make -k PRED=5p21 PRED2=5p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5p/5p21/struct-align/5p21.fssp-w0.5.mod', needed by `5p21/5p21-T0104-fssp-global.pw.a2m.gz'. /projects/compbio/bin/scripts/w0.5 T0104.t2k.a2m.gz T0104.t2k-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-30480 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp -alignfile T0104.t2k.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.1b (February 24, 1999) compiled 04/18/00_11:44:50 Reading alignment file T0104.t2k.a2m.gz (29 sequences, 158 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m. Dropping 1 (of 29) duplicate sequences with differing IDs Dropping 4 (of 29) sequences with > 80.0% id 24 sequences left after dropping 5 of 29 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m (24 sequences, 158 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.mod T0104.t2k-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-30480 80.0% id 515 sequences left after dropping 972 of 1487 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-10755/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-10755/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-10755/tmp.a2m (515 sequences, 166 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-10755/tmp.mod /projects/compbio/experiments/models.97/pdb/5p/5p21/nostruct-align/5p21.t2k-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-10755 80.0% id 37 sequences left after dropping 52 of 89 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-15183/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-15183/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-15183/tmp.a2m (37 sequences, 166 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-15183/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1ctqA/struct-align/1ctqA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-15183 80.0% id 13 sequences left after dropping 16 of 29 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-23113/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-23113/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-23113/tmp.a2m (13 sequences, 202 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-23113/tmp.mod /projects/compbio/experiments/models.97/pdb/1b/1byuA/struct-align/1byuA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-23113 80.0% id 10 sequences left after dropping 1 of 11 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21184/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21184/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21184/tmp.a2m (10 sequences, 212 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21184/tmp.mod /projects/compbio/experiments/models.97/pdb/1c/1ckeA/struct-align/1ckeA.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-21184 80.0% id 8 sequences left after dropping 15 of 23 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-26306/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-26306/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.1b (February 24, 1999) compiled 04/18/00_11:44:13 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-26306/tmp.a2m (8 sequences, 470 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-26306/tmp.mod /projects/compbio/experiments/models.97/pdb/1s/1skyE/struct-align/1skyE.fssp-w0.5.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-26306 80.0% id 11 sequences left after dropping 9 of 20 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11834/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11834/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11834/tmp.a2m (11 sequences, 175 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11834/tmp.mod /projects/compbio/experiments/models.97/pdb/1t/1tc1A/struct-align/1tc1A.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1tc1A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 1tc1A fixmode 1tc1A make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/1tc1A-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tc1A/struct-align/1tc1A.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tc1A/struct-align/1tc1A.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1tc1A/struct-align/1tc1A.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-11834/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -101.044037 Database has 3 sequences with 553 residues. gzip -f 1tc1A/1tc1A-T0104-fssp-global.pw.a2m make 1tc1A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/T0104-1tc1A-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -52.310028 Database has 3 sequences with 553 residues. gzip -f 1tc1A/T0104-1tc1A-local.pw.a2m make 1tc1A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/1tc1A-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tc1A/nostruct-align/1tc1A.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tc1A/nostruct-align/1tc1A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1tc1A/nostruct-align/1tc1A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5256/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -103.520020 Database has 3 sequences with 553 residues. gzip -f 1tc1A/1tc1A-T0104-local.pw.a2m make 1tc1A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/T0104-1tc1A-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.759033 Database has 3 sequences with 553 residues. gzip -f 1tc1A/T0104-1tc1A-vit.pw.a2m make 1tc1A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/1tc1A-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1t/1tc1A/nostruct-align/1tc1A.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tc1A/nostruct-align/1tc1A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1tc1A/nostruct-align/1tc1A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5256/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -100.096367 Database has 3 sequences with 553 residues. gzip -f 1tc1A/1tc1A-T0104-vit.pw.a2m make 1tc1A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/T0104-1tc1A-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -35.349018 Database has 3 sequences with 553 residues. gzip -f 1tc1A/T0104-1tc1A-global.pw.a2m make 1tc1A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/1tc1A-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/1t/1tc1A/nostruct-align/1tc1A.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1t/1tc1A/nostruct-align/1tc1A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1t/1tc1A/nostruct-align/1tc1A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-5256/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -99.882347 Database has 3 sequences with 553 residues. gzip -f 1tc1A/1tc1A-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tc1A/xxxx-1tc1A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qk3A PRED2=1q joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qk3A/struct-align/1qk3A.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qk3A/struct-align/1qk3A.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9237 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9237/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1q/1qk3A/struct-align/1qk3A.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1q/1qk3A/struct-align/1qk3A.fssp.a2m.gz (32 sequences, 228 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9237/tmp.a2m. Dropping 9 (of 32) duplicate sequences with differing IDs Dropping 14 (of 32) sequences with > 80.0% id 9 sequences left after dropping 23 of 32 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9237/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9237/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9237/tmp.a2m (9 sequences, 228 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9237/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qk3A/struct-align/1qk3A.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1qk3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 1qk3A fixmode 1qk3A make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/1qk3A-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qk3A/struct-align/1qk3A.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qk3A/struct-align/1qk3A.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qk3A/struct-align/1qk3A.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9237/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -157.101044 Database has 3 sequences with 619 residues. gzip -f 1qk3A/1qk3A-T0104-fssp-global.pw.a2m make 1qk3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/T0104-1qk3A-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.745380 Database has 3 sequences with 619 residues. gzip -f 1qk3A/T0104-1qk3A-local.pw.a2m make 1qk3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/1qk3A-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qk3A/nostruct-align/1qk3A.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qk3A/nostruct-align/1qk3A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qk3A/nostruct-align/1qk3A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2479/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -121.916046 Database has 3 sequences with 619 residues. gzip -f 1qk3A/1qk3A-T0104-local.pw.a2m make 1qk3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/T0104-1qk3A-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -49.071697 Database has 3 sequences with 619 residues. gzip -f 1qk3A/T0104-1qk3A-vit.pw.a2m make 1qk3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/1qk3A-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1q/1qk3A/nostruct-align/1qk3A.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qk3A/nostruct-align/1qk3A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qk3A/nostruct-align/1qk3A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2479/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -118.882050 Database has 3 sequences with 619 residues. gzip -f 1qk3A/1qk3A-T0104-vit.pw.a2m make 1qk3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/T0104-1qk3A-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -34.121052 Database has 3 sequences with 619 residues. gzip -f 1qk3A/T0104-1qk3A-global.pw.a2m make 1qk3A make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/1qk3A-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qk3A/nostruct-align/1qk3A.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qk3A/nostruct-align/1qk3A.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qk3A/nostruct-align/1qk3A.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-2479/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -117.958374 Database has 3 sequences with 619 residues. gzip -f 1qk3A/1qk3A-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qk3A/xxxx-1qk3A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nulA PRED2=1n joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1n/1nulA/struct-align/1nulA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1n/1nulA/struct-align/1nulA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12317 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12317/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1n/1nulA/struct-align/1nulA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1n/1nulA/struct-align/1nulA.fssp.a2m.gz (25 sequences, 142 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12317/tmp.a2m. Dropping 5 (of 25) duplicate sequences with differing IDs Dropping 11 (of 25) sequences with > 80.0% id 9 sequences left after dropping 16 of 25 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12317/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12317/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12317/tmp.a2m (9 sequences, 142 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12317/tmp.mod /projects/compbio/experiments/models.97/pdb/1n/1nulA/struct-align/1nulA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1nulA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 1nulA fixmode 1nulA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/1nulA-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nulA/struct-align/1nulA.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nulA/struct-align/1nulA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nulA/struct-align/1nulA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12317/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -82.659355 Database has 3 sequences with 452 residues. gzip -f 1nulA/1nulA-T0104-fssp-global.pw.a2m make 1nulA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/T0104-1nulA-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -52.596905 Database has 3 sequences with 452 residues. gzip -f 1nulA/T0104-1nulA-local.pw.a2m make 1nulA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/1nulA-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nulA/nostruct-align/1nulA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nulA/nostruct-align/1nulA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nulA/nostruct-align/1nulA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14867/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -70.811584 Database has 3 sequences with 452 residues. gzip -f 1nulA/1nulA-T0104-local.pw.a2m make 1nulA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/T0104-1nulA-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -48.732574 Database has 3 sequences with 452 residues. gzip -f 1nulA/T0104-1nulA-vit.pw.a2m make 1nulA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/1nulA-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1n/1nulA/nostruct-align/1nulA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nulA/nostruct-align/1nulA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nulA/nostruct-align/1nulA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14867/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -66.750908 Database has 3 sequences with 452 residues. gzip -f 1nulA/1nulA-T0104-vit.pw.a2m make 1nulA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/T0104-1nulA-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -42.620361 Database has 3 sequences with 452 residues. gzip -f 1nulA/T0104-1nulA-global.pw.a2m make 1nulA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/1nulA-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nulA/nostruct-align/1nulA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nulA/nostruct-align/1nulA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nulA/nostruct-align/1nulA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-14867/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -69.044365 Database has 3 sequences with 452 residues. gzip -f 1nulA/1nulA-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nulA/xxxx-1nulA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1a3c PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1a/1a3c/struct-align/1a3c.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1a/1a3c/struct-align/1a3c.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10443 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10443/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1a/1a3c/struct-align/1a3c.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1a/1a3c/struct-align/1a3c.fssp.a2m.gz (12 sequences, 166 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10443/tmp.a2m. Dropping 3 (of 12) sequences with > 80.0% id 9 sequences left after dropping 3 of 12 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10443/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10443/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10443/tmp.a2m (9 sequences, 166 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10443/tmp.mod /projects/compbio/experiments/models.97/pdb/1a/1a3c/struct-align/1a3c.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1a3c make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 1a3c fixmode 1a3c make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/1a3c-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a3c/struct-align/1a3c.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a3c/struct-align/1a3c.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1a3c/struct-align/1a3c.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-10443/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -88.488686 Database has 3 sequences with 505 residues. gzip -f 1a3c/1a3c-T0104-fssp-global.pw.a2m make 1a3c make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/T0104-1a3c-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -52.612335 Database has 3 sequences with 505 residues. gzip -f 1a3c/T0104-1a3c-local.pw.a2m make 1a3c make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/1a3c-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a3c/nostruct-align/1a3c.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a3c/nostruct-align/1a3c.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1a3c/nostruct-align/1a3c.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24708/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -81.220673 Database has 3 sequences with 505 residues. gzip -f 1a3c/1a3c-T0104-local.pw.a2m make 1a3c make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/T0104-1a3c-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.827656 Database has 3 sequences with 505 residues. gzip -f 1a3c/T0104-1a3c-vit.pw.a2m make 1a3c make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/1a3c-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1a/1a3c/nostruct-align/1a3c.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a3c/nostruct-align/1a3c.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1a3c/nostruct-align/1a3c.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24708/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -77.851997 Database has 3 sequences with 505 residues. gzip -f 1a3c/1a3c-T0104-vit.pw.a2m make 1a3c make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/T0104-1a3c-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -41.270691 Database has 3 sequences with 505 residues. gzip -f 1a3c/T0104-1a3c-global.pw.a2m make 1a3c make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/1a3c-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/1a/1a3c/nostruct-align/1a3c.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1a/1a3c/nostruct-align/1a3c.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1a/1a3c/nostruct-align/1a3c.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-24708/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -78.335350 Database has 3 sequences with 505 residues. gzip -f 1a3c/1a3c-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a3c/xxxx-1a3c-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1opr PRED2=1o joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1o/1opr/struct-align/1opr.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1o/1opr/struct-align/1opr.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9562 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9562/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1o/1opr/struct-align/1opr.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1o/1opr/struct-align/1opr.fssp.a2m.gz (12 sequences, 213 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9562/tmp.a2m. Dropping 3 (of 12) sequences with > 80.0% id 9 sequences left after dropping 3 of 12 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9562/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9562/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9562/tmp.a2m (9 sequences, 213 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9562/tmp.mod /projects/compbio/experiments/models.97/pdb/1o/1opr/struct-align/1opr.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1opr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 1opr fixmode 1opr make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1opr/1opr-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1o/1opr/struct-align/1opr.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1o/1opr/struct-align/1opr.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1o/1opr/struct-align/1opr.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9562/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -129.871017 Database has 3 sequences with 584 residues. gzip -f 1opr/1opr-T0104-fssp-global.pw.a2m make 1opr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1opr/T0104-1opr-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -52.354309 Database has 3 sequences with 584 residues. gzip -f 1opr/T0104-1opr-local.pw.a2m make 1opr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1opr/1opr-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6700/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -115.080963 Database has 3 sequences with 584 residues. gzip -f 1opr/1opr-T0104-local.pw.a2m make 1opr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1opr/T0104-1opr-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -47.177654 Database has 3 sequences with 584 residues. gzip -f 1opr/T0104-1opr-vit.pw.a2m make 1opr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1opr/1opr-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6700/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -111.749969 Database has 3 sequences with 584 residues. gzip -f 1opr/1opr-T0104-vit.pw.a2m make 1opr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1opr/T0104-1opr-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -33.653687 Database has 3 sequences with 584 residues. gzip -f 1opr/T0104-1opr-global.pw.a2m make 1opr make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1opr/1opr-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1o/1opr/nostruct-align/1opr.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6700/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -113.508720 Database has 3 sequences with 584 residues. gzip -f 1opr/1opr-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1opr/xxxx-1opr-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1 hits now trying 3.31.1 hits make -k PRED=5p21 PRED2=5p joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5p/5p21/struct-align/5p21.fssp-w0.5.mod', needed by `5p21/5p21-T0104-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5p21/xxxx-5p21-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1ctqA PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ctqA/xxxx-1ctqA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1kao PRED2=1k joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1k/1kao/struct-align/1kao.fssp-w0.5.mod', needed by `1kao/1kao-T0104-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1kao/xxxx-1kao-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1byuA PRED2=1b joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1byuA/xxxx-1byuA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3vtk PRED2=3v joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/3v/3vtk/struct-align/3vtk.fssp-w0.5.mod', needed by `3vtk/3vtk-T0104-fssp-global.pw.a2m.gz'. make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3vtk/xxxx-3vtk-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1skyE PRED2=1s joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1skyE/xxxx-1skyE-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1d2mA PRED2=1d joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d2mA/xxxx-1d2mA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1.1 hits now trying 3.31.1.1 hits make -k PRED=1ckeA PRED2=1c joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ckeA/xxxx-1ckeA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1zin PRED2=1z joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1z/1zin/struct-align/1zin.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1z/1zin/struct-align/1zin.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12565 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12565/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1z/1zin/struct-align/1zin.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1z/1zin/struct-align/1zin.fssp.a2m.gz (43 sequences, 217 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12565/tmp.a2m. Dropping 17 (of 43) duplicate sequences with differing IDs Dropping 5 (of 43) sequences with > 80.0% id 21 sequences left after dropping 22 of 43 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12565/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12565/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12565/tmp.a2m (21 sequences, 217 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12565/tmp.mod /projects/compbio/experiments/models.97/pdb/1z/1zin/struct-align/1zin.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1zin make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 1zin fixmode 1zin make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1zin/1zin-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1z/1zin/struct-align/1zin.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1z/1zin/struct-align/1zin.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1z/1zin/struct-align/1zin.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-12565/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -126.066704 Database has 3 sequences with 592 residues. gzip -f 1zin/1zin-T0104-fssp-global.pw.a2m make 1zin make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1zin/T0104-1zin-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.657246 Database has 3 sequences with 592 residues. gzip -f 1zin/T0104-1zin-local.pw.a2m make 1zin make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1zin/1zin-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/1z/1zin/nostruct-align/1zin.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1z/1zin/nostruct-align/1zin.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1z/1zin/nostruct-align/1zin.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31675/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -142.427567 Database has 3 sequences with 592 residues. gzip -f 1zin/1zin-T0104-local.pw.a2m make 1zin make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1zin/T0104-1zin-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -52.367229 Database has 3 sequences with 592 residues. gzip -f 1zin/T0104-1zin-vit.pw.a2m make 1zin make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1zin/1zin-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1z/1zin/nostruct-align/1zin.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1z/1zin/nostruct-align/1zin.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1z/1zin/nostruct-align/1zin.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31675/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -139.145889 Database has 3 sequences with 592 residues. gzip -f 1zin/1zin-T0104-vit.pw.a2m make 1zin make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1zin/T0104-1zin-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -32.897663 Database has 3 sequences with 592 residues. gzip -f 1zin/T0104-1zin-global.pw.a2m make 1zin make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1zin/1zin-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/1z/1zin/nostruct-align/1zin.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1z/1zin/nostruct-align/1zin.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1z/1zin/nostruct-align/1zin.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-31675/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -140.463684 Database has 3 sequences with 592 residues. gzip -f 1zin/1zin-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1zin/xxxx-1zin-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nksA PRED2=1n joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1n/1nksA/struct-align/1nksA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1n/1nksA/struct-align/1nksA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6543 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6543/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1n/1nksA/struct-align/1nksA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1n/1nksA/struct-align/1nksA.fssp.a2m.gz (22 sequences, 194 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6543/tmp.a2m. Dropping 5 (of 22) duplicate sequences with differing IDs 17 sequences left after dropping 5 of 22 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6543/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6543/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6543/tmp.a2m (17 sequences, 194 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6543/tmp.mod /projects/compbio/experiments/models.97/pdb/1n/1nksA/struct-align/1nksA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1nksA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 1nksA fixmode 1nksA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/1nksA-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nksA/struct-align/1nksA.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nksA/struct-align/1nksA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nksA/struct-align/1nksA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-6543/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -89.462013 Database has 3 sequences with 546 residues. gzip -f 1nksA/1nksA-T0104-fssp-global.pw.a2m make 1nksA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/T0104-1nksA-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.557232 Database has 3 sequences with 546 residues. gzip -f 1nksA/T0104-1nksA-local.pw.a2m make 1nksA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/1nksA-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nksA/nostruct-align/1nksA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nksA/nostruct-align/1nksA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nksA/nostruct-align/1nksA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-15016/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -96.930565 Database has 3 sequences with 546 residues. gzip -f 1nksA/1nksA-T0104-local.pw.a2m make 1nksA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/T0104-1nksA-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -49.921223 Database has 3 sequences with 546 residues. gzip -f 1nksA/T0104-1nksA-vit.pw.a2m make 1nksA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/1nksA-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1n/1nksA/nostruct-align/1nksA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nksA/nostruct-align/1nksA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nksA/nostruct-align/1nksA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-15016/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -92.927238 Database has 3 sequences with 546 residues. gzip -f 1nksA/1nksA-T0104-vit.pw.a2m make 1nksA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/T0104-1nksA-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -36.175049 Database has 3 sequences with 546 residues. gzip -f 1nksA/T0104-1nksA-global.pw.a2m make 1nksA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/1nksA-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/1n/1nksA/nostruct-align/1nksA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1n/1nksA/nostruct-align/1nksA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1n/1nksA/nostruct-align/1nksA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-15016/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -96.202698 Database has 3 sequences with 546 residues. gzip -f 1nksA/1nksA-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nksA/xxxx-1nksA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3tmkA PRED2=3t joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/3t/3tmkA/struct-align/3tmkA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/3t/3tmkA/struct-align/3tmkA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7347 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7347/tmp -alignfile /projects/compbio/experiments/models.97/pdb/3t/3tmkA/struct-align/3tmkA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/3t/3tmkA/struct-align/3tmkA.fssp.a2m.gz (22 sequences, 216 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7347/tmp.a2m. Dropping 7 (of 22) duplicate sequences with differing IDs Dropping 4 (of 22) sequences with > 80.0% id 11 sequences left after dropping 11 of 22 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7347/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7347/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7347/tmp.a2m (11 sequences, 216 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7347/tmp.mod /projects/compbio/experiments/models.97/pdb/3t/3tmkA/struct-align/3tmkA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 3tmkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 3tmkA fixmode 3tmkA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/3tmkA-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/3t/3tmkA/struct-align/3tmkA.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/3t/3tmkA/struct-align/3tmkA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/3t/3tmkA/struct-align/3tmkA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-7347/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -129.156677 Database has 3 sequences with 590 residues. gzip -f 3tmkA/3tmkA-T0104-fssp-global.pw.a2m make 3tmkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/T0104-3tmkA-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -54.121643 Database has 3 sequences with 590 residues. gzip -f 3tmkA/T0104-3tmkA-local.pw.a2m make 3tmkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/3tmkA-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6177/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -121.938942 Database has 3 sequences with 590 residues. gzip -f 3tmkA/3tmkA-T0104-local.pw.a2m make 3tmkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/T0104-3tmkA-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -50.554974 Database has 3 sequences with 590 residues. gzip -f 3tmkA/T0104-3tmkA-vit.pw.a2m make 3tmkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/3tmkA-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6177/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -117.499947 Database has 3 sequences with 590 residues. gzip -f 3tmkA/3tmkA-T0104-vit.pw.a2m make 3tmkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/T0104-3tmkA-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -35.203693 Database has 3 sequences with 590 residues. gzip -f 3tmkA/T0104-3tmkA-global.pw.a2m make 3tmkA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/3tmkA-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/3t/3tmkA/nostruct-align/3tmkA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-6177/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -121.065361 Database has 3 sequences with 590 residues. gzip -f 3tmkA/3tmkA-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3tmkA/xxxx-3tmkA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1dekA PRED2=1d joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1d/1dekA/struct-align/1dekA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1d/1dekA/struct-align/1dekA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9661 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9661/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1d/1dekA/struct-align/1dekA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1d/1dekA/struct-align/1dekA.fssp.a2m.gz (14 sequences, 241 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9661/tmp.a2m. Dropping 3 (of 14) sequences with > 80.0% id 11 sequences left after dropping 3 of 14 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9661/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9661/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9661/tmp.a2m (11 sequences, 241 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9661/tmp.mod /projects/compbio/experiments/models.97/pdb/1d/1dekA/struct-align/1dekA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1dekA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 1dekA fixmode 1dekA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/1dekA-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dekA/struct-align/1dekA.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dekA/struct-align/1dekA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dekA/struct-align/1dekA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9661/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -151.521027 Database has 3 sequences with 640 residues. gzip -f 1dekA/1dekA-T0104-fssp-global.pw.a2m make 1dekA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/T0104-1dekA-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.143940 Database has 3 sequences with 640 residues. gzip -f 1dekA/T0104-1dekA-local.pw.a2m make 1dekA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/1dekA-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dekA/nostruct-align/1dekA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dekA/nostruct-align/1dekA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dekA/nostruct-align/1dekA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30158/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -195.949295 Database has 3 sequences with 640 residues. gzip -f 1dekA/1dekA-T0104-local.pw.a2m make 1dekA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/T0104-1dekA-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -49.427288 Database has 3 sequences with 640 residues. gzip -f 1dekA/T0104-1dekA-vit.pw.a2m make 1dekA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/1dekA-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1d/1dekA/nostruct-align/1dekA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dekA/nostruct-align/1dekA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dekA/nostruct-align/1dekA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30158/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -192.611954 Database has 3 sequences with 640 residues. gzip -f 1dekA/1dekA-T0104-vit.pw.a2m make 1dekA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/T0104-1dekA-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -30.071045 Database has 3 sequences with 640 residues. gzip -f 1dekA/T0104-1dekA-global.pw.a2m make 1dekA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/1dekA-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/1d/1dekA/nostruct-align/1dekA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1d/1dekA/nostruct-align/1dekA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1d/1dekA/nostruct-align/1dekA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-30158/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -190.048050 Database has 3 sequences with 640 residues. gzip -f 1dekA/1dekA-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dekA/xxxx-1dekA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1gky PRED2=1g joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1g/1gky/struct-align/1gky.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1g/1gky/struct-align/1gky.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8169 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8169/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1g/1gky/struct-align/1gky.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1g/1gky/struct-align/1gky.fssp.a2m.gz (12 sequences, 186 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8169/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8169/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8169/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8169/tmp.a2m (12 sequences, 186 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8169/tmp.mod /projects/compbio/experiments/models.97/pdb/1g/1gky/struct-align/1gky.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1gky make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 1gky fixmode 1gky make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1gky/1gky-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gky/struct-align/1gky.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gky/struct-align/1gky.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1g/1gky/struct-align/1gky.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-8169/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -101.618034 Database has 3 sequences with 531 residues. gzip -f 1gky/1gky-T0104-fssp-global.pw.a2m make 1gky make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1gky/T0104-1gky-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -59.951538 Database has 3 sequences with 531 residues. gzip -f 1gky/T0104-1gky-local.pw.a2m make 1gky make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1gky/1gky-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gky/nostruct-align/1gky.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gky/nostruct-align/1gky.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1g/1gky/nostruct-align/1gky.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26439/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -117.618553 Database has 3 sequences with 531 residues. gzip -f 1gky/1gky-T0104-local.pw.a2m make 1gky make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1gky/T0104-1gky-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -54.868877 Database has 3 sequences with 531 residues. gzip -f 1gky/T0104-1gky-vit.pw.a2m make 1gky make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1gky/1gky-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1g/1gky/nostruct-align/1gky.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gky/nostruct-align/1gky.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1g/1gky/nostruct-align/1gky.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26439/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -113.688545 Database has 3 sequences with 531 residues. gzip -f 1gky/1gky-T0104-vit.pw.a2m make 1gky make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1gky/T0104-1gky-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -41.058716 Database has 3 sequences with 531 residues. gzip -f 1gky/T0104-1gky-global.pw.a2m make 1gky make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1gky/1gky-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/1g/1gky/nostruct-align/1gky.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1g/1gky/nostruct-align/1gky.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1g/1gky/nostruct-align/1gky.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-26439/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -113.911018 Database has 3 sequences with 531 residues. gzip -f 1gky/1gky-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gky/xxxx-1gky-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=5tmpA PRED2=5t joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5t/5tmpA/struct-align/5tmpA.fssp-w0.5.mod', needed by `5tmpA/5tmpA-T0104-fssp-global.pw.a2m.gz'. make 5tmpA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 5tmpA fixmode 5tmpA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/T0104-5tmpA-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.738708 Database has 3 sequences with 581 residues. gzip -f 5tmpA/T0104-5tmpA-local.pw.a2m make 5tmpA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/5tmpA-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-28047/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -115.082031 Database has 3 sequences with 581 residues. gzip -f 5tmpA/5tmpA-T0104-local.pw.a2m make 5tmpA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/T0104-5tmpA-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.499714 Database has 3 sequences with 581 residues. gzip -f 5tmpA/T0104-5tmpA-vit.pw.a2m make 5tmpA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/5tmpA-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-28047/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -110.401695 Database has 3 sequences with 581 residues. gzip -f 5tmpA/5tmpA-T0104-vit.pw.a2m make 5tmpA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/T0104-5tmpA-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -33.434040 Database has 3 sequences with 581 residues. gzip -f 5tmpA/T0104-5tmpA-global.pw.a2m make 5tmpA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/5tmpA-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/5t/5tmpA/nostruct-align/5tmpA.t99-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-28047/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -112.004372 Database has 3 sequences with 581 residues. gzip -f 5tmpA/5tmpA-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5tmpA/xxxx-5tmpA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qhiA PRED2=1q joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' /projects/compbio/bin/scripts/w0.5 /projects/compbio/experiments/models.97/pdb/1q/1qhiA/struct-align/1qhiA.fssp.a2m.gz /projects/compbio/experiments/models.97/pdb/1q/1qhiA/struct-align/1qhiA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9901 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9901/tmp -alignfile /projects/compbio/experiments/models.97/pdb/1q/1qhiA/struct-align/1qhiA.fssp.a2m.gz \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file /projects/compbio/experiments/models.97/pdb/1q/1qhiA/struct-align/1qhiA.fssp.a2m.gz (27 sequences, 300 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9901/tmp.a2m. Dropping 10 (of 27) duplicate sequences with differing IDs Dropping 10 (of 27) sequences with > 80.0% id 7 sequences left after dropping 20 of 27 sequences. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9901/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9901/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (June, 2000) compiled 07/06/00_15:43:15 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9901/tmp.a2m (7 sequences, 300 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9901/tmp.mod /projects/compbio/experiments/models.97/pdb/1q/1qhiA/struct-align/1qhiA.fssp-w0.5.mod Reading /projects/compbio/bin/scripts/sam-t99.confmake 1qhiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' mkdir 1qhiA fixmode 1qhiA make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/1qhiA-T0104-fssp-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qhiA/struct-align/1qhiA.fssp-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qhiA/struct-align/1qhiA.fssp-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qhiA/struct-align/1qhiA.fssp-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-9901/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -194.249390 Database has 3 sequences with 824 residues. gzip -f 1qhiA/1qhiA-T0104-fssp-global.pw.a2m make 1qhiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/T0104-1qhiA-local.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.724018 Database has 3 sequences with 824 residues. gzip -f 1qhiA/T0104-1qhiA-local.pw.a2m make 1qhiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/1qhiA-T0104-local.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qhiA/nostruct-align/1qhiA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq \ -adpstyle 5 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qhiA/nostruct-align/1qhiA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qhiA/nostruct-align/1qhiA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12376/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -191.478027 Database has 3 sequences with 824 residues. gzip -f 1qhiA/1qhiA-T0104-local.pw.a2m make 1qhiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/T0104-1qhiA-vit.pw \ -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.495686 Database has 3 sequences with 824 residues. gzip -f 1qhiA/T0104-1qhiA-vit.pw.a2m make 1qhiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/1qhiA-T0104-vit.pw \ -i /projects/compbio/experiments/models.97/pdb/1q/1qhiA/nostruct-align/1qhiA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq \ -viterbi 1 -sw 2 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qhiA/nostruct-align/1qhiA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qhiA/nostruct-align/1qhiA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12376/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -188.384689 Database has 3 sequences with 824 residues. gzip -f 1qhiA/1qhiA-T0104-vit.pw.a2m make 1qhiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/T0104-1qhiA-global.pw -i T0104.t2k-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file T0104.t2k-w0.5.mod T0104.t2k-w0.5.mod(23): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -15.793355 Database has 3 sequences with 824 residues. gzip -f 1qhiA/T0104-1qhiA-global.pw.a2m make 1qhiA make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/1qhiA-T0104-global.pw -i /projects/compbio/experiments/models.97/pdb/1q/1qhiA/nostruct-align/1qhiA.t99-w0.5.mod -db T0104.seq -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq \ -adpstyle 5 -sw 0 \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 Reading parameter file /projects/compbio/experiments/models.97/pdb/1q/1qhiA/nostruct-align/1qhiA.t99-w0.5.mod /projects/compbio/experiments/models.97/pdb/1q/1qhiA/nostruct-align/1qhiA.t99-w0.5.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-alpha-12376/tmp.a2m SAM: hmmscore v3.2 (June, 2000) compiled 07/06/00_15:43:01 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: -182.821350 Database has 3 sequences with 824 residues. gzip -f 1qhiA/1qhiA-T0104-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qhiA/xxxx-1qhiA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo "now trying 3.56.1 hits (not ours)" now trying 3.56.1 hits (not ours) make -k PRED=1tc1A PRED2=1t joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tc1A/xxxx-1tc1A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qk3A PRED2=1q joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qk3A/xxxx-1qk3A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nulA PRED2=1n joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nulA/xxxx-1nulA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1a3c PRED2=1a joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a3c/xxxx-1a3c-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1opr PRED2=1o joint make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1opr/xxxx-1opr-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1 hits now trying 3.31.1 hits make -k PRED=5p21 PRED2=5p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5p/5p21/struct-align/5p21.fssp-w0.5.mod', needed by `5p21/5p21-T0104-fssp-global.pw.a2m.gz'. /projects/compbio/experiments/models.97/scripts/2nd-rdb-to-sam-model T0104.t2k.2d.rdb T0104.t2k-2d.mod make 5p21 make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5p21' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5p21/T0104-5p21-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 5p21 Error in locating FIM delete in 5p21 . Average NLL-Simple NULL score: -59.481480 Database has 3 sequences with 490 residues. gzip -f 5p21/T0104-5p21-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5p21/xxxx-5p21-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1ctqA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1ctqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ctqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ctqA/T0104-1ctqA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1ctqA Error in locating FIM delete in 1ctqA . Average NLL-Simple NULL score: -60.847813 Database has 3 sequences with 490 residues. gzip -f 1ctqA/T0104-1ctqA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ctqA/xxxx-1ctqA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1kao PRED2=1k joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1k/1kao/struct-align/1kao.fssp-w0.5.mod', needed by `1kao/1kao-T0104-fssp-global.pw.a2m.gz'. make 1kao make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1kao' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1kao/T0104-1kao-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1kao Error in locating FIM delete in 1kao . Average NLL-Simple NULL score: -58.494503 Database has 3 sequences with 492 residues. gzip -f 1kao/T0104-1kao-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1kao/xxxx-1kao-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1byuA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1byuA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1byuA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1byuA/T0104-1byuA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1byuA Error in locating FIM delete in 1byuA . Average NLL-Simple NULL score: -55.154972 Database has 3 sequences with 576 residues. gzip -f 1byuA/T0104-1byuA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1byuA/xxxx-1byuA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3vtk PRED2=3v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/3v/3vtk/struct-align/3vtk.fssp-w0.5.mod', needed by `3vtk/3vtk-T0104-fssp-global.pw.a2m.gz'. make 3vtk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3vtk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3vtk/T0104-3vtk-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 3vtk Error in locating FIM delete in 3vtk . Average NLL-Simple NULL score: -53.356014 Database has 3 sequences with 814 residues. gzip -f 3vtk/T0104-3vtk-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3vtk/xxxx-3vtk-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1skyE PRED2=1s joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1skyE make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1skyE' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1skyE/T0104-1skyE-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1skyE Error in locating FIM delete in 1skyE . Average NLL-Simple NULL score: -57.738560 Database has 3 sequences with 1101 residues. gzip -f 1skyE/T0104-1skyE-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1skyE/xxxx-1skyE-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1d2mA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1d2mA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1d2mA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1d2mA/T0104-1d2mA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1d2mA Error in locating FIM delete in 1d2mA . Average NLL-Simple NULL score: -60.616024 Database has 3 sequences with 1375 residues. gzip -f 1d2mA/T0104-1d2mA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d2mA/xxxx-1d2mA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1.1 hits now trying 3.31.1.1 hits make -k PRED=1ckeA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1ckeA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ckeA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ckeA/T0104-1ckeA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1ckeA Error in locating FIM delete in 1ckeA . Average NLL-Simple NULL score: -59.419144 Database has 3 sequences with 597 residues. gzip -f 1ckeA/T0104-1ckeA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ckeA/xxxx-1ckeA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1zin PRED2=1z joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1zin make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1zin/T0104-1zin-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1zin Error in locating FIM delete in 1zin . Average NLL-Simple NULL score: -55.506912 Database has 3 sequences with 592 residues. gzip -f 1zin/T0104-1zin-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1zin/xxxx-1zin-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nksA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1nksA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/T0104-1nksA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1nksA Error in locating FIM delete in 1nksA . Average NLL-Simple NULL score: -53.281590 Database has 3 sequences with 546 residues. gzip -f 1nksA/T0104-1nksA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nksA/xxxx-1nksA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3tmkA PRED2=3t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 3tmkA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/T0104-3tmkA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 3tmkA Error in locating FIM delete in 3tmkA . Average NLL-Simple NULL score: -56.238621 Database has 3 sequences with 590 residues. gzip -f 3tmkA/T0104-3tmkA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3tmkA/xxxx-3tmkA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1dekA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1dekA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/T0104-1dekA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1dekA Error in locating FIM delete in 1dekA . Average NLL-Simple NULL score: -52.947628 Database has 3 sequences with 640 residues. gzip -f 1dekA/T0104-1dekA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dekA/xxxx-1dekA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1gky PRED2=1g joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1gky make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1gky/T0104-1gky-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1gky Error in locating FIM delete in 1gky . Average NLL-Simple NULL score: -56.437534 Database has 3 sequences with 531 residues. gzip -f 1gky/T0104-1gky-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gky/xxxx-1gky-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=5tmpA PRED2=5t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5t/5tmpA/struct-align/5tmpA.fssp-w0.5.mod', needed by `5tmpA/5tmpA-T0104-fssp-global.pw.a2m.gz'. make 5tmpA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/T0104-5tmpA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 5tmpA Error in locating FIM delete in 5tmpA . Average NLL-Simple NULL score: -55.707188 Database has 3 sequences with 581 residues. gzip -f 5tmpA/T0104-5tmpA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5tmpA/xxxx-5tmpA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qhiA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1qhiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/T0104-1qhiA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 5 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) Error in locating FIM delete in 1qhiA Error in locating FIM delete in 1qhiA . Average NLL-Simple NULL score: -53.227005 Database has 3 sequences with 824 residues. gzip -f 1qhiA/T0104-1qhiA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qhiA/xxxx-1qhiA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo "now trying 3.56.1 hits (not ours)" now trying 3.56.1 hits (not ours) make -k PRED=1tc1A PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1tc1A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/T0104-1tc1A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.740025 Database has 3 sequences with 553 residues. gzip -f 1tc1A/T0104-1tc1A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tc1A/xxxx-1tc1A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qk3A PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1qk3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/T0104-1qk3A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.016026 Database has 3 sequences with 619 residues. gzip -f 1qk3A/T0104-1qk3A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qk3A/xxxx-1qk3A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nulA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1nulA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/T0104-1nulA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.812748 Database has 3 sequences with 452 residues. gzip -f 1nulA/T0104-1nulA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nulA/xxxx-1nulA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1a3c PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1a3c make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/T0104-1a3c-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -61.175327 Database has 3 sequences with 505 residues. gzip -f 1a3c/T0104-1a3c-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a3c/xxxx-1a3c-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1opr PRED2=1o joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1opr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1opr/T0104-1opr-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -54.337948 Database has 3 sequences with 584 residues. gzip -f 1opr/T0104-1opr-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1opr/xxxx-1opr-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1 hits now trying 3.31.1 hits make -k PRED=5p21 PRED2=5p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5p/5p21/struct-align/5p21.fssp-w0.5.mod', needed by `5p21/5p21-T0104-fssp-global.pw.a2m.gz'. make 5p21 make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5p21' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5p21/T0104-5p21-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -59.481480 Database has 3 sequences with 490 residues. gzip -f 5p21/T0104-5p21-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5p21/xxxx-5p21-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1ctqA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1ctqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ctqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ctqA/T0104-1ctqA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -60.847813 Database has 3 sequences with 490 residues. gzip -f 1ctqA/T0104-1ctqA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ctqA/xxxx-1ctqA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1kao PRED2=1k joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1k/1kao/struct-align/1kao.fssp-w0.5.mod', needed by `1kao/1kao-T0104-fssp-global.pw.a2m.gz'. make 1kao make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1kao' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1kao/T0104-1kao-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -58.494503 Database has 3 sequences with 492 residues. gzip -f 1kao/T0104-1kao-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1kao/xxxx-1kao-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1byuA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1byuA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1byuA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1byuA/T0104-1byuA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.154972 Database has 3 sequences with 576 residues. gzip -f 1byuA/T0104-1byuA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1byuA/xxxx-1byuA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3vtk PRED2=3v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/3v/3vtk/struct-align/3vtk.fssp-w0.5.mod', needed by `3vtk/3vtk-T0104-fssp-global.pw.a2m.gz'. make 3vtk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3vtk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3vtk/T0104-3vtk-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.356014 Database has 3 sequences with 814 residues. gzip -f 3vtk/T0104-3vtk-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3vtk/xxxx-3vtk-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1skyE PRED2=1s joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1skyE make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1skyE' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1skyE/T0104-1skyE-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -57.738560 Database has 3 sequences with 1101 residues. gzip -f 1skyE/T0104-1skyE-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1skyE/xxxx-1skyE-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1d2mA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1d2mA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1d2mA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1d2mA/T0104-1d2mA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -60.616024 Database has 3 sequences with 1375 residues. gzip -f 1d2mA/T0104-1d2mA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d2mA/xxxx-1d2mA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1.1 hits now trying 3.31.1.1 hits make -k PRED=1ckeA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1ckeA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ckeA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ckeA/T0104-1ckeA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -59.419144 Database has 3 sequences with 597 residues. gzip -f 1ckeA/T0104-1ckeA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ckeA/xxxx-1ckeA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1zin PRED2=1z joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1zin make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1zin/T0104-1zin-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.506912 Database has 3 sequences with 592 residues. gzip -f 1zin/T0104-1zin-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1zin/xxxx-1zin-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nksA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1nksA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/T0104-1nksA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.281590 Database has 3 sequences with 546 residues. gzip -f 1nksA/T0104-1nksA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nksA/xxxx-1nksA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3tmkA PRED2=3t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 3tmkA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/T0104-3tmkA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.238621 Database has 3 sequences with 590 residues. gzip -f 3tmkA/T0104-3tmkA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3tmkA/xxxx-3tmkA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1dekA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1dekA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/T0104-1dekA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -52.947628 Database has 3 sequences with 640 residues. gzip -f 1dekA/T0104-1dekA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dekA/xxxx-1dekA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1gky PRED2=1g joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1gky make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1gky/T0104-1gky-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.437534 Database has 3 sequences with 531 residues. gzip -f 1gky/T0104-1gky-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gky/xxxx-1gky-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=5tmpA PRED2=5t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5t/5tmpA/struct-align/5tmpA.fssp-w0.5.mod', needed by `5tmpA/5tmpA-T0104-fssp-global.pw.a2m.gz'. make 5tmpA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/T0104-5tmpA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.707188 Database has 3 sequences with 581 residues. gzip -f 5tmpA/T0104-5tmpA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5tmpA/xxxx-5tmpA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qhiA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1qhiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/T0104-1qhiA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.227005 Database has 3 sequences with 824 residues. gzip -f 1qhiA/T0104-1qhiA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qhiA/xxxx-1qhiA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo "now trying 3.56.1 hits (not ours)" now trying 3.56.1 hits (not ours) make -k PRED=1tc1A PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1tc1A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/T0104-1tc1A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.740025 Database has 3 sequences with 553 residues. gzip -f 1tc1A/T0104-1tc1A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tc1A/xxxx-1tc1A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qk3A PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1qk3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/T0104-1qk3A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.016026 Database has 3 sequences with 619 residues. gzip -f 1qk3A/T0104-1qk3A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qk3A/xxxx-1qk3A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nulA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1nulA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/T0104-1nulA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.812748 Database has 3 sequences with 452 residues. gzip -f 1nulA/T0104-1nulA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nulA/xxxx-1nulA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1a3c PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1a3c make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/T0104-1a3c-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -61.175327 Database has 3 sequences with 505 residues. gzip -f 1a3c/T0104-1a3c-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a3c/xxxx-1a3c-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1opr PRED2=1o joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1opr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1opr/T0104-1opr-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (June, 2000) compiled 07/18/00_10:49:49 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -54.337948 Database has 3 sequences with 584 residues. gzip -f 1opr/T0104-1opr-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1opr/xxxx-1opr-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1 hits now trying 3.31.1 hits make -k PRED=5p21 PRED2=5p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5p/5p21/struct-align/5p21.fssp-w0.5.mod', needed by `5p21/5p21-T0104-fssp-global.pw.a2m.gz'. make 5p21 make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5p21' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5p21/T0104-5p21-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -59.481480 Database has 3 sequences with 490 residues. gzip -f 5p21/T0104-5p21-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5p21/xxxx-5p21-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1ctqA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1ctqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ctqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ctqA/T0104-1ctqA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -60.847813 Database has 3 sequences with 490 residues. gzip -f 1ctqA/T0104-1ctqA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ctqA/xxxx-1ctqA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1kao PRED2=1k joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1k/1kao/struct-align/1kao.fssp-w0.5.mod', needed by `1kao/1kao-T0104-fssp-global.pw.a2m.gz'. make 1kao make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1kao' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1kao/T0104-1kao-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -58.494503 Database has 3 sequences with 492 residues. gzip -f 1kao/T0104-1kao-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1kao/xxxx-1kao-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1byuA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1byuA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1byuA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1byuA/T0104-1byuA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.154972 Database has 3 sequences with 576 residues. gzip -f 1byuA/T0104-1byuA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1byuA/xxxx-1byuA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3vtk PRED2=3v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/3v/3vtk/struct-align/3vtk.fssp-w0.5.mod', needed by `3vtk/3vtk-T0104-fssp-global.pw.a2m.gz'. make 3vtk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3vtk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3vtk/T0104-3vtk-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.356014 Database has 3 sequences with 814 residues. gzip -f 3vtk/T0104-3vtk-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3vtk/xxxx-3vtk-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1skyE PRED2=1s joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1skyE make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1skyE' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1skyE/T0104-1skyE-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -57.738560 Database has 3 sequences with 1101 residues. gzip -f 1skyE/T0104-1skyE-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1skyE/xxxx-1skyE-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1d2mA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1d2mA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1d2mA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1d2mA/T0104-1d2mA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -60.616024 Database has 3 sequences with 1375 residues. gzip -f 1d2mA/T0104-1d2mA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d2mA/xxxx-1d2mA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1.1 hits now trying 3.31.1.1 hits make -k PRED=1ckeA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1ckeA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ckeA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ckeA/T0104-1ckeA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -59.419144 Database has 3 sequences with 597 residues. gzip -f 1ckeA/T0104-1ckeA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ckeA/xxxx-1ckeA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1zin PRED2=1z joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1zin make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1zin/T0104-1zin-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.506912 Database has 3 sequences with 592 residues. gzip -f 1zin/T0104-1zin-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1zin/xxxx-1zin-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nksA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1nksA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/T0104-1nksA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.281590 Database has 3 sequences with 546 residues. gzip -f 1nksA/T0104-1nksA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nksA/xxxx-1nksA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3tmkA PRED2=3t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 3tmkA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/T0104-3tmkA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.238621 Database has 3 sequences with 590 residues. gzip -f 3tmkA/T0104-3tmkA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3tmkA/xxxx-3tmkA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1dekA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1dekA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/T0104-1dekA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -52.947628 Database has 3 sequences with 640 residues. gzip -f 1dekA/T0104-1dekA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dekA/xxxx-1dekA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1gky PRED2=1g joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1gky make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1gky/T0104-1gky-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.437534 Database has 3 sequences with 531 residues. gzip -f 1gky/T0104-1gky-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gky/xxxx-1gky-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=5tmpA PRED2=5t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5t/5tmpA/struct-align/5tmpA.fssp-w0.5.mod', needed by `5tmpA/5tmpA-T0104-fssp-global.pw.a2m.gz'. make 5tmpA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/T0104-5tmpA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.707188 Database has 3 sequences with 581 residues. gzip -f 5tmpA/T0104-5tmpA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5tmpA/xxxx-5tmpA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qhiA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1qhiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/T0104-1qhiA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -53.227005 Database has 3 sequences with 824 residues. gzip -f 1qhiA/T0104-1qhiA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qhiA/xxxx-1qhiA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo "now trying 3.56.1 hits (not ours)" now trying 3.56.1 hits (not ours) make -k PRED=1tc1A PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1tc1A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/T0104-1tc1A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.740025 Database has 3 sequences with 553 residues. gzip -f 1tc1A/T0104-1tc1A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tc1A/xxxx-1tc1A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qk3A PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1qk3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/T0104-1qk3A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -55.016026 Database has 3 sequences with 619 residues. gzip -f 1qk3A/T0104-1qk3A-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qk3A/xxxx-1qk3A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nulA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1nulA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/T0104-1nulA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -56.812748 Database has 3 sequences with 452 residues. gzip -f 1nulA/T0104-1nulA-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nulA/xxxx-1nulA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1a3c PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1a3c make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/T0104-1a3c-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -61.175327 Database has 3 sequences with 505 residues. gzip -f 1a3c/T0104-1a3c-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a3c/xxxx-1a3c-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1opr PRED2=1o joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1opr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1opr/T0104-1opr-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.2d \ -subtract_null 4 -simplethreshold 1 \ -select_align 8 SAM: hmmscore v3.2 (July 31, 2000) compiled 07/31/00_14:08:17 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -54.337948 Database has 3 sequences with 584 residues. gzip -f 1opr/T0104-1opr-2track-local.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1opr/xxxx-1opr-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1 hits now trying 3.31.1 hits make -k PRED=5p21 PRED2=5p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5p/5p21/struct-align/5p21.fssp-w0.5.mod', needed by `5p21/5p21-T0104-fssp-global.pw.a2m.gz'. make 5p21 make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5p21' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5p21/T0104-5p21-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 390.804108 Database has 3 sequences with 490 residues. gzip -f 5p21/T0104-5p21-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5p21/xxxx-5p21-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1ctqA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1ctqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ctqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ctqA/T0104-1ctqA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 362.488861 Database has 3 sequences with 490 residues. gzip -f 1ctqA/T0104-1ctqA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ctqA/xxxx-1ctqA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1kao PRED2=1k joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1k/1kao/struct-align/1kao.fssp-w0.5.mod', needed by `1kao/1kao-T0104-fssp-global.pw.a2m.gz'. make 1kao make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1kao' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1kao/T0104-1kao-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 451.915131 Database has 3 sequences with 492 residues. gzip -f 1kao/T0104-1kao-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1kao/xxxx-1kao-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1byuA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1byuA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1byuA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1byuA/T0104-1byuA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 1153.072876 Database has 3 sequences with 576 residues. gzip -f 1byuA/T0104-1byuA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1byuA/xxxx-1byuA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3vtk PRED2=3v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/3v/3vtk/struct-align/3vtk.fssp-w0.5.mod', needed by `3vtk/3vtk-T0104-fssp-global.pw.a2m.gz'. make 3vtk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3vtk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3vtk/T0104-3vtk-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 4091.910889 Database has 3 sequences with 814 residues. gzip -f 3vtk/T0104-3vtk-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3vtk/xxxx-3vtk-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1skyE PRED2=1s joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1skyE make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1skyE' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1skyE/T0104-1skyE-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 8231.918945 Database has 3 sequences with 1101 residues. gzip -f 1skyE/T0104-1skyE-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1skyE/xxxx-1skyE-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1d2mA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1d2mA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1d2mA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1d2mA/T0104-1d2mA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 10412.090820 Database has 3 sequences with 1375 residues. gzip -f 1d2mA/T0104-1d2mA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d2mA/xxxx-1d2mA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1.1 hits now trying 3.31.1.1 hits make -k PRED=1ckeA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1ckeA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ckeA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ckeA/T0104-1ckeA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 1459.643921 Database has 3 sequences with 597 residues. gzip -f 1ckeA/T0104-1ckeA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ckeA/xxxx-1ckeA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1zin PRED2=1z joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1zin make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1zin/T0104-1zin-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 1543.411133 Database has 3 sequences with 592 residues. gzip -f 1zin/T0104-1zin-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1zin/xxxx-1zin-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nksA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1nksA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/T0104-1nksA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 950.906189 Database has 3 sequences with 546 residues. gzip -f 1nksA/T0104-1nksA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nksA/xxxx-1nksA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3tmkA PRED2=3t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 3tmkA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/T0104-3tmkA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 1517.105103 Database has 3 sequences with 590 residues. gzip -f 3tmkA/T0104-3tmkA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3tmkA/xxxx-3tmkA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1dekA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1dekA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/T0104-1dekA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 2171.206299 Database has 3 sequences with 640 residues. gzip -f 1dekA/T0104-1dekA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dekA/xxxx-1dekA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1gky PRED2=1g joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1gky make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1gky/T0104-1gky-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 732.313782 Database has 3 sequences with 531 residues. gzip -f 1gky/T0104-1gky-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gky/xxxx-1gky-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=5tmpA PRED2=5t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5t/5tmpA/struct-align/5tmpA.fssp-w0.5.mod', needed by `5tmpA/5tmpA-T0104-fssp-global.pw.a2m.gz'. make 5tmpA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/T0104-5tmpA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 1351.422974 Database has 3 sequences with 581 residues. gzip -f 5tmpA/T0104-5tmpA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5tmpA/xxxx-5tmpA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qhiA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1qhiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/T0104-1qhiA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 3752.978271 Database has 3 sequences with 824 residues. gzip -f 1qhiA/T0104-1qhiA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qhiA/xxxx-1qhiA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo "now trying 3.56.1 hits (not ours)" now trying 3.56.1 hits (not ours) make -k PRED=1tc1A PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1tc1A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/T0104-1tc1A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 406.067841 Database has 3 sequences with 553 residues. gzip -f 1tc1A/T0104-1tc1A-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tc1A/xxxx-1tc1A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qk3A PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1qk3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/T0104-1qk3A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 1803.793945 Database has 3 sequences with 619 residues. gzip -f 1qk3A/T0104-1qk3A-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qk3A/xxxx-1qk3A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nulA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1nulA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/T0104-1nulA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: -46.159336 Database has 3 sequences with 452 residues. gzip -f 1nulA/T0104-1nulA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nulA/xxxx-1nulA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1a3c PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1a3c make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/T0104-1a3c-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 310.584137 Database has 3 sequences with 505 residues. gzip -f 1a3c/T0104-1a3c-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a3c/xxxx-1a3c-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1opr PRED2=1o joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1opr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1opr/T0104-1opr-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/tmp.a2m T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.t2k.2d.rdb Calculating Distances (. = 1000 sequences) . Average NLL-Simple NULL score: 1415.983765 Database has 3 sequences with 584 residues. gzip -f 1opr/T0104-1opr-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1opr/xxxx-1opr-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1 hits now trying 3.31.1 hits make -k PRED=5p21 PRED2=5p joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5p/5p21/struct-align/5p21.fssp-w0.5.mod', needed by `5p21/5p21-T0104-fssp-global.pw.a2m.gz'. make 5p21 make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5p21' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5p21/T0104-5p21-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6227.064941 Database has 3 sequences with 490 residues. gzip -f 5p21/T0104-5p21-2track-local.pw.a2m make 5p21 make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5p21' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5p21/T0104-5p21-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.stride.seq,/projects/compbio/experiments/models.97/pdb/5p/5p21/info/5p21.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6230.537109 Database has 3 sequences with 490 residues. gzip -f 5p21/T0104-5p21-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5p21/xxxx-5p21-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1ctqA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1ctqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ctqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ctqA/T0104-1ctqA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6225.144531 Database has 3 sequences with 490 residues. gzip -f 1ctqA/T0104-1ctqA-2track-local.pw.a2m make 1ctqA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ctqA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ctqA/T0104-1ctqA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ctqA/info/1ctqA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6228.606934 Database has 3 sequences with 490 residues. gzip -f 1ctqA/T0104-1ctqA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ctqA/xxxx-1ctqA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1kao PRED2=1k joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/1k/1kao/struct-align/1kao.fssp-w0.5.mod', needed by `1kao/1kao-T0104-fssp-global.pw.a2m.gz'. make 1kao make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1kao' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1kao/T0104-1kao-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6225.302246 Database has 3 sequences with 492 residues. gzip -f 1kao/T0104-1kao-2track-local.pw.a2m make 1kao make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1kao' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1kao/T0104-1kao-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.stride.seq,/projects/compbio/experiments/models.97/pdb/1k/1kao/info/1kao.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6228.045410 Database has 3 sequences with 492 residues. gzip -f 1kao/T0104-1kao-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1kao/xxxx-1kao-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1byuA PRED2=1b joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1byuA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1byuA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1byuA/T0104-1byuA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6244.080566 Database has 3 sequences with 576 residues. gzip -f 1byuA/T0104-1byuA-2track-local.pw.a2m make 1byuA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1byuA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1byuA/T0104-1byuA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.stride.seq,/projects/compbio/experiments/models.97/pdb/1b/1byuA/info/1byuA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6240.888672 Database has 3 sequences with 576 residues. gzip -f 1byuA/T0104-1byuA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1byuA/xxxx-1byuA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3vtk PRED2=3v joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/3v/3vtk/struct-align/3vtk.fssp-w0.5.mod', needed by `3vtk/3vtk-T0104-fssp-global.pw.a2m.gz'. make 3vtk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3vtk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3vtk/T0104-3vtk-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6251.599121 Database has 3 sequences with 814 residues. gzip -f 3vtk/T0104-3vtk-2track-local.pw.a2m make 3vtk make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3vtk' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3vtk/T0104-3vtk-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.stride.seq,/projects/compbio/experiments/models.97/pdb/3v/3vtk/info/3vtk.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6230.906250 Database has 3 sequences with 814 residues. gzip -f 3vtk/T0104-3vtk-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3vtk/xxxx-3vtk-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1skyE PRED2=1s joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1skyE make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1skyE' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1skyE/T0104-1skyE-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6267.895996 Database has 3 sequences with 1101 residues. gzip -f 1skyE/T0104-1skyE-2track-local.pw.a2m make 1skyE make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1skyE' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1skyE/T0104-1skyE-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.stride.seq,/projects/compbio/experiments/models.97/pdb/1s/1skyE/info/1skyE.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6211.098145 Database has 3 sequences with 1101 residues. gzip -f 1skyE/T0104-1skyE-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1skyE/xxxx-1skyE-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1d2mA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1d2mA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1d2mA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1d2mA/T0104-1d2mA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6265.626465 Database has 3 sequences with 1375 residues. gzip -f 1d2mA/T0104-1d2mA-2track-local.pw.a2m make 1d2mA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1d2mA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1d2mA/T0104-1d2mA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1d2mA/info/1d2mA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6197.978516 Database has 3 sequences with 1375 residues. gzip -f 1d2mA/T0104-1d2mA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1d2mA/xxxx-1d2mA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo now trying 3.31.1.1 hits now trying 3.31.1.1 hits make -k PRED=1ckeA PRED2=1c joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1ckeA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ckeA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ckeA/T0104-1ckeA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6245.835937 Database has 3 sequences with 597 residues. gzip -f 1ckeA/T0104-1ckeA-2track-local.pw.a2m make 1ckeA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1ckeA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1ckeA/T0104-1ckeA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.stride.seq,/projects/compbio/experiments/models.97/pdb/1c/1ckeA/info/1ckeA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6242.069824 Database has 3 sequences with 597 residues. gzip -f 1ckeA/T0104-1ckeA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1ckeA/xxxx-1ckeA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1zin PRED2=1z joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1zin make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1zin/T0104-1zin-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6251.617187 Database has 3 sequences with 592 residues. gzip -f 1zin/T0104-1zin-2track-local.pw.a2m make 1zin make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1zin' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1zin/T0104-1zin-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.stride.seq,/projects/compbio/experiments/models.97/pdb/1z/1zin/info/1zin.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6251.300781 Database has 3 sequences with 592 residues. gzip -f 1zin/T0104-1zin-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1zin/xxxx-1zin-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nksA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1nksA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/T0104-1nksA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6244.105469 Database has 3 sequences with 546 residues. gzip -f 1nksA/T0104-1nksA-2track-local.pw.a2m make 1nksA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nksA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nksA/T0104-1nksA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nksA/info/1nksA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6246.614746 Database has 3 sequences with 546 residues. gzip -f 1nksA/T0104-1nksA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nksA/xxxx-1nksA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=3tmkA PRED2=3t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 3tmkA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/T0104-3tmkA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6248.904785 Database has 3 sequences with 590 residues. gzip -f 3tmkA/T0104-3tmkA-2track-local.pw.a2m make 3tmkA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `3tmkA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 3tmkA/T0104-3tmkA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.stride.seq,/projects/compbio/experiments/models.97/pdb/3t/3tmkA/info/3tmkA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6246.394043 Database has 3 sequences with 590 residues. gzip -f 3tmkA/T0104-3tmkA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `3tmkA/xxxx-3tmkA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1dekA PRED2=1d joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1dekA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/T0104-1dekA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6259.765625 Database has 3 sequences with 640 residues. gzip -f 1dekA/T0104-1dekA-2track-local.pw.a2m make 1dekA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1dekA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1dekA/T0104-1dekA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.stride.seq,/projects/compbio/experiments/models.97/pdb/1d/1dekA/info/1dekA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6252.097168 Database has 3 sequences with 640 residues. gzip -f 1dekA/T0104-1dekA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1dekA/xxxx-1dekA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1gky PRED2=1g joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1gky make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1gky/T0104-1gky-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6245.191406 Database has 3 sequences with 531 residues. gzip -f 1gky/T0104-1gky-2track-local.pw.a2m make 1gky make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1gky' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1gky/T0104-1gky-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.stride.seq,/projects/compbio/experiments/models.97/pdb/1g/1gky/info/1gky.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6245.417969 Database has 3 sequences with 531 residues. gzip -f 1gky/T0104-1gky-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1gky/xxxx-1gky-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=5tmpA PRED2=5t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[1]: *** No rule to make target `/projects/compbio/experiments/models.97/pdb/5t/5tmpA/struct-align/5tmpA.fssp-w0.5.mod', needed by `5tmpA/5tmpA-T0104-fssp-global.pw.a2m.gz'. make 5tmpA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/T0104-5tmpA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6260.099121 Database has 3 sequences with 581 residues. gzip -f 5tmpA/T0104-5tmpA-2track-local.pw.a2m make 5tmpA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `5tmpA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 5tmpA/T0104-5tmpA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.stride.seq,/projects/compbio/experiments/models.97/pdb/5t/5tmpA/info/5tmpA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6257.902344 Database has 3 sequences with 581 residues. gzip -f 5tmpA/T0104-5tmpA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `5tmpA/xxxx-5tmpA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qhiA PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1qhiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/T0104-1qhiA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6251.188965 Database has 3 sequences with 824 residues. gzip -f 1qhiA/T0104-1qhiA-2track-local.pw.a2m make 1qhiA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qhiA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qhiA/T0104-1qhiA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qhiA/info/1qhiA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6228.202637 Database has 3 sequences with 824 residues. gzip -f 1qhiA/T0104-1qhiA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qhiA/xxxx-1qhiA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) echo "now trying 3.56.1 hits (not ours)" now trying 3.56.1 hits (not ours) make -k PRED=1tc1A PRED2=1t joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1tc1A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/T0104-1tc1A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6274.109375 Database has 3 sequences with 553 residues. gzip -f 1tc1A/T0104-1tc1A-2track-local.pw.a2m make 1tc1A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1tc1A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1tc1A/T0104-1tc1A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.stride.seq,/projects/compbio/experiments/models.97/pdb/1t/1tc1A/info/1tc1A.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6271.037598 Database has 3 sequences with 553 residues. gzip -f 1tc1A/T0104-1tc1A-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1tc1A/xxxx-1tc1A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1qk3A PRED2=1q joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1qk3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/T0104-1qk3A-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6278.515625 Database has 3 sequences with 619 residues. gzip -f 1qk3A/T0104-1qk3A-2track-local.pw.a2m make 1qk3A make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1qk3A' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1qk3A/T0104-1qk3A-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.stride.seq,/projects/compbio/experiments/models.97/pdb/1q/1qk3A/info/1qk3A.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6268.643066 Database has 3 sequences with 619 residues. gzip -f 1qk3A/T0104-1qk3A-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1qk3A/xxxx-1qk3A-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1nulA PRED2=1n joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1nulA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/T0104-1nulA-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -5854.291504 Database has 3 sequences with 452 residues. gzip -f 1nulA/T0104-1nulA-2track-local.pw.a2m make 1nulA make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1nulA' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1nulA/T0104-1nulA-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.stride.seq,/projects/compbio/experiments/models.97/pdb/1n/1nulA/info/1nulA.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -5856.354980 Database has 3 sequences with 452 residues. gzip -f 1nulA/T0104-1nulA-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1nulA/xxxx-1nulA-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1a3c PRED2=1a joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1a3c make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/T0104-1a3c-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6244.112793 Database has 3 sequences with 505 residues. gzip -f 1a3c/T0104-1a3c-2track-local.pw.a2m make 1a3c make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1a3c' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1a3c/T0104-1a3c-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.stride.seq,/projects/compbio/experiments/models.97/pdb/1a/1a3c/info/1a3c.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6243.803223 Database has 3 sequences with 505 residues. gzip -f 1a3c/T0104-1a3c-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1a3c/xxxx-1a3c-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored) make -k PRED=1opr PRED2=1o joint make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make 1opr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1opr/T0104-1opr-2track-local.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 2 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.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 T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6272.070312 Database has 3 sequences with 584 residues. gzip -f 1opr/T0104-1opr-2track-local.pw.a2m make 1opr make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t104' make[2]: `1opr' is up to date. make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' hmmscore 1opr/T0104-1opr-2track-global.pw \ -alphabet protein,EHL2 \ -trackcoeff 0.5,0.5 \ -sw 0 -adpstyle 1 \ -trackmod T0104.t2k-w0.5.mod,T0104.t2k-2d.mod \ -db T0104.seq,T0104.t2k.2d.seq \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride-mixed.2d \ -db /projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.stride.seq,/projects/compbio/experiments/models.97/pdb/1o/1opr/info/1opr.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. T0104.t2k-w0.5.mod(23): Reading track 0 model from MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-30480/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. T0104.t2k-2d.mod(971): Reading track 1 model from MODEL -- Model from 2nd structure file T0104.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: -6266.239746 Database has 3 sequences with 584 residues. gzip -f 1opr/T0104-1opr-2track-global.pw.a2m make[1]: *** No rule to make target `yyy/xxxx-w0.5.mod', needed by `1opr/xxxx-1opr-T0104-local.pw.a2m.gz'. make[1]: Target `joint' not remade because of errors. make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t104' make: [joints] Error 2 (ignored)