make -k und/T0086-5csmA-local.index und/5csmA-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/T0086-5csmA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/T0086-5csmA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 5csmA/T0086-5csmA-local.pw.a2m.gz \ -target T0086 -template 5csmA \ -out T0086-5csmA-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/5csmA-orig.a2m Writing a2m file: tmp/5csmA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11011 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11011/tmp -alignfile tmp/5csmA-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/5csmA-orig.a2m (1 sequences, 256 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11011/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11011/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11011/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-11011/tmp.a2m (1 sequences, 256 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11011/tmp.mod tmp/5csmA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/5csmA-align.mod tmp/5csmA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11011/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/5csmA-orig.a2m tmp/5csmA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/5csmA-align.mod Running w0.5 tmp/5csmA-orig.a2m tmp/5csmA-align.mod Running align2model tmp/5csmA-align -i tmp/5csmA-align.mod -db tmp/5csmA-orig.a2m -db tmp/5csmA-pdb.a2m Debugging on ! Reading sequence file Reading input structure 58 residues read Measuring phi and psi Getting chi values LEU 1 2 ARG 2 27 LEU 4 3 ARG 5 26 TYR 6 2 CYS 7 2 LYS 8 25 LEU 13 3 ASP 14 5 PRO 15 2 GLN 16 10 LEU 17 3 LEU 21 3 LEU 23 3 GLU 24 12 ASP 27 4 MET 29 11 THR 30 1 LYS 31 17 GLN 35 14 GLN 36 15 LYS 38 27 VAL 42 3 SER 43 2 VAL 44 3 THR 45 2 MET 46 11 ARG 48 31 GLU 49 14 VAL 52 2 GLU 53 13 GLN 54 14 ASN 55 5 GLU 56 12 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 3 rotamers of residue L 14 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 21 25 43.7961 keepclash 30 49 31.0511 turnclash 30 9 52 0 48.8095 Cluster 1 = 21 25 Cluster 2 = 30 49 52 5 clashing residues after turn Residue clashes: 21-25 30-49 30-52 cluster 1 has 2 members and 0.000e+00 combinations: 21 25 Energy 43.7961 Searching cluster 21 Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search 0.000000 < 43.796093: keeping Solved cluster 1: residual clashing 0.20 cluster 2 has 3 members and 0.000e+00 combinations: 52 30 49 Energy 39.6870 Searching cluster 30 Combinations for 3 members in cluster 2 OK: 0.000e+00 - Sending to search 4.569699 < 39.687042: keeping 0.000000 < 5.300319: keeping Solved cluster 2: residual clashing 1.07 Still clashes at these sidechain pairs: Residual clashes = 13.93536 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/5csmA-T0086-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/5csmA-T0086-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 5csmA/5csmA-T0086-local.pw.a2m.gz \ -target T0086 -template 5csmA \ -out 5csmA-T0086-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/5csmA-orig.a2m Writing a2m file: tmp/5csmA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-1353 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-1353/tmp -alignfile tmp/5csmA-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/5csmA-orig.a2m (1 sequences, 256 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-1353/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-1353/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-1353/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-1353/tmp.a2m (1 sequences, 256 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-1353/tmp.mod tmp/5csmA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/5csmA-align.mod tmp/5csmA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-1353/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/5csmA-orig.a2m tmp/5csmA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/5csmA-align.mod Running w0.5 tmp/5csmA-orig.a2m tmp/5csmA-align.mod Running align2model tmp/5csmA-align -i tmp/5csmA-align.mod -db tmp/5csmA-orig.a2m -db tmp/5csmA-pdb.a2m Debugging on ! Reading sequence file Reading input structure 59 residues read Measuring phi and psi Getting chi values ARG 1 26 TYR 2 2 CYS 3 2 LYS 4 25 LEU 9 3 ASP 10 5 PRO 11 2 GLN 12 10 LEU 13 3 LEU 17 3 LEU 19 3 GLU 20 12 ASP 21 4 MET 25 11 THR 26 1 LYS 27 17 GLN 31 14 GLN 32 15 LYS 34 27 VAL 38 3 SER 39 2 VAL 40 3 THR 41 2 MET 42 11 ARG 44 31 GLU 45 14 VAL 48 2 GLU 49 13 GLN 50 14 ASN 51 5 GLU 52 12 ILE 53 2 GLU 55 13 GLU 56 12 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 3 rotamers of residue L 10 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 17 21 43.7961 keepclash 26 45 31.0511 turnclash 26 9 48 0 48.8095 Cluster 1 = 17 21 Cluster 2 = 26 45 48 5 clashing residues after turn Residue clashes: 17-21 26-45 26-48 cluster 1 has 2 members and 0.000e+00 combinations: 17 21 Energy 43.7961 Searching cluster 17 Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search 0.000000 < 43.796093: keeping Solved cluster 1: residual clashing 0.20 cluster 2 has 3 members and 0.000e+00 combinations: 48 26 45 Energy 39.6870 Searching cluster 26 Combinations for 3 members in cluster 2 OK: 0.000e+00 - Sending to search 4.569699 < 39.687042: keeping 0.000000 < 5.300319: keeping Solved cluster 2: residual clashing 1.07 Still clashes at these sidechain pairs: Residual clashes = 14.86249 Printing make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86'