make -k und/T0086-1auiA-local.index und/1auiA-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/T0086-1auiA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/T0086-1auiA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1auiA/T0086-1auiA-local.pw.a2m.gz \ -target T0086 -template 1auiA \ -out T0086-1auiA-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1auiA-orig.a2m Writing a2m file: tmp/1auiA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-13727 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-13727/tmp -alignfile tmp/1auiA-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/1auiA-orig.a2m (1 sequences, 521 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-13727/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-13727/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-13727/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-13727/tmp.a2m (1 sequences, 521 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-13727/tmp.mod tmp/1auiA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1auiA-align.mod tmp/1auiA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-13727/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1auiA-orig.a2m tmp/1auiA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1auiA-align.mod Running w0.5 tmp/1auiA-orig.a2m tmp/1auiA-align.mod Running align2model tmp/1auiA-align -i tmp/1auiA-align.mod -db tmp/1auiA-orig.a2m -db tmp/1auiA-pdb.a2m Debugging on ! Reading sequence file Reading input structure 107 residues read Measuring phi and psi Getting chi values GLU 1 12 GLN 2 14 GLN 3 11 LYS 5 26 THR 6 2 VAL 7 1 SER 8 3 VAL 9 1 THR 10 2 MET 11 10 ILE 12 4 ARG 13 22 PHE 16 3 VAL 17 2 GLN 19 9 ASN 20 4 GLU 21 12 GLU 24 12 PRO 26 2 LEU 27 3 LEU 28 3 PRO 29 2 LYS 30 30 GLU 31 12 SER 32 3 ARG 33 32 TYR 34 3 TRP 35 5 LEU 36 3 ARG 37 27 ILE 39 5 LEU 40 3 CYS 42 2 ASP 44 6 GLU 46 14 TRP 48 4 VAL 51 1 PRO 52 2 VAL 53 2 SER 54 3 THR 55 2 LEU 56 3 SER 57 2 PRO 59 2 GLU 60 13 LEU 61 3 GLN 64 11 LYS 70 31 THR 71 2 LEU 73 3 THR 81 2 SER 82 3 SER 83 2 THR 84 2 LEU 85 2 THR 86 2 ASP 88 5 PHE 89 2 ILE 90 3 GLU 91 12 ARG 94 26 ASP 95 4 ARG 101 32 ARG 102 27 SER 103 3 ARG 104 29 LEU 105 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 12 rotamers of residue E 22 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 12 rotamers of residue E 25 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 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 12 rotamers of residue E 32 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 4 rotamers of residue W 49 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 1 rotamers of residue V 52 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 53 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 60 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 5 rotamers of residue D 89 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 I 91 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 12 rotamers of residue E 92 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 26 rotamers of residue R 95 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 18 25 20.0000 keepclash 26 30 29.4622 keepclash 32 100 16.2158 keepclash 49 78 20.4646 keepclash 57 95 20.4660 Cluster 1 = 18 25 Cluster 2 = 26 30 Cluster 3 = 32 100 Cluster 4 = 49 78 Cluster 5 = 57 95 10 clashing residues after turn Residue clashes: 18-25 26-30 32-100 49-78 57-95 cluster 1 has 2 members and 1.200e+01 combinations: 18 25 Energy 31.5869 Searching cluster 18 Combinations for 2 members in cluster 1 OK: 1.200e+01 - Sending to search 0.000000 < 31.586948: keeping Solved cluster 1: residual clashing 14.50 cluster 2 has 2 members and 0.000e+00 combinations: 26 30 Energy 29.4622 Searching cluster 26 Combinations for 2 members in cluster 2 OK: 0.000e+00 - Sending to search Solved cluster 2: residual clashing 29.46 cluster 3 has 2 members and 0.000e+00 combinations: 100 32 Energy 121.8858 Searching cluster 32 Combinations for 2 members in cluster 3 OK: 0.000e+00 - Sending to search 10.597643 < 121.885757: keeping 35.478809 < 110.619164: keeping 7.798311 < 58.725586: keeping 1.654405 < 48.683891: keeping Solved cluster 3: residual clashing 44.02 cluster 4 has 2 members and 0.000e+00 combinations: 49 78 Energy 284.4938 Searching cluster 49 Combinations for 2 members in cluster 4 OK: 0.000e+00 - Sending to search 0.000000 < 284.493835: keeping Solved cluster 4: residual clashing 51.53 cluster 5 has 2 members and 5.200e+01 combinations: 57 95 Energy 60.1312 Searching cluster 57 Combinations for 2 members in cluster 5 OK: 5.200e+01 - Sending to search 0.000000 < 60.131184: keeping 0.576947 < 30.991985: keeping 6.499789 < 27.036335: keeping 0.000000 < 18.706787: keeping Solved cluster 5: residual clashing 15.61 Still clashes at these sidechain pairs: ires= 26 irot= 1 jres= 30 jrot= 1 29.4622 ires= 32 irot= 10 jres= 103 jrot= 1 21.6284 ires= 49 irot= 4 jres= 53 jrot= 1 51.8059 ires= 85 irot= 1 jres= 95 jrot= 26 28.5319 Residual clashes = 178.63239 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/1auiA-T0086-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/1auiA-T0086-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1auiA/1auiA-T0086-local.pw.a2m.gz \ -target T0086 -template 1auiA \ -out 1auiA-T0086-local -outdir und Sequence named T0086 has all gap columns. It will be included anyway. PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1auiA-orig.a2m Writing a2m file: tmp/1auiA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-21105 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-21105/tmp -alignfile tmp/1auiA-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/1auiA-orig.a2m (1 sequences, 521 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-21105/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-21105/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-21105/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-21105/tmp.a2m (1 sequences, 521 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-21105/tmp.mod tmp/1auiA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1auiA-align.mod tmp/1auiA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-21105/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1auiA-orig.a2m tmp/1auiA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1auiA-align.mod Running w0.5 tmp/1auiA-orig.a2m tmp/1auiA-align.mod Running align2model tmp/1auiA-align -i tmp/1auiA-align.mod -db tmp/1auiA-orig.a2m -db tmp/1auiA-pdb.a2m /projects/kestrel/users/karplus/burial/slicer/slicer: no segments found make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86'