make -k PRED=1dbgA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dbgA/1dbgA-T0101-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7413/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -462.332123
Database has 3 sequences with 1387 residues.
gzip -f 1dbgA/1dbgA-T0101-local.pw.a2m
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dbgA/1dbgA-T0101-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7413/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -460.208466
Database has 3 sequences with 1387 residues.
gzip -f 1dbgA/1dbgA-T0101-vit.pw.a2m
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dbgA/1dbgA-T0101-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dbgA/nostruct-align/1dbgA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-7413/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -459.776093
Database has 3 sequences with 1387 residues.
gzip -f 1dbgA/1dbgA-T0101-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbgA/xxxx-1dbgA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1rmg  PRED2=1r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1rmg/1rmg-T0101-local.pw -i /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14068/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -227.905838
Database has 3 sequences with 1244 residues.
gzip -f 1rmg/1rmg-T0101-local.pw.a2m
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1rmg/1rmg-T0101-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14068/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -218.557541
Database has 3 sequences with 1244 residues.
gzip -f 1rmg/1rmg-T0101-vit.pw.a2m
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1rmg/1rmg-T0101-global.pw -i /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1r/1rmg/nostruct-align/1rmg.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14068/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -238.639404
Database has 3 sequences with 1244 residues.
gzip -f 1rmg/1rmg-T0101-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1rmg/xxxx-1rmg-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1bhe  PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1bhe/1bhe-T0101-local.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4921/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -179.549194
Database has 3 sequences with 1152 residues.
gzip -f 1bhe/1bhe-T0101-local.pw.a2m
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1bhe/1bhe-T0101-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4921/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -171.449219
Database has 3 sequences with 1152 residues.
gzip -f 1bhe/1bhe-T0101-vit.pw.a2m
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1bhe/1bhe-T0101-global.pw -i /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1b/1bhe/nostruct-align/1bhe.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-4921/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -183.594727
Database has 3 sequences with 1152 residues.
gzip -f 1bhe/1bhe-T0101-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bhe/xxxx-1bhe-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1czfA  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1czfA/1czfA-T0101-local.pw -i /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12403/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -201.545303
Database has 3 sequences with 1097 residues.
gzip -f 1czfA/1czfA-T0101-local.pw.a2m
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1czfA/1czfA-T0101-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12403/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -197.653992
Database has 3 sequences with 1097 residues.
gzip -f 1czfA/1czfA-T0101-vit.pw.a2m
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1czfA/1czfA-T0101-global.pw -i /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1c/1czfA/nostruct-align/1czfA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12403/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -196.299728
Database has 3 sequences with 1097 residues.
gzip -f 1czfA/1czfA-T0101-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1czfA/xxxx-1czfA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1air  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/1air-T0101-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -193.426559
Database has 3 sequences with 1105 residues.
gzip -f 1air/1air-T0101-local.pw.a2m
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/1air-T0101-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -189.224197
Database has 3 sequences with 1105 residues.
gzip -f 1air/1air-T0101-vit.pw.a2m
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/1air-T0101-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-937/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -188.222717
Database has 3 sequences with 1105 residues.
gzip -f 1air/1air-T0101-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1air/xxxx-1air-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qa1A  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qa1A/1qa1A-T0101-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31080/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -576.269836
Database has 3 sequences with 1496 residues.
gzip -f 1qa1A/1qa1A-T0101-local.pw.a2m
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qa1A/1qa1A-T0101-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31080/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -573.939148
Database has 3 sequences with 1496 residues.
gzip -f 1qa1A/1qa1A-T0101-vit.pw.a2m
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qa1A/1qa1A-T0101-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qa1A/nostruct-align/1qa1A.t99-w0.5.mod(23):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31080/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -784.386414
Database has 3 sequences with 1496 residues.
gzip -f 1qa1A/1qa1A-T0101-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qa1A/xxxx-1qa1A-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qcxA  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qcxA/1qcxA-T0101-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20881/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -204.434082
Database has 3 sequences with 1118 residues.
gzip -f 1qcxA/1qcxA-T0101-local.pw.a2m
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qcxA/1qcxA-T0101-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20881/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -199.429398
Database has 3 sequences with 1118 residues.
gzip -f 1qcxA/1qcxA-T0101-vit.pw.a2m
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qcxA/1qcxA-T0101-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1q/1qcxA/nostruct-align/1qcxA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-20881/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -201.152420
Database has 3 sequences with 1118 residues.
gzip -f 1qcxA/1qcxA-T0101-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qcxA/xxxx-1qcxA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dabA  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dabA/1dabA-T0101-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-1167/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -277.574707
Database has 3 sequences with 1478 residues.
gzip -f 1dabA/1dabA-T0101-local.pw.a2m
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dabA/1dabA-T0101-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-1167/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -269.907440
Database has 3 sequences with 1478 residues.
gzip -f 1dabA/1dabA-T0101-vit.pw.a2m
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dabA/1dabA-T0101-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1d/1dabA/nostruct-align/1dabA.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-1167/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -259.686737
Database has 3 sequences with 1478 residues.
gzip -f 1dabA/1dabA-T0101-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dabA/xxxx-1dabA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1tyv  PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1tyv/1tyv-T0101-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22469/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -579.150452
Database has 3 sequences with 1484 residues.
gzip -f 1tyv/1tyv-T0101-local.pw.a2m
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1tyv/1tyv-T0101-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22469/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -576.720093
Database has 3 sequences with 1484 residues.
gzip -f 1tyv/1tyv-T0101-vit.pw.a2m
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1tyv/1tyv-T0101-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1t/1tyv/nostruct-align/1tyv.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-22469/tmp.a2m
SAM: hmmscore v3.1b (February 24, 1999) compiled 05/16/00_17:09:35
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.

Warning: First model node is not a FIM but
null model probabilities are being taken from it
anyway.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -785.550354
Database has 3 sequences with 1484 residues.
gzip -f 1tyv/1tyv-T0101-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tyv/xxxx-1tyv-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dbgA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
/projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0101.t2k.2d.rdb T0101.t2k-2d.mod
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dbgA/T0101-1dbgA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -120.056267
Database has 3 sequences with 1387 residues.
gzip -f 1dbgA/T0101-1dbgA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbgA/xxxx-1dbgA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1rmg  PRED2=1r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1rmg/T0101-1rmg-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -114.500740
Database has 3 sequences with 1244 residues.
gzip -f 1rmg/T0101-1rmg-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1rmg/xxxx-1rmg-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1bhe  PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1bhe/T0101-1bhe-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -110.531670
Database has 3 sequences with 1152 residues.
gzip -f 1bhe/T0101-1bhe-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bhe/xxxx-1bhe-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1czfA  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1czfA/T0101-1czfA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -107.389618
Database has 3 sequences with 1097 residues.
gzip -f 1czfA/T0101-1czfA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1czfA/xxxx-1czfA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1air  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/1air-T0101-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq \
	-adpstyle 5 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29188/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -180.749939
Database has 3 sequences with 1105 residues.
gzip -f 1air/1air-T0101-local.pw.a2m
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/T0101-1air-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 5 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -110.019684
Database has 3 sequences with 1105 residues.
gzip -f 1air/T0101-1air-2track-local.pw.a2m
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/1air-T0101-vit.pw \
	-i /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq \
	-viterbi 1 -sw 2 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29188/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -177.020264
Database has 3 sequences with 1105 residues.
gzip -f 1air/1air-T0101-vit.pw.a2m
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/1air-T0101-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod -db T0101.seq -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq \
	-db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq \
	-adpstyle 5 -sw 0 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod
/projects/compbio/experiments/models.97/pdb/1a/1air/nostruct-align/1air.t99-w0.5.mod(21):  Reading MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-29188/tmp.a2m
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -175.864395
Database has 3 sequences with 1105 residues.
gzip -f 1air/1air-T0101-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1air/xxxx-1air-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qa1A  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qa1A/T0101-1qa1A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -106.777275
Database has 3 sequences with 1496 residues.
gzip -f 1qa1A/T0101-1qa1A-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qa1A/xxxx-1qa1A-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qcxA  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qcxA/T0101-1qcxA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -111.863533
Database has 3 sequences with 1118 residues.
gzip -f 1qcxA/T0101-1qcxA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qcxA/xxxx-1qcxA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dabA  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dabA/T0101-1dabA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -106.031219
Database has 3 sequences with 1478 residues.
gzip -f 1dabA/T0101-1dabA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dabA/xxxx-1dabA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1tyv  PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1tyv/T0101-1tyv-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -106.800507
Database has 3 sequences with 1484 residues.
gzip -f 1tyv/T0101-1tyv-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tyv/xxxx-1tyv-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dbgA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dbgA/T0101-1dbgA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -120.056267
Database has 3 sequences with 1387 residues.
gzip -f 1dbgA/T0101-1dbgA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbgA/xxxx-1dbgA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1rmg  PRED2=1r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1rmg/T0101-1rmg-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -114.500740
Database has 3 sequences with 1244 residues.
gzip -f 1rmg/T0101-1rmg-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1rmg/xxxx-1rmg-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1bhe  PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1bhe/T0101-1bhe-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -110.531670
Database has 3 sequences with 1152 residues.
gzip -f 1bhe/T0101-1bhe-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bhe/xxxx-1bhe-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1czfA  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1czfA/T0101-1czfA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -107.389618
Database has 3 sequences with 1097 residues.
gzip -f 1czfA/T0101-1czfA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1czfA/xxxx-1czfA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1air  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/T0101-1air-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -110.019684
Database has 3 sequences with 1105 residues.
gzip -f 1air/T0101-1air-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1air/xxxx-1air-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qa1A  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qa1A/T0101-1qa1A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -106.777275
Database has 3 sequences with 1496 residues.
gzip -f 1qa1A/T0101-1qa1A-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qa1A/xxxx-1qa1A-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qcxA  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qcxA/T0101-1qcxA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -111.863533
Database has 3 sequences with 1118 residues.
gzip -f 1qcxA/T0101-1qcxA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qcxA/xxxx-1qcxA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dabA  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dabA/T0101-1dabA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -106.031219
Database has 3 sequences with 1478 residues.
gzip -f 1dabA/T0101-1dabA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dabA/xxxx-1dabA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1tyv  PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1tyv/T0101-1tyv-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -106.800507
Database has 3 sequences with 1484 residues.
gzip -f 1tyv/T0101-1tyv-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tyv/xxxx-1tyv-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dbgA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dbgA/T0101-1dbgA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -120.056267
Database has 3 sequences with 1387 residues.
gzip -f 1dbgA/T0101-1dbgA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbgA/xxxx-1dbgA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1rmg  PRED2=1r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1rmg/T0101-1rmg-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -114.500740
Database has 3 sequences with 1244 residues.
gzip -f 1rmg/T0101-1rmg-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1rmg/xxxx-1rmg-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1bhe  PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1bhe/T0101-1bhe-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -110.531670
Database has 3 sequences with 1152 residues.
gzip -f 1bhe/T0101-1bhe-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bhe/xxxx-1bhe-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1czfA  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1czfA/T0101-1czfA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -107.389618
Database has 3 sequences with 1097 residues.
gzip -f 1czfA/T0101-1czfA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1czfA/xxxx-1czfA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1air  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/T0101-1air-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -110.019684
Database has 3 sequences with 1105 residues.
gzip -f 1air/T0101-1air-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1air/xxxx-1air-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qa1A  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qa1A/T0101-1qa1A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -106.777275
Database has 3 sequences with 1496 residues.
gzip -f 1qa1A/T0101-1qa1A-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qa1A/xxxx-1qa1A-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qcxA  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qcxA/T0101-1qcxA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -111.863533
Database has 3 sequences with 1118 residues.
gzip -f 1qcxA/T0101-1qcxA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qcxA/xxxx-1qcxA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dabA  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dabA/T0101-1dabA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -106.031219
Database has 3 sequences with 1478 residues.
gzip -f 1dabA/T0101-1dabA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dabA/xxxx-1dabA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1tyv  PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1tyv/T0101-1tyv-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -106.800507
Database has 3 sequences with 1484 residues.
gzip -f 1tyv/T0101-1tyv-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tyv/xxxx-1tyv-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dbgA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dbgA/T0101-1dbgA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -120.056267
Database has 3 sequences with 1387 residues.
gzip -f 1dbgA/T0101-1dbgA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbgA/xxxx-1dbgA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1rmg  PRED2=1r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1rmg/T0101-1rmg-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -114.500740
Database has 3 sequences with 1244 residues.
gzip -f 1rmg/T0101-1rmg-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1rmg/xxxx-1rmg-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1bhe  PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1bhe/T0101-1bhe-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -110.531670
Database has 3 sequences with 1152 residues.
gzip -f 1bhe/T0101-1bhe-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bhe/xxxx-1bhe-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1czfA  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1czfA/T0101-1czfA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -107.389618
Database has 3 sequences with 1097 residues.
gzip -f 1czfA/T0101-1czfA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1czfA/xxxx-1czfA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1air  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/T0101-1air-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -110.019684
Database has 3 sequences with 1105 residues.
gzip -f 1air/T0101-1air-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1air/xxxx-1air-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qa1A  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qa1A/T0101-1qa1A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -106.777275
Database has 3 sequences with 1496 residues.
gzip -f 1qa1A/T0101-1qa1A-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qa1A/xxxx-1qa1A-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qcxA  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qcxA/T0101-1qcxA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -111.863533
Database has 3 sequences with 1118 residues.
gzip -f 1qcxA/T0101-1qcxA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qcxA/xxxx-1qcxA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dabA  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dabA/T0101-1dabA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -106.031219
Database has 3 sequences with 1478 residues.
gzip -f 1dabA/T0101-1dabA-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dabA/xxxx-1dabA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1tyv  PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1tyv/T0101-1tyv-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)



.
Average NLL-Simple NULL score:        -106.800507
Database has 3 sequences with 1484 residues.
gzip -f 1tyv/T0101-1tyv-2track-local.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tyv/xxxx-1tyv-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dbgA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dbgA/T0101-1dbgA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        2078.720703
Database has 3 sequences with 1387 residues.
gzip -f 1dbgA/T0101-1dbgA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbgA/xxxx-1dbgA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1rmg  PRED2=1r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1rmg/T0101-1rmg-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        514.014099
Database has 3 sequences with 1244 residues.
gzip -f 1rmg/T0101-1rmg-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1rmg/xxxx-1rmg-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1bhe  PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1bhe/T0101-1bhe-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -67.097870
Database has 3 sequences with 1152 residues.
gzip -f 1bhe/T0101-1bhe-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bhe/xxxx-1bhe-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1czfA  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1czfA/T0101-1czfA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -76.637360
Database has 3 sequences with 1097 residues.
gzip -f 1czfA/T0101-1czfA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1czfA/xxxx-1czfA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1air  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/T0101-1air-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -78.696869
Database has 3 sequences with 1105 residues.
gzip -f 1air/T0101-1air-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1air/xxxx-1air-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qa1A  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qa1A/T0101-1qa1A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        3692.738281
Database has 3 sequences with 1496 residues.
gzip -f 1qa1A/T0101-1qa1A-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qa1A/xxxx-1qa1A-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qcxA  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qcxA/T0101-1qcxA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -97.332527
Database has 3 sequences with 1118 residues.
gzip -f 1qcxA/T0101-1qcxA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qcxA/xxxx-1qcxA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dabA  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dabA/T0101-1dabA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        3620.690186
Database has 3 sequences with 1478 residues.
gzip -f 1dabA/T0101-1dabA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dabA/xxxx-1dabA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1tyv  PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1tyv/T0101-1tyv-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.2d \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        3689.288330
Database has 3 sequences with 1484 residues.
gzip -f 1tyv/T0101-1tyv-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tyv/xxxx-1tyv-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dbgA PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dbgA/T0101-1dbgA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15887.644531
Database has 3 sequences with 1387 residues.
gzip -f 1dbgA/T0101-1dbgA-2track-local.pw.a2m
make 1dbgA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dbgA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dbgA/T0101-1dbgA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dbgA/info/1dbgA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15878.442383
Database has 3 sequences with 1387 residues.
gzip -f 1dbgA/T0101-1dbgA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dbgA/xxxx-1dbgA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1rmg  PRED2=1r joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1rmg/T0101-1rmg-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15883.246094
Database has 3 sequences with 1244 residues.
gzip -f 1rmg/T0101-1rmg-2track-local.pw.a2m
make 1rmg
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1rmg' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1rmg/T0101-1rmg-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.seq,/projects/compbio/experiments/models.97/pdb/1r/1rmg/info/1rmg.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15883.426758
Database has 3 sequences with 1244 residues.
gzip -f 1rmg/T0101-1rmg-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1rmg/xxxx-1rmg-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1bhe  PRED2=1b joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1bhe/T0101-1bhe-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15256.464844
Database has 3 sequences with 1152 residues.
gzip -f 1bhe/T0101-1bhe-2track-local.pw.a2m
make 1bhe
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1bhe' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1bhe/T0101-1bhe-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1bhe/info/1bhe.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15260.209961
Database has 3 sequences with 1152 residues.
gzip -f 1bhe/T0101-1bhe-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1bhe/xxxx-1bhe-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1czfA  PRED2=1c joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1czfA/T0101-1czfA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -14183.071289
Database has 3 sequences with 1097 residues.
gzip -f 1czfA/T0101-1czfA-2track-local.pw.a2m
make 1czfA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1czfA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1czfA/T0101-1czfA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1czfA/info/1czfA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -14185.383789
Database has 3 sequences with 1097 residues.
gzip -f 1czfA/T0101-1czfA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1czfA/xxxx-1czfA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1air  PRED2=1a joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/T0101-1air-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -14627.250000
Database has 3 sequences with 1105 residues.
gzip -f 1air/T0101-1air-2track-local.pw.a2m
make 1air
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1air' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1air/T0101-1air-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1air/info/1air.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -14630.309570
Database has 3 sequences with 1105 residues.
gzip -f 1air/T0101-1air-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1air/xxxx-1air-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qa1A  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qa1A/T0101-1qa1A-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15887.522461
Database has 3 sequences with 1496 residues.
gzip -f 1qa1A/T0101-1qa1A-2track-local.pw.a2m
make 1qa1A
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qa1A' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qa1A/T0101-1qa1A-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qa1A/info/1qa1A.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15868.940430
Database has 3 sequences with 1496 residues.
gzip -f 1qa1A/T0101-1qa1A-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qa1A/xxxx-1qa1A-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1qcxA  PRED2=1q joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qcxA/T0101-1qcxA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -14826.277344
Database has 3 sequences with 1118 residues.
gzip -f 1qcxA/T0101-1qcxA-2track-local.pw.a2m
make 1qcxA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1qcxA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1qcxA/T0101-1qcxA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qcxA/info/1qcxA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -14829.546875
Database has 3 sequences with 1118 residues.
gzip -f 1qcxA/T0101-1qcxA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qcxA/xxxx-1qcxA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1dabA  PRED2=1d joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dabA/T0101-1dabA-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15883.760742
Database has 3 sequences with 1478 residues.
gzip -f 1dabA/T0101-1dabA-2track-local.pw.a2m
make 1dabA
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1dabA' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1dabA/T0101-1dabA-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dabA/info/1dabA.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15878.303711
Database has 3 sequences with 1478 residues.
gzip -f 1dabA/T0101-1dabA-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dabA/xxxx-1dabA-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)
make -k PRED=1tyv  PRED2=1t joint
make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1tyv/T0101-1tyv-2track-local.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 2 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15888.465820
Database has 3 sequences with 1484 residues.
gzip -f 1tyv/T0101-1tyv-2track-local.pw.a2m
make 1tyv
make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t101'
make[2]: `1tyv' is up to date.
make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
hmmscore 1tyv/T0101-1tyv-2track-global.pw \
	-alphabet protein,EHL2 \
	-trackcoeff 0.5,0.5 \
	-sw 0 -adpstyle 1 \
	-trackmod T0101.t2k-w0.5.mod,T0101.t2k-2d.mod \
 -db T0101.seq,T0101.t2k.2d.seq \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride-mixed.2d \
 -db /projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tyv/info/1tyv.stride.2d \
	-fim_method_score 5 -insert_method_score 5 \
	-subtract_null 4 -simplethreshold 1 \
	-select_align 8
SAM: hmmscore v3.2 (July 31, 2000) compiled 08/04/00_11:31:33
You are performing full sequence database search.
  Experience has shown that fully local scoring
  is usually the best choice.  Use '-SW 2' to enable.
T0101.t2k-w0.5.mod(23):  Reading track 0 model from MODEL --  Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30400/tmp.a2m
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
T0101.t2k-2d.mod(2423):  Reading track 1 model from MODEL -- Model from 2nd structure file T0101.t2k.2d.rdb
FIM_method 5 (the generic node) not available in model.
 Tables not modified.
Insert_method 5 (the generic node) not available in model.
 Tables not modified.
Calculating Distances (. = 1000 sequences)
.
Average NLL-Simple NULL score:        -15868.868164
Database has 3 sequences with 1484 residues.
gzip -f 1tyv/T0101-1tyv-2track-global.pw.a2m
make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tyv/xxxx-1tyv-T0101-local.pw.a2m.gz'.
make[1]: Target `joint' not remade because of errors.
make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t101'
make: [joints] Error 2 (ignored)