bct.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8429 80.0% id 11 sequences left after dropping 3 of 14 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8359/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8359/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8359/tmp.a2m (11 sequences, 871 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8359/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qgrA/struct-align/1qgrA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8359 80.0% id 8 sequences left after dropping 3 of 11 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8523/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8523/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8523/tmp.a2m (8 sequences, 422 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8523/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1bk5A/struct-align/1bk5A.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8523 80.0% id 5 sequences left after dropping 1 of 6 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8688/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8688/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8688/tmp.a2m (5 sequences, 233 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8688/tmp.mod /projects/compbio/experiments/models.97/pdb/1l/1lrv/struct-align/1lrv.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8688 80.0% id 8 sequences left after dropping 9 of 17 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8883/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8883/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8883/tmp.a2m (8 sequences, 156 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8883/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1bd8/struct-align/1bd8.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8883 80.0% id 5 sequences left after dropping 1 of 6 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9127/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9127/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9127/tmp.a2m (5 sequences, 254 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9127/tmp.mod /projects/compbio/experiments/models.97/pdb/1s/1sw6A/struct-align/1sw6A.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9127 80.0% id 4 sequences left after dropping 2 of 6 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9322/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9322/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9322/tmp.a2m (4 sequences, 618 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9322/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qsaA/struct-align/1qsaA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9322 80.0% id 5 sequences left after dropping 5 of 10 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9300/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9300/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9300/tmp.a2m (5 sequences, 315 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9300/tmp.mod /projects/compbio/experiments/models.97/pdb/1f/1ft1A/struct-align/1ft1A.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9300 80.0% id 8 sequences left after dropping 11 of 19 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9376/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9376/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9376/tmp.a2m (8 sequences, 217 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9376/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qjaA/struct-align/1qjaA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9376 80.0% id 14 sequences left after dropping 6 of 20 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9531/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9531/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9531/tmp.a2m (14 sequences, 487 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9531/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1bpoA/struct-align/1bpoA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9531 80.0% id 1 sequences left after dropping 9 of 10 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9612/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9612/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9612/tmp.a2m (1 sequences, 105 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9612/tmp.mod /projects/compbio/experiments/models.97/pdb/2o/2occE/struct-align/2occE.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9612