make -k PRED=1k89 PRED2=1k joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 1k89
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1k89' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1k89/T0115-1k89-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1k/1k89/info/1k89.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1k89/info/1k89.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1k/1k89/info/1k89.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1k89/info/1k89.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1k89/T0115-1k89-2track-local.pw.a2m
make 1k89
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1k89' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1k89/T0115-1k89-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1k/1k89/info/1k89.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1k89/info/1k89.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1k/1k89/info/1k89.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1k89/info/1k89.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1k89/T0115-1k89-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
make -k PRED=1do0A PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1do0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/T0115-1do0A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1do0A/T0115-1do0A-2track-local.pw.a2m
make 1do0A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1do0A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1do0A/T0115-1do0A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1do0A/info/1do0A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1do0A/T0115-1do0A-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
make -k PRED=1bmtA PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 1bmtA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1bmtA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1bmtA/T0115-1bmtA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bmtA/info/1bmtA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bmtA/info/1bmtA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bmtA/info/1bmtA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bmtA/info/1bmtA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bmtA/T0115-1bmtA-2track-local.pw.a2m
make 1bmtA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1bmtA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1bmtA/T0115-1bmtA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bmtA/info/1bmtA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bmtA/info/1bmtA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bmtA/info/1bmtA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bmtA/info/1bmtA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1bmtA/T0115-1bmtA-2track-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
make -k PRED=1csn  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 1csn
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
mkdir 1csn
fixmode 1csn
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1csn/T0115-1csn-local.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1csn/T0115-1csn-local.pw.a2m
make 1csn
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1csn' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1csn/1csn-T0115-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1csn/nostruct-align/1csn.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1csn/1csn-T0115-local.pw.a2m
make 1csn
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1csn' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1csn/T0115-1csn-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1csn/T0115-1csn-2track-local.pw.a2m
make 1csn
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1csn' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1csn/T0115-1csn-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1csn/T0115-1csn-2track-global.pw.a2m
make 1csn
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1csn' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1csn/T0115-1csn-vit.pw \
	-i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1csn/T0115-1csn-vit.pw.a2m
make 1csn
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1csn' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1csn/1csn-T0115-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1csn/nostruct-align/1csn.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1csn/1csn-T0115-vit.pw.a2m
make 1csn
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1csn' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1csn/T0115-1csn-global.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1csn/T0115-1csn-global.pw.a2m
make 1csn
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1csn' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1csn/1csn-T0115-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1csn/nostruct-align/1csn.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1csn/1csn-T0115-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1c/1csn/struct-align/1csn.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1c/1csn/struct-align/1csn.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1csn
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1csn' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1csn/1csn-T0115-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1csn/struct-align/1csn.fssp-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1csn/info/1csn.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1csn/1csn-T0115-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
make -k PRED=1rdr  PRED2=1r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 1rdr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
mkdir 1rdr
fixmode 1rdr
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1rdr/T0115-1rdr-local.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1rdr/T0115-1rdr-local.pw.a2m
make 1rdr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1rdr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1rdr/1rdr-T0115-local.pw -i /projects/compbio/experiments/models.97/pdb/1r/1rdr/nostruct-align/1rdr.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1rdr/1rdr-T0115-local.pw.a2m
make 1rdr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1rdr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1rdr/T0115-1rdr-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.seq,/projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1rdr/T0115-1rdr-2track-local.pw.a2m
make 1rdr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1rdr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1rdr/T0115-1rdr-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.seq,/projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1rdr/T0115-1rdr-2track-global.pw.a2m
make 1rdr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1rdr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1rdr/T0115-1rdr-vit.pw \
	-i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1rdr/T0115-1rdr-vit.pw.a2m
make 1rdr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1rdr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1rdr/1rdr-T0115-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1r/1rdr/nostruct-align/1rdr.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1rdr/1rdr-T0115-vit.pw.a2m
make 1rdr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1rdr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1rdr/T0115-1rdr-global.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1rdr/T0115-1rdr-global.pw.a2m
make 1rdr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1rdr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1rdr/1rdr-T0115-global.pw -i /projects/compbio/experiments/models.97/pdb/1r/1rdr/nostruct-align/1rdr.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1rdr/1rdr-T0115-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1r/1rdr/struct-align/1rdr.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1r/1rdr/struct-align/1rdr.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1rdr
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1rdr' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1rdr/1rdr-T0115-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1r/1rdr/struct-align/1rdr.fssp-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rdr/info/1rdr.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1rdr/1rdr-T0115-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
make -k PRED=1dgfA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 1dgfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
mkdir 1dgfA
fixmode 1dgfA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1dgfA/T0115-1dgfA-local.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dgfA/T0115-1dgfA-local.pw.a2m
make 1dgfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1dgfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1dgfA/1dgfA-T0115-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dgfA/nostruct-align/1dgfA.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dgfA/1dgfA-T0115-local.pw.a2m
make 1dgfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1dgfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1dgfA/T0115-1dgfA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dgfA/T0115-1dgfA-2track-local.pw.a2m
make 1dgfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1dgfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1dgfA/T0115-1dgfA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dgfA/T0115-1dgfA-2track-global.pw.a2m
make 1dgfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1dgfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1dgfA/T0115-1dgfA-vit.pw \
	-i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dgfA/T0115-1dgfA-vit.pw.a2m
make 1dgfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1dgfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1dgfA/1dgfA-T0115-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1dgfA/nostruct-align/1dgfA.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dgfA/1dgfA-T0115-vit.pw.a2m
make 1dgfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1dgfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1dgfA/T0115-1dgfA-global.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dgfA/T0115-1dgfA-global.pw.a2m
make 1dgfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1dgfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1dgfA/1dgfA-T0115-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dgfA/nostruct-align/1dgfA.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dgfA/info/1dgfA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1dgfA/1dgfA-T0115-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
make -k PRED=1gtxA PRED2=1g joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 1gtxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
mkdir 1gtxA
fixmode 1gtxA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1gtxA/T0115-1gtxA-local.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1gtxA/T0115-1gtxA-local.pw.a2m
make 1gtxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1gtxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1gtxA/1gtxA-T0115-local.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gtxA/nostruct-align/1gtxA.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1gtxA/1gtxA-T0115-local.pw.a2m
make 1gtxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1gtxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1gtxA/T0115-1gtxA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1gtxA/T0115-1gtxA-2track-local.pw.a2m
make 1gtxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1gtxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1gtxA/T0115-1gtxA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1gtxA/T0115-1gtxA-2track-global.pw.a2m
make 1gtxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1gtxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1gtxA/T0115-1gtxA-vit.pw \
	-i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1gtxA/T0115-1gtxA-vit.pw.a2m
make 1gtxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1gtxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1gtxA/1gtxA-T0115-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1g/1gtxA/nostruct-align/1gtxA.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1gtxA/1gtxA-T0115-vit.pw.a2m
make 1gtxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1gtxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1gtxA/T0115-1gtxA-global.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1gtxA/T0115-1gtxA-global.pw.a2m
make 1gtxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1gtxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1gtxA/1gtxA-T0115-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gtxA/nostruct-align/1gtxA.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1gtxA/1gtxA-T0115-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1g/1gtxA/struct-align/1gtxA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1g/1gtxA/struct-align/1gtxA.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1gtxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1gtxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1gtxA/1gtxA-T0115-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gtxA/struct-align/1gtxA.fssp-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1g/1gtxA/info/1gtxA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1gtxA/1gtxA-T0115-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
make -k PRED=2cae  PRED2=2c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 2cae
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
mkdir 2cae
fixmode 2cae
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 2cae/T0115-2cae-local.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2cae/T0115-2cae-local.pw.a2m
make 2cae
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `2cae' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 2cae/2cae-T0115-local.pw -i /projects/compbio/experiments/models.97/pdb/2c/2cae/nostruct-align/2cae.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2cae/2cae-T0115-local.pw.a2m
make 2cae
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `2cae' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 2cae/T0115-2cae-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride.seq,/projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2cae/T0115-2cae-2track-local.pw.a2m
make 2cae
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `2cae' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 2cae/T0115-2cae-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride.seq,/projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2cae/T0115-2cae-2track-global.pw.a2m
make 2cae
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `2cae' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 2cae/T0115-2cae-vit.pw \
	-i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2cae/T0115-2cae-vit.pw.a2m
make 2cae
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `2cae' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 2cae/2cae-T0115-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/2c/2cae/nostruct-align/2cae.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2cae/2cae-T0115-vit.pw.a2m
make 2cae
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `2cae' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 2cae/T0115-2cae-global.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2cae/T0115-2cae-global.pw.a2m
make 2cae
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `2cae' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 2cae/2cae-T0115-global.pw -i /projects/compbio/experiments/models.97/pdb/2c/2cae/nostruct-align/2cae.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/2c/2cae/info/2cae.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 2cae/2cae-T0115-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
make -k PRED=1nozA PRED2=1n joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 1nozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
mkdir 1nozA
fixmode 1nozA
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1nozA/T0115-1nozA-local.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1nozA/T0115-1nozA-local.pw.a2m
make 1nozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1nozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1nozA/1nozA-T0115-local.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nozA/nostruct-align/1nozA.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1nozA/1nozA-T0115-local.pw.a2m
make 1nozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1nozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1nozA/T0115-1nozA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1nozA/T0115-1nozA-2track-local.pw.a2m
make 1nozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1nozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1nozA/T0115-1nozA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1nozA/T0115-1nozA-2track-global.pw.a2m
make 1nozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1nozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1nozA/T0115-1nozA-vit.pw \
	-i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1nozA/T0115-1nozA-vit.pw.a2m
make 1nozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1nozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1nozA/1nozA-T0115-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1n/1nozA/nostruct-align/1nozA.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1nozA/1nozA-T0115-vit.pw.a2m
make 1nozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1nozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1nozA/T0115-1nozA-global.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1nozA/T0115-1nozA-global.pw.a2m
make 1nozA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1nozA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1nozA/1nozA-T0115-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nozA/nostruct-align/1nozA.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1n/1nozA/info/1nozA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1nozA/1nozA-T0115-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
make -k PRED=1b6cB PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 1b6cB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
mkdir 1b6cB
fixmode 1b6cB
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1b6cB/T0115-1b6cB-local.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b6cB/T0115-1b6cB-local.pw.a2m
make 1b6cB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1b6cB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1b6cB/1b6cB-T0115-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b6cB/nostruct-align/1b6cB.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b6cB/1b6cB-T0115-local.pw.a2m
make 1b6cB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1b6cB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1b6cB/T0115-1b6cB-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b6cB/T0115-1b6cB-2track-local.pw.a2m
make 1b6cB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1b6cB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1b6cB/T0115-1b6cB-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b6cB/T0115-1b6cB-2track-global.pw.a2m
make 1b6cB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1b6cB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1b6cB/T0115-1b6cB-vit.pw \
	-i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b6cB/T0115-1b6cB-vit.pw.a2m
make 1b6cB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1b6cB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1b6cB/1b6cB-T0115-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1b6cB/nostruct-align/1b6cB.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b6cB/1b6cB-T0115-vit.pw.a2m
make 1b6cB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1b6cB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1b6cB/T0115-1b6cB-global.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b6cB/T0115-1b6cB-global.pw.a2m
make 1b6cB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1b6cB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1b6cB/1b6cB-T0115-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b6cB/nostruct-align/1b6cB.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b6cB/1b6cB-T0115-global.pw.a2m
/projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1b/1b6cB/struct-align/1b6cB.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1b/1b6cB/struct-align/1b6cB.fssp-w0.5.mod
Reading /projects/compbio/bin/scripts/sam-t99.confReading /projects/compbio/bin/scripts/sam-t99.confmake 1b6cB
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1b6cB' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1b6cB/1b6cB-T0115-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1b6cB/struct-align/1b6cB.fssp-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1b6cB/info/1b6cB.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1b6cB/1b6cB-T0115-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
make -k PRED=1cf9A PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
mkdir 1cf9A
fixmode 1cf9A
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/T0115-1cf9A-local.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/T0115-1cf9A-local.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/1cf9A-T0115-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cf9A/nostruct-align/1cf9A.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/1cf9A-T0115-local.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/T0115-1cf9A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/T0115-1cf9A-2track-local.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/T0115-1cf9A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0115.t2k-w0.5.mod,T0115.t2k-2d.mod \
 -db T0115.seq,T0115.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/T0115-1cf9A-2track-global.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/T0115-1cf9A-vit.pw \
	-i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/T0115-1cf9A-vit.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/1cf9A-T0115-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1cf9A/nostruct-align/1cf9A.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/1cf9A-T0115-vit.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/T0115-1cf9A-global.pw -i T0115.t2k-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/T0115-1cf9A-global.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/1cf9A-T0115-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cf9A/nostruct-align/1cf9A.t99-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/1cf9A-T0115-global.pw.a2m
make 1cf9A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t115'
make[2]: `1cf9A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'
/projects/compbio/bin/alpha.new/hmmscore 1cf9A/1cf9A-T0115-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1cf9A/struct-align/1cf9A.fssp-w0.5.mod -db T0115.seq -db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1cf9A/info/1cf9A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
gzip -f 1cf9A/1cf9A-T0115-fssp-global.pw.a2m
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t115'