make -k und/T0086-1adjA-local.index und/1adjA-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/T0086-1adjA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/T0086-1adjA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1adjA/T0086-1adjA-local.pw.a2m.gz \ -target T0086 -template 1adjA \ -out T0086-1adjA-local -outdir und Sequence named 1adjA has all gap columns. It will be included anyway. Sequence named 1adjA has all gap columns. It will be included anyway. PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1adjA-orig.a2m Writing a2m file: tmp/1adjA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-27960 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-27960/tmp -alignfile tmp/1adjA-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/1adjA-orig.a2m (1 sequences, 421 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-27960/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-27960/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-27960/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-27960/tmp.a2m (1 sequences, 421 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-27960/tmp.mod tmp/1adjA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1adjA-align.mod tmp/1adjA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-27960/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1adjA-orig.a2m tmp/1adjA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1adjA-align.mod Running w0.5 tmp/1adjA-orig.a2m tmp/1adjA-align.mod Running align2model tmp/1adjA-align -i tmp/1adjA-align.mod -db tmp/1adjA-orig.a2m -db tmp/1adjA-pdb.a2m /projects/kestrel/users/karplus/burial/slicer/slicer: no segments found mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/1adjA-T0086-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/1adjA-T0086-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1adjA/1adjA-T0086-local.pw.a2m.gz \ -target T0086 -template 1adjA \ -out 1adjA-T0086-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1adjA-orig.a2m Writing a2m file: tmp/1adjA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-32284 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-32284/tmp -alignfile tmp/1adjA-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/1adjA-orig.a2m (1 sequences, 421 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-32284/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-32284/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-32284/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-32284/tmp.a2m (1 sequences, 421 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-32284/tmp.mod tmp/1adjA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1adjA-align.mod tmp/1adjA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-32284/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1adjA-orig.a2m tmp/1adjA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1adjA-align.mod Running w0.5 tmp/1adjA-orig.a2m tmp/1adjA-align.mod Running align2model tmp/1adjA-align -i tmp/1adjA-align.mod -db tmp/1adjA-orig.a2m -db tmp/1adjA-pdb.a2m Debugging on ! Reading sequence file Reading input structure 53 residues read Measuring phi and psi Getting chi values LEU 1 4 PRO 2 2 LEU 4 2 PRO 5 2 SER 8 3 TYR 10 3 TRP 11 6 LEU 12 3 LEU 17 3 LEU 18 3 CYS 19 2 ASP 21 5 GLU 23 12 PRO 24 2 TRP 25 5 LEU 26 3 ARG 29 30 THR 30 2 VAL 31 1 VAL 32 2 PRO 33 2 VAL 34 3 SER 35 3 THR 36 2 LEU 37 5 SER 38 3 PRO 40 2 GLU 41 12 LEU 42 3 LEU 44 3 GLN 45 12 LYS 46 25 LEU 47 3 LYS 49 28 THR 50 1 PRO 51 2 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 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 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. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: keepclash 7 11 14.5826 keepclash 22 26 72.7657 keepclash 26 32 18.3738 Cluster 1 = 7 11 Cluster 2 = 22 26 32 5 clashing residues after turn Residue clashes: 7-11 22-26 26-32 cluster 1 has 2 members and 0.000e+00 combinations: 7 11 Energy 14.5826 Searching cluster 7 Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search 0.000000 < 14.582605: keeping Solved cluster 1: residual clashing 1.91 cluster 2 has 3 members and 2.000e+00 combinations: 32 26 22 Energy 92.6363 Searching cluster 22 Combinations for 3 members in cluster 2 OK: 2.000e+00 - Sending to search 81.947556 < 92.636261: keeping Solved cluster 2: residual clashing 83.57 Still clashes at these sidechain pairs: ires= 22 irot= 4 jres= 26 jrot= 3 63.5737 ires= 26 irot= 3 jres= 32 jrot= 1 18.3738 Residual clashes = 82.93806 Printing make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86'