make -k und/T0086-1cg2A-local.index und/1cg2A-T0086-local.index make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/T0086-1cg2A-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/T0086-1cg2A-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1cg2A/T0086-1cg2A-local.pw.a2m.gz \ -target T0086 -template 1cg2A \ -out T0086-1cg2A-local -outdir und Sequence named 1cg2A has all gap columns. It will be included anyway. Sequence named 1cg2A has all gap columns. It will be included anyway. PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1cg2A-orig.a2m Writing a2m file: tmp/1cg2A-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-7909 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp -alignfile tmp/1cg2A-orig.a2m \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file tmp/1cg2A-orig.a2m (1 sequences, 393 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/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-beta-7909/tmp.a2m (1 sequences, 393 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp.mod tmp/1cg2A-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cg2A-align.mod tmp/1cg2A-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-7909/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1cg2A-orig.a2m tmp/1cg2A-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1cg2A-align.mod Running w0.5 tmp/1cg2A-orig.a2m tmp/1cg2A-align.mod Running align2model tmp/1cg2A-align -i tmp/1cg2A-align.mod -db tmp/1cg2A-orig.a2m -db tmp/1cg2A-pdb.a2m /projects/kestrel/users/karplus/burial/slicer/slicer: no segments found mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/1cg2A-T0086-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/1cg2A-T0086-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1cg2A/1cg2A-T0086-local.pw.a2m.gz \ -target T0086 -template 1cg2A \ -out 1cg2A-T0086-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1cg2A-orig.a2m Writing a2m file: tmp/1cg2A-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-22520 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-22520/tmp -alignfile tmp/1cg2A-orig.a2m \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (June, 2000) compiled 07/06/00_15:43:59 Reading alignment file tmp/1cg2A-orig.a2m (1 sequences, 393 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-22520/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-22520/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-22520/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-beta-22520/tmp.a2m (1 sequences, 393 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-22520/tmp.mod tmp/1cg2A-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1cg2A-align.mod tmp/1cg2A-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-22520/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1cg2A-orig.a2m tmp/1cg2A-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1cg2A-align.mod Running w0.5 tmp/1cg2A-orig.a2m tmp/1cg2A-align.mod Running align2model tmp/1cg2A-align -i tmp/1cg2A-align.mod -db tmp/1cg2A-orig.a2m -db tmp/1cg2A-pdb.a2m Debugging on ! Reading sequence file Reading input structure 124 residues read Measuring phi and psi Getting chi values LYS 1 30 GLU 2 14 ILE 3 3 PRO 4 2 LEU 6 3 PRO 8 2 GLN 9 14 LEU 10 3 LEU 11 2 ASP 12 4 THR 15 2 VAL 16 1 SER 17 3 VAL 18 1 MET 20 10 ILE 21 4 ARG 22 32 PHE 26 3 VAL 27 3 GLU 28 12 GLN 29 15 GLU 31 14 GLU 34 15 GLU 35 16 LEU 36 5 PRO 37 2 LEU 39 3 PRO 42 2 LYS 43 30 GLU 44 15 SER 45 2 ARG 46 26 TYR 47 3 TRP 48 5 LEU 49 3 ARG 50 27 GLU 51 12 ILE 52 3 LEU 54 3 CYS 55 2 ASP 57 4 GLU 59 10 PRO 60 2 TRP 61 6 ARG 65 30 THR 66 2 VAL 68 1 PRO 69 2 VAL 70 1 SER 71 2 LEU 73 3 SER 74 3 GLU 77 16 LEU 80 3 LEU 82 3 GLN 83 12 LYS 84 26 LEU 85 2 LYS 89 26 THR 90 2 PRO 91 2 LEU 92 3 ARG 94 29 TYR 95 2 PHE 98 3 THR 99 1 SER 100 2 SER 101 2 LEU 103 4 THR 104 2 ARG 105 32 ASP 106 4 PHE 107 3 ILE 108 5 GLU 109 15 ILE 110 4 ARG 112 29 ASP 113 5 LEU 118 2 TRP 119 4 ARG 121 29 ARG 122 30 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 2 rotamers of residue P 5 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 2 rotamers of residue P 9 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 32 rotamers of residue R 23 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 3 rotamers of residue F 27 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 2 rotamers of residue P 38 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 2 rotamers of residue P 61 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 2 rotamers of residue Y 96 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 3 rotamers of residue F 99 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: keepclash 3 62 12.6790 keepclash 21 40 17.9650 keepclash 47 74 29.6988 turnclash 47 4 51 0 26.3932 turnclash 47 12 78 4 40.7469 Cluster 1 = 3 62 Cluster 2 = 21 40 Cluster 3 = 47 51 74 78 8 clashing residues after turn Residue clashes: 3-62 21-40 47-74 47-51 47-78 cluster 1 has 2 members and 8.400e+01 combinations: 62 3 Energy 12.6790 Searching cluster 3 Combinations for 2 members in cluster 1 OK: 8.400e+01 - Sending to search 1.584533 < 12.678951: keeping 0.000000 < 2.181602: keeping Solved cluster 1: residual clashing 0.76 cluster 2 has 2 members and 1.800e+01 combinations: 40 21 Energy 18.5586 Searching cluster 21 Combinations for 2 members in cluster 2 OK: 1.800e+01 - Sending to search 0.000000 < 18.558586: keeping 0.000000 < 0.767698: keeping Solved cluster 2: residual clashing 0.75 cluster 3 has 4 members and 6.552e+03 combinations: 78 51 74 47 Energy 30.4577 Searching cluster 47 Combinations for 4 members in cluster 3 OK: 6.552e+03 - Sending to search 0.000000 < 30.457653: keeping Solved cluster 3: residual clashing 0.89 Still clashes at these sidechain pairs: Residual clashes = 38.95290 Printing make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86'