make -k und/T0086-1ecmA-local.index und/1ecmA-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/T0086-1ecmA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/T0086-1ecmA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1ecmA/T0086-1ecmA-local.pw.a2m.gz \ -target T0086 -template 1ecmA \ -out T0086-1ecmA-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1ecmA-orig.a2m Writing a2m file: tmp/1ecmA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-25450 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-25450/tmp -alignfile tmp/1ecmA-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/1ecmA-orig.a2m (1 sequences, 109 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-25450/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-25450/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-25450/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-25450/tmp.a2m (1 sequences, 109 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-25450/tmp.mod tmp/1ecmA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ecmA-align.mod tmp/1ecmA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-25450/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1ecmA-orig.a2m tmp/1ecmA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1ecmA-align.mod Running w0.5 tmp/1ecmA-orig.a2m tmp/1ecmA-align.mod Running align2model tmp/1ecmA-align -i tmp/1ecmA-align.mod -db tmp/1ecmA-orig.a2m -db tmp/1ecmA-pdb.a2m Debugging on ! Reading sequence file Reading input structure 39 residues read Measuring phi and psi Getting chi values TYR 1 2 CYS 2 2 LYS 3 30 GLU 4 12 PRO 6 2 PRO 10 2 GLN 11 12 ASP 14 5 TRP 15 7 LEU 17 3 LEU 18 3 GLU 19 15 ASP 20 4 SER 21 3 MET 22 10 THR 23 2 LYS 24 25 ARG 25 26 PHE 26 4 GLU 27 12 GLN 28 11 THR 33 2 VAL 34 1 VAL 36 3 THR 37 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 7 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 11 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 11 rotamers of residue Q 29 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 27 33 22.7537 Cluster 1 = 27 33 2 clashing residues after turn Residue clashes: 27-33 cluster 1 has 2 members and 0.000e+00 combinations: 33 27 Energy 23.8817 Searching cluster 27 Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search 22.753738 < 23.881666: keeping 0.000000 < 23.881664: keeping Solved cluster 1: residual clashing 1.70 Still clashes at these sidechain pairs: Residual clashes = 13.98548 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/1ecmA-T0086-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/1ecmA-T0086-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1ecmA/1ecmA-T0086-local.pw.a2m.gz \ -target T0086 -template 1ecmA \ -out 1ecmA-T0086-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1ecmA-orig.a2m Writing a2m file: tmp/1ecmA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-14673 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-14673/tmp -alignfile tmp/1ecmA-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/1ecmA-orig.a2m (1 sequences, 109 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-14673/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-14673/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-14673/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-14673/tmp.a2m (1 sequences, 109 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-14673/tmp.mod tmp/1ecmA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1ecmA-align.mod tmp/1ecmA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-14673/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1ecmA-orig.a2m tmp/1ecmA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1ecmA-align.mod Running w0.5 tmp/1ecmA-orig.a2m tmp/1ecmA-align.mod Running align2model tmp/1ecmA-align -i tmp/1ecmA-align.mod -db tmp/1ecmA-orig.a2m -db tmp/1ecmA-pdb.a2m Debugging on ! Reading sequence file Reading input structure 23 residues read Measuring phi and psi Getting chi values ARG 2 28 LYS 8 30 GLU 9 12 PRO 11 2 PRO 15 2 GLN 16 12 ASP 19 5 TRP 20 7 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 30 rotamers of residue K 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 2 rotamers of residue P 12 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 16 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 6 12 28.3445 Cluster 1 = 6 12 2 clashing residues after turn Residue clashes: 6-12 cluster 1 has 2 members and 0.000e+00 combinations: 6 12 Energy 131.2089 Searching cluster 6 Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search 29.057457 < 131.208923: keeping Solved cluster 1: residual clashing 77.78 Still clashes at these sidechain pairs: ires= 6 irot= 1 jres= 12 jrot= 2 29.0575 Residual clashes = 39.77569 Printing make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86'