make -k und/T0086-1pysA-local.index und/1pysA-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/T0086-1pysA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/T0086-1pysA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1pysA/T0086-1pysA-local.pw.a2m.gz \ -target T0086 -template 1pysA \ -out T0086-1pysA-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1pysA-orig.a2m Writing a2m file: tmp/1pysA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-3737 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-3737/tmp -alignfile tmp/1pysA-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/1pysA-orig.a2m (1 sequences, 350 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-3737/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-3737/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-3737/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-3737/tmp.a2m (1 sequences, 350 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-3737/tmp.mod tmp/1pysA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pysA-align.mod tmp/1pysA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-3737/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1pysA-orig.a2m tmp/1pysA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1pysA-align.mod Running w0.5 tmp/1pysA-orig.a2m tmp/1pysA-align.mod Running align2model tmp/1pysA-align -i tmp/1pysA-align.mod -db tmp/1pysA-orig.a2m -db tmp/1pysA-pdb.a2m Debugging on ! Reading sequence file Reading input structure 16 residues read Measuring phi and psi Getting chi values LEU 2 3 ASP 4 5 SER 5 3 MET 6 11 THR 7 2 LYS 8 30 ARG 9 26 GLU 11 12 GLN 12 15 GLN 13 8 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/1pysA-T0086-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/1pysA-T0086-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1pysA/1pysA-T0086-local.pw.a2m.gz \ -target T0086 -template 1pysA \ -out 1pysA-T0086-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1pysA-orig.a2m Writing a2m file: tmp/1pysA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-11033 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-11033/tmp -alignfile tmp/1pysA-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/1pysA-orig.a2m (1 sequences, 350 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-11033/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-11033/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-11033/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-11033/tmp.a2m (1 sequences, 350 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-11033/tmp.mod tmp/1pysA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1pysA-align.mod tmp/1pysA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-11033/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1pysA-orig.a2m tmp/1pysA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1pysA-align.mod Running w0.5 tmp/1pysA-orig.a2m tmp/1pysA-align.mod Running align2model tmp/1pysA-align -i tmp/1pysA-align.mod -db tmp/1pysA-orig.a2m -db tmp/1pysA-pdb.a2m Debugging on ! Reading sequence file Reading input structure 32 residues read Measuring phi and psi Getting chi values ARG 1 32 GLU 2 12 PHE 4 3 VAL 5 2 GLU 6 12 GLN 9 14 ASN 10 5 GLU 11 10 GLU 15 11 LEU 16 4 LEU 18 3 LEU 19 3 PRO 20 2 LYS 21 30 GLU 22 13 SER 23 2 ARG 24 30 TYR 25 2 ARG 28 30 GLU 29 13 ILE 30 5 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 21 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 21 37.7891 Cluster 1 = 18 21 2 clashing residues after turn Residue clashes: 18-21 cluster 1 has 2 members and 0.000e+00 combinations: 18 21 Energy 49.3098 Searching cluster 18 Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search 30.448179 < 49.309814: keeping Solved cluster 1: residual clashing 42.18 Still clashes at these sidechain pairs: ires= 18 irot= 1 jres= 21 jrot= 2 30.4482 Residual clashes = 32.94681 Printing make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86'