mkdir und mkdir: cannot create und. und: File exists make: [fragment-indexes] Error 2 (ignored) /projects/compbio/experiments/casp4/scripts/fragments-to-indexes gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' mkdir und mkdir: cannot create und. und: File exists gmake[1]: [und/T0107-153l.40.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0107-153l.40.4.a2m \ -target T0107 -template 153l \ -out T0107-153l.40.4 -outdir und partial PDB gets fragment 135 through 144 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LYS 2 30 VAL 3 2 ARG 4 27 VAL 5 1 LEU 6 3 TRP 7 6 ASP 8 4 GLU 9 12 ASN 10 4 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 gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' T0107-153l.40.4 done gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' mkdir und mkdir: cannot create und. und: File exists gmake[1]: [und/T0107-153l.43.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0107-153l.43.4.a2m \ -target T0107 -template 153l \ -out T0107-153l.43.4 -outdir und partial PDB gets fragment 132 through 141 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ARG 1 21 VAL 2 2 LEU 3 2 TRP 4 6 GLU 6 13 ASN 7 4 TYR 8 2 LEU 9 3 TYR 10 3 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: keepclash 3 8 17.2060 Cluster 1 = 3 8 2 clashing residues after turn Residue clashes: 3-8 cluster 1 has 2 members and 2.000e+00 combinations: 3 8 Energy 17.3288 Searching cluster 3 Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search 0.000000 < 17.328785: keeping Solved cluster 1: residual clashing 0.90 Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' T0107-153l.43.4 done gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' mkdir und mkdir: cannot create und. und: File exists gmake[1]: [und/T0107-19hcA.0.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0107-19hcA.0.5.a2m \ -target T0107 -template 19hcA \ -out T0107-19hcA.0.5 -outdir und Skipped atom 422, because occupancy 0.34 <= existing 0.660001 Skipped atom 426, because occupancy 0.34 <= existing 0.660001 Skipped atom 428, because occupancy 0.34 <= existing 0.660001 Skipped atom 540, because occupancy 0.47 <= existing 0.530001 Skipped atom 544, because occupancy 0.47 <= existing 0.530001 Skipped atom 546, because occupancy 0.47 <= existing 0.530001 Skipped atom 548, because occupancy 0.47 <= existing 0.530001 Skipped atom 550, because occupancy 0.47 <= existing 0.530001 Skipped atom 746, because occupancy 0.3 <= existing 0.700001 Skipped atom 748, because occupancy 0.3 <= existing 0.700001 Skipped atom 750, because occupancy 0.3 <= existing 0.700001 Skipped atom 752, because occupancy 0.3 <= existing 0.700001 Skipped atom 754, because occupancy 0.3 <= existing 0.700001 Skipped atom 756, because occupancy 0.3 <= existing 0.700001 Skipped atom 758, because occupancy 0.3 <= existing 0.700001 Skipped atom 760, because occupancy 0.3 <= existing 0.700001 Skipped atom 762, because occupancy 0.3 <= existing 0.700001 Skipped atom 764, because occupancy 0.3 <= existing 0.700001 Skipped atom 766, because occupancy 0.3 <= existing 0.700001 Skipped atom 768, because occupancy 0.3 <= existing 0.700001 Skipped atom 770, because occupancy 0.3 <= existing 0.700001 Skipped atom 772, because occupancy 0.3 <= existing 0.700001 Skipped atom 774, because occupancy 0.3 <= existing 0.700001 Skipped atom 1275, because occupancy 0.48 <= existing 0.520001 Skipped atom 1277, because occupancy 0.48 <= existing 0.520001 Skipped atom 1279, because occupancy 0.48 <= existing 0.520001 Skipped atom 1548, because occupancy 0.38 <= existing 0.620001 Skipped atom 1552, because occupancy 0.38 <= existing 0.620001 Skipped atom 1554, because occupancy 0.38 <= existing 0.620001 Skipped atom 1556, because occupancy 0.38 <= existing 0.620001 Skipped atom 1558, because occupancy 0.38 <= existing 0.620001 Skipped atom 1560, because occupancy 0.38 <= existing 0.620001 Skipped atom 1838, because occupancy 0.44 <= existing 0.560001 Skipped atom 1842, because occupancy 0.44 <= existing 0.560001 Skipped atom 1844, because occupancy 0.44 <= existing 0.560001 partial PDB gets fragment 277 through 286 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values VAL 1 2 THR 3 2 LYS 5 21 TYR 6 2 PRO 9 2 VAL 10 3 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 Y 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. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: keepclash 7 10 98.2750 Cluster 1 = 7 10 2 clashing residues after turn Residue clashes: 7-10 cluster 1 has 2 members and 4.000e+00 combinations: 7 10 Energy 152.6453 Searching cluster 7 Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search 74.476883 < 152.645264: keeping 0.000000 < 130.021164: keeping Solved cluster 1: residual clashing 13.87 Still clashes at these sidechain pairs: ires= 4 irot= 1 jres= 7 jrot= 2 31.7982 Residual clashes = 36.81367 Printing gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' T0107-19hcA.0.5 done gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' mkdir und mkdir: cannot create und. und: File exists gmake[1]: [und/T0107-19hcA.67.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0107-19hcA.67.2.a2m \ -target T0107 -template 19hcA \ -out T0107-19hcA.67.2 -outdir und Skipped atom 422, because occupancy 0.34 <= existing 0.660001 Skipped atom 426, because occupancy 0.34 <= existing 0.660001 Skipped atom 428, because occupancy 0.34 <= existing 0.660001 Skipped atom 540, because occupancy 0.47 <= existing 0.530001 Skipped atom 544, because occupancy 0.47 <= existing 0.530001 Skipped atom 546, because occupancy 0.47 <= existing 0.530001 Skipped atom 548, because occupancy 0.47 <= existing 0.530001 Skipped atom 550, because occupancy 0.47 <= existing 0.530001 Skipped atom 746, because occupancy 0.3 <= existing 0.700001 Skipped atom 748, because occupancy 0.3 <= existing 0.700001 Skipped atom 750, because occupancy 0.3 <= existing 0.700001 Skipped atom 752, because occupancy 0.3 <= existing 0.700001 Skipped atom 754, because occupancy 0.3 <= existing 0.700001 Skipped atom 756, because occupancy 0.3 <= existing 0.700001 Skipped atom 758, because occupancy 0.3 <= existing 0.700001 Skipped atom 760, because occupancy 0.3 <= existing 0.700001 Skipped atom 762, because occupancy 0.3 <= existing 0.700001 Skipped atom 764, because occupancy 0.3 <= existing 0.700001 Skipped atom 766, because occupancy 0.3 <= existing 0.700001 Skipped atom 768, because occupancy 0.3 <= existing 0.700001 Skipped atom 770, because occupancy 0.3 <= existing 0.700001 Skipped atom 772, because occupancy 0.3 <= existing 0.700001 Skipped atom 774, because occupancy 0.3 <= existing 0.700001 Skipped atom 1275, because occupancy 0.48 <= existing 0.520001 Skipped atom 1277, because occupancy 0.48 <= existing 0.520001 Skipped atom 1279, because occupancy 0.48 <= existing 0.520001 Skipped atom 1548, because occupancy 0.38 <= existing 0.620001 Skipped atom 1552, because occupancy 0.38 <= existing 0.620001 Skipped atom 1554, because occupancy 0.38 <= existing 0.620001 Skipped atom 1556, because occupancy 0.38 <= existing 0.620001 Skipped atom 1558, because occupancy 0.38 <= existing 0.620001 Skipped atom 1560, because occupancy 0.38 <= existing 0.620001 Skipped atom 1838, because occupancy 0.44 <= existing 0.560001 Skipped atom 1842, because occupancy 0.44 <= existing 0.560001 Skipped atom 1844, because occupancy 0.44 <= existing 0.560001 partial PDB gets fragment 186 through 195 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values SER 1 3 ASN 2 4 PRO 3 2 TRP 4 4 GLN 6 11 ASP 7 5 SER 8 3 VAL 9 1 GLU 10 11 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 gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' T0107-19hcA.67.2 done gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' mkdir und mkdir: cannot create und. und: File exists gmake[1]: [und/T0107-19hcA.67.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0107-19hcA.67.5.a2m \ -target T0107 -template 19hcA \ -out T0107-19hcA.67.5 -outdir und Skipped atom 422, because occupancy 0.34 <= existing 0.660001 Skipped atom 426, because occupancy 0.34 <= existing 0.660001 Skipped atom 428, because occupancy 0.34 <= existing 0.660001 Skipped atom 540, because occupancy 0.47 <= existing 0.530001 Skipped atom 544, because occupancy 0.47 <= existing 0.530001 Skipped atom 546, because occupancy 0.47 <= existing 0.530001 Skipped atom 548, because occupancy 0.47 <= existing 0.530001 Skipped atom 550, because occupancy 0.47 <= existing 0.530001 Skipped atom 746, because occupancy 0.3 <= existing 0.700001 Skipped atom 748, because occupancy 0.3 <= existing 0.700001 Skipped atom 750, because occupancy 0.3 <= existing 0.700001 Skipped atom 752, because occupancy 0.3 <= existing 0.700001 Skipped atom 754, because occupancy 0.3 <= existing 0.700001 Skipped atom 756, because occupancy 0.3 <= existing 0.700001 Skipped atom 758, because occupancy 0.3 <= existing 0.700001 Skipped atom 760, because occupancy 0.3 <= existing 0.700001 Skipped atom 762, because occupancy 0.3 <= existing 0.700001 Skipped atom 764, because occupancy 0.3 <= existing 0.700001 Skipped atom 766, because occupancy 0.3 <= existing 0.700001 Skipped atom 768, because occupancy 0.3 <= existing 0.700001 Skipped atom 770, because occupancy 0.3 <= existing 0.700001 Skipped atom 772, because occupancy 0.3 <= existing 0.700001 Skipped atom 774, because occupancy 0.3 <= existing 0.700001 Skipped atom 1275, because occupancy 0.48 <= existing 0.520001 Skipped atom 1277, because occupancy 0.48 <= existing 0.520001 Skipped atom 1279, because occupancy 0.48 <= existing 0.520001 Skipped atom 1548, because occupancy 0.38 <= existing 0.620001 Skipped atom 1552, because occupancy 0.38 <= existing 0.620001 Skipped atom 1554, because occupancy 0.38 <= existing 0.620001 Skipped atom 1556, because occupancy 0.38 <= existing 0.620001 Skipped atom 1558, because occupancy 0.38 <= existing 0.620001 Skipped atom 1560, because occupancy 0.38 <= existing 0.620001 Skipped atom 1838, because occupancy 0.44 <= existing 0.560001 Skipped atom 1842, because occupancy 0.44 <= existing 0.560001 Skipped atom 1844, because occupancy 0.44 <= existing 0.560001 partial PDB gets fragment 184 through 193 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values SER 1 3 ASN 2 5 PRO 3 2 TRP 4 3 GLU 5 15 GLN 6 10 ASP 7 6 SER 8 3 VAL 9 1 GLU 10 11 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 4 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: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' T0107-19hcA.67.5 done gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' mkdir und mkdir: cannot create und. und: File exists gmake[1]: [und/T0107-19hcA.68.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0107-19hcA.68.4.a2m \ -target T0107 -template 19hcA \ -out T0107-19hcA.68.4 -outdir und Skipped atom 422, because occupancy 0.34 <= existing 0.660001 Skipped atom 426, because occupancy 0.34 <= existing 0.660001 Skipped atom 428, because occupancy 0.34 <= existing 0.660001 Skipped atom 540, because occupancy 0.47 <= existing 0.530001 Skipped atom 544, because occupancy 0.47 <= existing 0.530001 Skipped atom 546, because occupancy 0.47 <= existing 0.530001 Skipped atom 548, because occupancy 0.47 <= existing 0.530001 Skipped atom 550, because occupancy 0.47 <= existing 0.530001 Skipped atom 746, because occupancy 0.3 <= existing 0.700001 Skipped atom 748, because occupancy 0.3 <= existing 0.700001 Skipped atom 750, because occupancy 0.3 <= existing 0.700001 Skipped atom 752, because occupancy 0.3 <= existing 0.700001 Skipped atom 754, because occupancy 0.3 <= existing 0.700001 Skipped atom 756, because occupancy 0.3 <= existing 0.700001 Skipped atom 758, because occupancy 0.3 <= existing 0.700001 Skipped atom 760, because occupancy 0.3 <= existing 0.700001 Skipped atom 762, because occupancy 0.3 <= existing 0.700001 Skipped atom 764, because occupancy 0.3 <= existing 0.700001 Skipped atom 766, because occupancy 0.3 <= existing 0.700001 Skipped atom 768, because occupancy 0.3 <= existing 0.700001 Skipped atom 770, because occupancy 0.3 <= existing 0.700001 Skipped atom 772, because occupancy 0.3 <= existing 0.700001 Skipped atom 774, because occupancy 0.3 <= existing 0.700001 Skipped atom 1275, because occupancy 0.48 <= existing 0.520001 Skipped atom 1277, because occupancy 0.48 <= existing 0.520001 Skipped atom 1279, because occupancy 0.48 <= existing 0.520001 Skipped atom 1548, because occupancy 0.38 <= existing 0.620001 Skipped atom 1552, because occupancy 0.38 <= existing 0.620001 Skipped atom 1554, because occupancy 0.38 <= existing 0.620001 Skipped atom 1556, because occupancy 0.38 <= existing 0.620001 Skipped atom 1558, because occupancy 0.38 <= existing 0.620001 Skipped atom 1560, because occupancy 0.38 <= existing 0.620001 Skipped atom 1838, because occupancy 0.44 <= existing 0.560001 Skipped atom 1842, because occupancy 0.44 <= existing 0.560001 Skipped atom 1844, because occupancy 0.44 <= existing 0.560001 partial PDB gets fragment 185 through 194 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASN 1 5 PRO 2 2 TRP 3 3 GLU 4 15 GLN 5 10 ASP 6 6 SER 7 3 VAL 8 1 GLU 9 11 ILE 10 3 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 3 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: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing gmake[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t107' T0107-19hcA.68.4 done gmake[1]: Entering directory `/export/projects/compbio/experiments/casp4/t107' mkdir und mkdir: cannot create und. und: File exists gmake[1]: [und/T0107-1a34A.49.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0107-1a34A.49.4.a2m \ -target T0107 -template 1a34A \ -out T0107-1a34A.49.4 -outdir und Skipped atom 203, because occupancy 0.4 <= existing 0.600001 Skipped atom 205, because occupancy 0.4 <= existing 0.600001 Skipped atom 564, because occupancy 0.5 <= existing 0.500001 Skipped atom 566, because occupancy 0.5 <= existing 0.500001 Skipped atom 1012, because occupancy 0.45 <= existing 0.550001 Skipped atom 1014, because occupancy 0.45 <= existing 0.550001 Skipped atom 1016, because occupancy 0.45 <= existing 0.550001 Skipped atom 1018, because occupancy 0.45 <= existing 0.550001 Skipped atom 1020, because occupancy 0.45 <= existing 0.550001 Skipped atom 1022, because occupancy 0.45 <= existing 0.550001 Skipped atom 1024, because occupancy 0.45 <= existing 0.550001 Skipped atom 1466, because occupancy 0.45 <= existing 0.550001 Skipped atom 1468, because occupancy 0.45 <= existing 0.550001 Skipped atom 1660, because occupancy 0.4 <= existing 0.600001 Skipped atom 1662, because occupancy 0.4 <= existing 0.600001 Skipped atom 1664, because occupancy 0.4 <= existing 0.600001 Skipped atom 2267, because occupancy 0.25 <= existing 0.750001 Skipped atom 2269, because occupancy 0.25 <= existing 0.750001 PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1a34A-orig.a2m Writing a2m file: tmp/1a34A-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-18570 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-18570/tmp -alignfile tmp/1a34A-orig.a2m \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp/1a34A-orig.a2m (1 sequences, 159 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-18570/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-18570/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-18570/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 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-beta-18570/tmp.a2m (1 sequences, 159 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-18570/tmp.mod tmp/1a34A-align.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-18570