make -k 1qh7A.indexes make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1qh7A-local.index und/1qh7A-T0114-local.index \ und/%-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' mkdir tmp mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0114-1qh7A-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qh7A/T0114-1qh7A-local.pw.a2m.gz \ -target T0114 -template 1qh7A \ -out T0114-1qh7A-local -outdir und Skipped atom 317, because occupancy 0.5 <= existing 0.500001 Skipped atom 319, because occupancy 0.5 <= existing 0.500001 Skipped atom 321, because occupancy 0.5 <= existing 0.500001 Skipped atom 328, because occupancy 0.5 <= existing 0.500001 Skipped atom 330, because occupancy 0.5 <= existing 0.500001 Skipped atom 332, because occupancy 0.5 <= existing 0.500001 Skipped atom 346, because occupancy 0.4 <= existing 0.600001 Skipped atom 348, because occupancy 0.4 <= existing 0.600001 Skipped atom 350, because occupancy 0.4 <= existing 0.600001 Skipped atom 1395, because occupancy 0.33 <= existing 0.770001 Skipped atom 1397, because occupancy 0.33 <= existing 0.770001 Skipped atom 1399, because occupancy 0.33 <= existing 0.770001 Skipped atom 1495, because occupancy 0.3 <= existing 0.700001 Skipped atom 1497, because occupancy 0.3 <= existing 0.700001 Skipped atom 1499, because occupancy 0.3 <= existing 0.700001 Skipped atom 1501, because occupancy 0.3 <= existing 0.700001 Skipped atom 1503, because occupancy 0.3 <= existing 0.700001 Skipped atom 1505, because occupancy 0.3 <= existing 0.700001 Skipped atom 1507, because occupancy 0.3 <= existing 0.700001 Skipped atom 1514, because occupancy 0.5 <= existing 0.500001 Skipped atom 1516, because occupancy 0.5 <= existing 0.500001 Skipped atom 1518, because occupancy 0.5 <= existing 0.500001 Skipped atom 1520, because occupancy 0.5 <= existing 0.500001 PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1qh7A-orig.a2m Writing a2m file: tmp/1qh7A-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-1417 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-1417/tmp -alignfile tmp/1qh7A-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/1qh7A-orig.a2m (1 sequences, 208 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-1417/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-1417/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-1417/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-purr-1417/tmp.a2m (1 sequences, 208 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-1417/tmp.mod tmp/1qh7A-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qh7A-align.mod tmp/1qh7A-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-1417/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1qh7A-orig.a2m tmp/1qh7A-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1qh7A-align.mod Running w0.5 tmp/1qh7A-orig.a2m tmp/1qh7A-align.mod Running align2model tmp/1qh7A-align -i tmp/1qh7A-align.mod -db tmp/1qh7A-orig.a2m -db tmp/1qh7A-pdb.a2m partial PDB gets fragment 51 through 66 extending start extending end partial PDB gets fragment 67 through 82 extending start extending end partial PDB gets fragment 83 through 106 extending start extending end Debugging on ! Reading sequence file Reading input structure 62 residues read Measuring phi and psi Getting chi values GLU 1 14 ARG 3 21 ASP 4 5 LEU 6 3 CYS 7 2 PHE 8 4 ASN 10 4 THR 13 2 PRO 15 2 VAL 16 1 ILE 19 3 VAL 22 3 TRP 24 5 VAL 25 2 GLU 26 15 SER 27 2 ASN 30 5 VAL 31 2 VAL 32 1 THR 33 2 LEU 34 3 GLN 37 15 ARG 38 29 ASN 39 6 LEU 40 2 SER 41 3 ARG 44 30 LEU 45 4 THR 47 2 ILE 48 5 THR 49 1 LEU 50 3 GLN 51 12 LYS 52 29 SER 55 2 ASN 57 5 HIS 60 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 1 rotamers of residue V 17 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 3 rotamers of residue I 20 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 15 rotamers of residue E 27 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 T 34 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 3 rotamers of residue L 35 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 15 rotamers of residue Q 38 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 3 rotamers of residue L 51 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 9 39 12.5890 keepclash 9 41 27.6569 keepclash 21 52 31.9945 keepclash 25 27 62.9091 keepclash 25 33 23.1927 keepclash 34 38 12.7383 keepclash 57 61 146.7569 Cluster 1 = 9 39 41 Cluster 2 = 21 52 Cluster 3 = 25 27 33 Cluster 4 = 34 38 Cluster 5 = 57 61 12 clashing residues after turn Residue clashes: 9-39 9-41 21-52 25-27 25-33 34-38 39-41 57-61 cluster 1 has 3 members and 1.200e+02 combinations: 41 9 39 Energy 40.2458 Searching cluster 9 Combinations for 3 members in cluster 1 OK: 1.200e+02 - Sending to search 27.656879 < 40.245834: keeping 0.000000 < 28.091534: keeping Solved cluster 1: residual clashing 1.63 cluster 2 has 2 members and 0.000e+00 combinations: 21 52 Energy 31.9945 Searching cluster 21 Combinations for 2 members in cluster 2 OK: 0.000e+00 - Sending to search 18.662220 < 31.994513: keeping 17.712893 < 18.716942: keeping 0.000000 < 17.821346: keeping Solved cluster 2: residual clashing 0.11 cluster 3 has 3 members and 1.500e+01 combinations: 33 25 27 Energy 128.2095 Searching cluster 25 Combinations for 3 members in cluster 3 OK: 1.500e+01 - Sending to search 59.554070 < 128.209457: keeping 23.192713 < 86.288620: keeping 23.192713 < 80.333755: keeping 23.192713 < 49.248856: keeping Solved cluster 3: residual clashing 43.60 cluster 4 has 2 members and 3.000e+01 combinations: 34 38 Energy 42.7550 Searching cluster 34 Combinations for 2 members in cluster 4 OK: 3.000e+01 - Sending to search 12.253425 < 42.755035: keeping 0.000000 < 42.378647: keeping 0.000000 < 34.484501: keeping Solved cluster 4: residual clashing 20.52 cluster 5 has 2 members and 0.000e+00 combinations: 57 61 Energy 146.7569 Searching cluster 57 Combinations for 2 members in cluster 5 OK: 0.000e+00 - Sending to search 0.000000 < 146.756897: keeping Solved cluster 5: residual clashing 2.00 Still clashes at these sidechain pairs: ires= 25 irot= 2 jres= 33 jrot= 1 23.1927 ires= 27 irot= 13 jres= 31 jrot= 1 76.1172 Residual clashes = 139.30994 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1qh7A-T0114-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1qh7A-T0114-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qh7A/1qh7A-T0114-local.pw.a2m.gz \ -target T0114 -template 1qh7A \ -out 1qh7A-T0114-local -outdir und Skipped atom 317, because occupancy 0.5 <= existing 0.500001 Skipped atom 319, because occupancy 0.5 <= existing 0.500001 Skipped atom 321, because occupancy 0.5 <= existing 0.500001 Skipped atom 328, because occupancy 0.5 <= existing 0.500001 Skipped atom 330, because occupancy 0.5 <= existing 0.500001 Skipped atom 332, because occupancy 0.5 <= existing 0.500001 Skipped atom 346, because occupancy 0.4 <= existing 0.600001 Skipped atom 348, because occupancy 0.4 <= existing 0.600001 Skipped atom 350, because occupancy 0.4 <= existing 0.600001 Skipped atom 1395, because occupancy 0.33 <= existing 0.770001 Skipped atom 1397, because occupancy 0.33 <= existing 0.770001 Skipped atom 1399, because occupancy 0.33 <= existing 0.770001 Skipped atom 1495, because occupancy 0.3 <= existing 0.700001 Skipped atom 1497, because occupancy 0.3 <= existing 0.700001 Skipped atom 1499, because occupancy 0.3 <= existing 0.700001 Skipped atom 1501, because occupancy 0.3 <= existing 0.700001 Skipped atom 1503, because occupancy 0.3 <= existing 0.700001 Skipped atom 1505, because occupancy 0.3 <= existing 0.700001 Skipped atom 1507, because occupancy 0.3 <= existing 0.700001 Skipped atom 1514, because occupancy 0.5 <= existing 0.500001 Skipped atom 1516, because occupancy 0.5 <= existing 0.500001 Skipped atom 1518, because occupancy 0.5 <= existing 0.500001 Skipped atom 1520, because occupancy 0.5 <= existing 0.500001 PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1qh7A-orig.a2m Writing a2m file: tmp/1qh7A-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-1444 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-1444/tmp -alignfile tmp/1qh7A-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/1qh7A-orig.a2m (1 sequences, 208 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-1444/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-1444/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-1444/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-purr-1444/tmp.a2m (1 sequences, 208 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-1444/tmp.mod tmp/1qh7A-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1qh7A-align.mod tmp/1qh7A-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-1444/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1qh7A-orig.a2m tmp/1qh7A-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1qh7A-align.mod Running w0.5 tmp/1qh7A-orig.a2m tmp/1qh7A-align.mod Running align2model tmp/1qh7A-align -i tmp/1qh7A-align.mod -db tmp/1qh7A-orig.a2m -db tmp/1qh7A-pdb.a2m partial PDB gets fragment 9 through 19 extending start extending end partial PDB gets fragment 21 through 38 extending start extending end partial PDB gets fragment 68 through 82 extending start extending end partial PDB gets fragment 89 through 107 extending start extending end Debugging on ! Reading sequence file Reading input structure 71 residues read Measuring phi and psi Getting chi values ASN 1 4 GLU 2 7 ASN 3 5 SER 4 3 TYR 5 2 LEU 6 2 ILE 8 4 HIS 9 3 ASN 10 6 ASN 11 6 GLU 14 14 ARG 16 32 ASP 17 6 LEU 19 3 CYS 20 2 PHE 21 3 ASN 23 6 MET 27 8 PRO 28 2 VAL 29 3 ILE 31 5 VAL 36 3 TRP 38 5 VAL 39 2 GLU 40 15 SER 41 2 ASN 44 5 VAL 45 2 VAL 46 1 THR 47 2 LEU 48 3 ARG 52 30 LEU 53 4 THR 55 2 ILE 56 5 THR 57 1 LEU 58 3 GLN 59 12 LYS 60 29 SER 63 2 ASN 65 5 HIS 68 3 ILE 69 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 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. All 15 rotamers of residue E 41 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 T 48 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 3 rotamers of residue L 59 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 9 20 11.3414 keepclash 18 32 20.0000 keepclash 22 28 20.0000 keepclash 35 60 31.9945 keepclash 39 41 62.9091 keepclash 39 47 23.1927 keepclash 65 69 146.7569 turnclash 28 3 7 0 38.4024 Cluster 1 = 7 9 20 22 28 Cluster 2 = 18 32 Cluster 3 = 35 60 Cluster 4 = 39 41 47 Cluster 5 = 65 69 14 clashing residues after turn Residue clashes: 9-20 18-32 20-22 20-28 22-28 28-7 35-60 39-41 39-47 65-69 cluster 1 has 5 members and 2.700e+01 combinations: 7 22 9 20 28 Energy 48.4681 Searching cluster 7 Combinations for 5 members in cluster 1 OK: 2.700e+01 - Sending to search 29.703533 < 48.468075: keeping 19.644352 < 32.945313: keeping Solved cluster 1: residual clashing 24.59 cluster 2 has 2 members and 9.000e+00 combinations: 18 32 Energy 24.5802 Searching cluster 18 Combinations for 2 members in cluster 2 OK: 9.000e+00 - Sending to search 0.000000 < 24.580202: keeping 0.000000 < 5.253963: keeping Solved cluster 2: residual clashing 0.91 cluster 3 has 2 members and 0.000e+00 combinations: 35 60 Energy 31.9945 Searching cluster 35 Combinations for 2 members in cluster 3 OK: 0.000e+00 - Sending to search 18.662220 < 31.994513: keeping 17.712893 < 18.716942: keeping 0.000000 < 17.821346: keeping Solved cluster 3: residual clashing 0.11 cluster 4 has 3 members and 1.500e+01 combinations: 47 39 41 Energy 128.2095 Searching cluster 39 Combinations for 3 members in cluster 4 OK: 1.500e+01 - Sending to search 59.554070 < 128.209457: keeping 23.192713 < 86.288620: keeping 23.192713 < 80.333755: keeping 23.192713 < 49.248856: keeping Solved cluster 4: residual clashing 43.60 cluster 5 has 2 members and 0.000e+00 combinations: 65 69 Energy 146.7569 Searching cluster 65 Combinations for 2 members in cluster 5 OK: 0.000e+00 - Sending to search 0.000000 < 146.756897: keeping Solved cluster 5: residual clashing 2.00 Still clashes at these sidechain pairs: ires= 7 irot= 1 jres= 28 jrot= 3 12.6982 ires= 39 irot= 2 jres= 47 jrot= 1 23.1927 ires= 41 irot= 13 jres= 45 jrot= 1 76.1172 Residual clashes = 155.80127 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/%-T0114-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/%-T0114-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m %/%-T0114-fssp-global.pw.a2m.gz \ -target T0114 -template % \ -out %-T0114-fssp-global -outdir und PDB file download failed: Can't locate PDB file for % /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Could not set defaults make[2]: *** [und/%-T0114-fssp-global.index] Error 1 make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make[1]: *** [1qh7A.indexes] Error 2 make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make: *** [indexes] Error 2 make -k 1qh7A.indexes \ 1qtsA.indexes \ 1axkA.indexes \ 1qhfA.indexes make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1qh7A-local.index und/1qh7A-T0114-local.index \ und/1qh7A-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' make[2]: `und/T0114-1qh7A-local.index' is up to date. make[2]: `und/1qh7A-T0114-local.index' is up to date. mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1qh7A-T0114-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1qh7A-T0114-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz \ -target T0114 -template 1qh7A \ -out 1qh7A-T0114-fssp-global -outdir und Couldn't open file 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz or 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz.gz for input Can't open A2M file 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz for input /projects/kestrel/users/karplus/burial/slicer/slicer: Error while reading the input a2m file. /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR read_input_alignment failed. make[2]: *** [und/1qh7A-T0114-fssp-global.index] Error 1 make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make[1]: *** [1qh7A.indexes] Error 2 make -k und/T0114-1qtsA-local.index und/1qtsA-T0114-local.index \ und/1qtsA-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/T0114-1qtsA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0114-1qtsA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qtsA/T0114-1qtsA-local.pw.a2m.gz \ -target T0114 -template 1qtsA \ -out T0114-1qtsA-local -outdir und Sequence named 1qtsA has all gap columns. It will be included anyway. Sequence named 1qtsA has all gap columns. It will be included anyway. /projects/kestrel/users/karplus/burial/slicer/slicer: no segments found mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1qtsA-T0114-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1qtsA-T0114-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qtsA/1qtsA-T0114-local.pw.a2m.gz \ -target T0114 -template 1qtsA \ -out 1qtsA-T0114-local -outdir und partial PDB gets fragment 36 through 87 extending start extending end Debugging on ! Reading sequence file Reading input structure 54 residues read Measuring phi and psi Getting chi values LEU 1 3 ILE 3 5 HIS 4 3 ASN 5 4 GLU 7 15 ASP 10 5 THR 11 2 LEU 12 3 CYS 13 2 PHE 14 3 THR 19 1 MET 20 11 PRO 21 2 VAL 22 3 ILE 24 3 TYR 25 2 VAL 27 1 ASN 28 6 TRP 29 5 VAL 30 2 GLU 31 12 SER 32 3 ASN 34 4 ASN 35 4 VAL 36 1 VAL 37 3 THR 38 2 GLN 40 12 PHE 41 3 ARG 43 28 ASN 44 5 LEU 45 3 SER 46 3 ARG 49 30 LEU 50 3 GLU 51 15 THR 52 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 1 rotamers of residue V 37 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 3 rotamers of residue T 53 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 2 11 26.9389 keepclash 13 30 13.7450 keepclash 15 26 32.8147 keepclash 15 28 12.1133 keepclash 30 44 116.6239 keepclash 32 42 36.0053 keepclash 40 42 11.2910 Cluster 1 = 2 11 Cluster 2 = 13 15 26 28 30 32 40 42 44 11 clashing residues after turn Residue clashes: 2-11 13-15 13-30 15-26 15-28 30-32 30-42 30-44 32-42 40-42 42-44 cluster 1 has 2 members and 8.000e+00 combinations: 2 11 Energy 28.8892 Searching cluster 2 Combinations for 2 members in cluster 1 OK: 8.000e+00 - Sending to search 26.938942 < 28.889179: keeping 0.000000 < 28.889177: keeping Solved cluster 1: residual clashing 3.05 cluster 2 has 9 members and 0.000e+00 combinations: 26 28 40 42 13 15 30 32 44 Energy 225.5311 Searching cluster 13 Combinations for 9 members in cluster 2 OK: 0.000e+00 - Sending to search 150.229553 < 225.531067: keeping 125.969292 < 153.674438: keeping 105.969292 < 129.580719: keeping 100.200485 < 110.190742: keeping 95.644875 < 105.019005: keeping 91.626846 < 100.513924: keeping 71.626846 < 95.997169: keeping 69.963959 < 76.607185: keeping 57.881886 < 75.939285: keeping 56.218994 < 64.067802: keeping 50.871845 < 63.399895: keeping 47.075733 < 57.679008: keeping Solved cluster 2: residual clashing 54.88 Still clashes at these sidechain pairs: ires= 15 irot= 1 jres= 26 jrot= 1 32.8147 ires= 15 irot= 1 jres= 28 jrot= 1 12.1133 Residual clashes = 55.29887 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1qtsA-T0114-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1qtsA-T0114-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qtsA/1qtsA-T0114-fssp-global.pw.a2m.gz \ -target T0114 -template 1qtsA \ -out 1qtsA-T0114-fssp-global -outdir und partial PDB gets fragment 29 through 34 extending start extending end partial PDB gets fragment 38 through 39 extending start extending end partial PDB gets fragment 40 through 58 extending start extending end partial PDB gets fragment 64 through 84 extending start extending end partial PDB gets fragment 101 through 131 extending start Debugging on ! Reading sequence file Reading input structure 88 residues read Measuring phi and psi Getting chi values MET 1 9 ILE 2 4 ASN 3 5 ARG 4 26 THR 5 2 ASP 6 7 ASN 9 6 SER 10 2 ASN 13 4 GLU 15 15 ASP 18 5 THR 19 2 LEU 20 3 CYS 21 2 PHE 22 3 THR 27 1 MET 28 11 PRO 29 2 VAL 30 3 ILE 34 3 TYR 35 3 VAL 37 2 ASN 38 4 TRP 39 6 VAL 40 1 GLU 41 12 SER 42 2 ASN 44 4 VAL 46 1 VAL 47 3 LEU 49 3 GLN 50 16 PHE 51 3 GLN 52 12 ARG 53 30 ASN 54 4 LEU 57 4 SER 58 3 ASP 59 6 PRO 60 2 ARG 61 30 LEU 62 3 GLU 63 15 THR 64 2 ILE 65 2 THR 66 2 LEU 67 3 LYS 69 21 TRP 70 5 SER 72 2 TRP 73 4 ASN 74 6 PRO 75 2 HIS 77 3 ILE 78 4 HIS 79 3 GLU 80 16 ILE 81 3 SER 83 3 ARG 85 27 ILE 86 3 TYR 87 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 S 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 4 rotamers of residue N 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. All 1 rotamers of residue V 41 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 I 66 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 5 66 24.0385 keepclash 47 64 16.6885 keepclash 67 80 20.3471 keepclash 78 80 55.0508 turnclash 5 4 81 0 34.2857 turnclash 5 14 23 0 131.1697 turnclash 23 1 3 0 26.6855 turnclash 5 25 68 0 21.1149 turnclash 64 6 35 0 36.5141 Cluster 1 = 3 5 23 66 68 81 Cluster 2 = 35 47 64 Cluster 3 = 67 78 80 12 clashing residues after turn Residue clashes: 5-66 5-81 5-23 5-3 5-68 47-64 64-35 67-80 78-80 23-3 23-68 cluster 1 has 6 members and 2.534e+04 combinations: 68 23 3 81 66 5 Energy 46.8815 Searching cluster 3 Combinations for 6 members in cluster 1 OK: 2.534e+04 - Sending to search 0.000000 < 46.881481: keeping 0.000000 < 27.080420: keeping 0.000000 < 23.072004: keeping Solved cluster 1: residual clashing 20.09 cluster 2 has 3 members and 2.400e+01 combinations: 35 47 64 Energy 17.0190 Searching cluster 35 Combinations for 3 members in cluster 2 OK: 2.400e+01 - Sending to search 14.656901 < 17.018990: keeping 8.216683 < 15.253975: keeping 0.330484 < 8.864285: keeping 0.330484 < 1.478822: keeping Solved cluster 2: residual clashing 1.48 cluster 3 has 3 members and 1.200e+01 combinations: 67 80 78 Energy 77.6848 Searching cluster 67 Combinations for 3 members in cluster 3 OK: 1.200e+01 - Sending to search 75.397812 < 77.684845: keeping 20.347061 < 77.684837: keeping 11.934566 < 23.045458: keeping 0.000000 < 13.718304: keeping Solved cluster 3: residual clashing 3.79 Still clashes at these sidechain pairs: Residual clashes = 23.98874 Printing make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1axkA-local.index und/1axkA-T0114-local.index \ und/1axkA-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/T0114-1axkA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0114-1axkA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1axkA/T0114-1axkA-local.pw.a2m.gz \ -target T0114 -template 1axkA \ -out T0114-1axkA-local -outdir und Skipped atom 2685, because occupancy 0.5 <= existing 0.500001 Skipped atom 2687, because occupancy 0.5 <= existing 0.500001 Skipped atom 2689, because occupancy 0.5 <= existing 0.500001 Skipped atom 2691, because occupancy 0.5 <= existing 0.500001 Skipped atom 2693, because occupancy 0.5 <= existing 0.500001 Skipped atom 2695, because occupancy 0.5 <= existing 0.500001 Skipped atom 2697, because occupancy 0.5 <= existing 0.500001 Skipped atom 2699, because occupancy 0.5 <= existing 0.500001 Skipped atom 2701, because occupancy 0.5 <= existing 0.500001 PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1axkA-orig.a2m Writing a2m file: tmp/1axkA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-1530 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-1530/tmp -alignfile tmp/1axkA-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/1axkA-orig.a2m (1 sequences, 394 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-1530/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-1530/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-1530/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-purr-1530/tmp.a2m (1 sequences, 394 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-1530/tmp.mod tmp/1axkA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1axkA-align.mod tmp/1axkA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-1530/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1axkA-orig.a2m tmp/1axkA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1axkA-align.mod Running w0.5 tmp/1axkA-orig.a2m tmp/1axkA-align.mod Running align2model tmp/1axkA-align -i tmp/1axkA-align.mod -db tmp/1axkA-orig.a2m -db tmp/1axkA-pdb.a2m partial PDB gets fragment 181 through 198 extending start extending end Debugging on ! Reading sequence file Reading input structure 20 residues read Measuring phi and psi Getting chi values VAL 6 1 GLU 7 10 SER 8 2 ASN 11 6 THR 14 2 LEU 15 2 GLN 16 13 PHE 17 3 GLN 18 12 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 14 15 12.9844 Cluster 1 = 14 15 2 clashing residues after turn Residue clashes: 14-15 cluster 1 has 2 members and 0.000e+00 combinations: 14 15 Energy 12.9844 Searching cluster 14 Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search 0.000000 < 12.984434: keeping Solved cluster 1: residual clashing 2.33 Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1axkA-T0114-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1axkA-T0114-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1axkA/1axkA-T0114-local.pw.a2m.gz \ -target T0114 -template 1axkA \ -out 1axkA-T0114-local -outdir und Skipped atom 2685, because occupancy 0.5 <= existing 0.500001 Skipped atom 2687, because occupancy 0.5 <= existing 0.500001 Skipped atom 2689, because occupancy 0.5 <= existing 0.500001 Skipped atom 2691, because occupancy 0.5 <= existing 0.500001 Skipped atom 2693, because occupancy 0.5 <= existing 0.500001 Skipped atom 2695, because occupancy 0.5 <= existing 0.500001 Skipped atom 2697, because occupancy 0.5 <= existing 0.500001 Skipped atom 2699, because occupancy 0.5 <= existing 0.500001 Skipped atom 2701, because occupancy 0.5 <= existing 0.500001 PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1axkA-orig.a2m Writing a2m file: tmp/1axkA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-1557 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-1557/tmp -alignfile tmp/1axkA-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/1axkA-orig.a2m (1 sequences, 394 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-1557/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-1557/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-1557/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-purr-1557/tmp.a2m (1 sequences, 394 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-1557/tmp.mod tmp/1axkA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1axkA-align.mod tmp/1axkA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-1557/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1axkA-orig.a2m tmp/1axkA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1axkA-align.mod Running w0.5 tmp/1axkA-orig.a2m tmp/1axkA-align.mod Running align2model tmp/1axkA-align -i tmp/1axkA-align.mod -db tmp/1axkA-orig.a2m -db tmp/1axkA-pdb.a2m partial PDB gets fragment 154 through 165 extending start extending end partial PDB gets fragment 167 through 191 extending start extending end partial PDB gets fragment 198 through 212 extending start extending end partial PDB gets fragment 228 through 247 extending start extending end Debugging on ! Reading sequence file Reading input structure 80 residues read Measuring phi and psi Getting chi values ASP 1 6 CYS 2 3 ASN 3 4 GLU 4 8 ASN 5 5 SER 6 2 LEU 8 3 GLU 9 12 ILE 10 4 HIS 11 3 ASN 12 6 ASN 15 5 GLU 16 14 ARG 18 27 ASP 19 3 THR 20 2 LEU 21 3 CYS 22 2 PHE 23 2 ASN 25 5 THR 28 3 MET 29 12 PRO 30 2 ILE 33 5 TYR 34 2 VAL 36 2 ASN 37 5 TRP 38 5 VAL 39 2 GLU 42 12 SER 43 2 ASN 45 5 ASN 46 5 VAL 47 2 VAL 48 3 LEU 50 3 GLN 51 13 PHE 52 2 GLN 53 14 ARG 54 27 ASN 55 4 LEU 56 3 SER 59 3 ASP 60 4 ARG 62 25 LEU 63 3 THR 65 2 ILE 66 5 THR 67 2 LEU 68 3 GLN 69 12 LYS 70 27 SER 73 2 TRP 74 5 ASN 75 5 HIS 78 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 6 rotamers of residue N 13 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 F 24 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. ssdist 3 1 23 1 17.3327 ssdist 3 1 23 2 19.8050 ssdist 3 2 23 1 19.3352 ssdist 3 2 23 2 21.7227 ssdist 3 3 23 1 16.6100 ssdist 3 3 23 2 18.9916 Found 0 disulfide bonds. Residue clashes: keepclash 9 24 59.6570 keepclash 13 20 14.6745 keepclash 13 40 14.6214 keepclash 46 48 15.7310 keepclash 53 70 24.2315 keepclash 55 71 12.6526 keepclash 72 76 39.4661 Cluster 1 = 9 24 Cluster 2 = 13 20 40 Cluster 3 = 46 48 Cluster 4 = 53 55 70 71 Cluster 5 = 72 76 13 clashing residues after turn Residue clashes: 9-24 13-20 13-40 46-48 53-70 55-71 70-71 72-76 cluster 1 has 2 members and 4.000e+00 combinations: 24 9 Energy 67.8180 Searching cluster 9 Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search 9.657747 < 67.817978: keeping Solved cluster 1: residual clashing 17.58 cluster 2 has 3 members and 1.800e+01 combinations: 40 13 20 Energy 41.1481 Searching cluster 13 Combinations for 3 members in cluster 2 OK: 1.800e+01 - Sending to search 18.011948 < 41.148140: keeping 14.613524 < 32.250713: keeping 10.477688 < 27.586201: keeping 7.097995 < 26.521889: keeping 7.780534 < 25.943001: keeping Solved cluster 2: residual clashing 16.59 cluster 3 has 2 members and 6.000e+00 combinations: 48 46 Energy 19.2741 Searching cluster 46 Combinations for 2 members in cluster 3 OK: 6.000e+00 - Sending to search 0.000000 < 19.274107: keeping Solved cluster 3: residual clashing 0.42 cluster 4 has 4 members and 1.555e+04 combinations: 53 70 55 71 Energy 36.8841 Searching cluster 53 Combinations for 4 members in cluster 4 OK: 1.555e+04 - Sending to search 24.231472 < 36.884071: keeping 23.097530 < 25.015049: keeping 12.652598 < 23.935831: keeping 0.000000 < 12.767075: keeping Solved cluster 4: residual clashing 0.90 cluster 5 has 2 members and 0.000e+00 combinations: 72 76 Energy 41.0257 Searching cluster 72 Combinations for 2 members in cluster 5 OK: 0.000e+00 - Sending to search 0.000000 < 41.025658: keeping Solved cluster 5: residual clashing 0.06 Still clashes at these sidechain pairs: ires= 11 irot= 1 jres= 24 jrot= 2 55.7022 Residual clashes = 83.14052 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1axkA-T0114-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1axkA-T0114-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1axkA/1axkA-T0114-fssp-global.pw.a2m.gz \ -target T0114 -template 1axkA \ -out 1axkA-T0114-fssp-global -outdir und Skipped atom 2685, because occupancy 0.5 <= existing 0.500001 Skipped atom 2687, because occupancy 0.5 <= existing 0.500001 Skipped atom 2689, because occupancy 0.5 <= existing 0.500001 Skipped atom 2691, because occupancy 0.5 <= existing 0.500001 Skipped atom 2693, because occupancy 0.5 <= existing 0.500001 Skipped atom 2695, because occupancy 0.5 <= existing 0.500001 Skipped atom 2697, because occupancy 0.5 <= existing 0.500001 Skipped atom 2699, because occupancy 0.5 <= existing 0.500001 Skipped atom 2701, because occupancy 0.5 <= existing 0.500001 PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1axkA-orig.a2m Writing a2m file: tmp/1axkA-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-purr-1584 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-purr-1584/tmp -alignfile tmp/1axkA-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/1axkA-orig.a2m (1 sequences, 394 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-purr-1584/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-purr-1584/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-purr-1584/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-purr-1584/tmp.a2m (1 sequences, 394 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-purr-1584/tmp.mod tmp/1axkA-align.mod Reading /projects/compbio/bin/scripts/sam-t99.confReading parameter file tmp/1axkA-align.mod tmp/1axkA-align.mod(21): Reading MODEL -- Model from alignment file /projects/compbio/tmp/tmp-build-weighted-model-purr-1584/tmp.a2m SAM: align2model v3.2 (June, 2000) compiled 07/06/00_15:43:05 Sequence Files: tmp/1axkA-orig.a2m tmp/1axkA-pdb.a2m Model FIM_method_score geometric mean of match probabilities (6). % Single Track Model: tmp/1axkA-align.mod Running w0.5 tmp/1axkA-orig.a2m tmp/1axkA-align.mod Running align2model tmp/1axkA-align -i tmp/1axkA-align.mod -db tmp/1axkA-orig.a2m -db tmp/1axkA-pdb.a2m partial PDB gets fragment 0 through 9 extending end partial PDB gets fragment 25 through 37 extending start extending end partial PDB gets fragment 41 through 46 extending start extending end partial PDB gets fragment 47 through 53 extending start extending end partial PDB gets fragment 103 through 112 extending start extending end partial PDB gets fragment 113 through 125 extending start extending end partial PDB gets fragment 211 through 216 extending start extending end partial PDB gets fragment 341 through 347 extending start extending end Debugging on ! Reading sequence file Reading input structure 87 residues read Measuring phi and psi Getting chi values THR 0 3 ASN 3 5 ASN 5 5 SER 6 3 TYR 7 3 LEU 8 3 GLU 9 13 ASN 13 6 GLU 14 9 ARG 16 32 ASP 17 5 THR 18 2 LEU 19 3 CYS 20 2 PHE 21 2 ASN 23 6 MET 29 8 PRO 30 2 VAL 31 1 TYR 35 3 VAL 37 1 ASN 38 5 TRP 39 5 VAL 40 1 GLU 41 15 ASN 45 5 ASN 46 5 VAL 47 3 VAL 48 2 LEU 50 3 GLN 51 15 PHE 52 3 GLN 53 11 SER 56 3 ASP 57 6 PRO 58 2 ARG 59 27 LEU 60 3 GLU 61 13 THR 62 2 THR 64 2 LEU 65 3 GLN 66 13 LYS 67 29 SER 72 3 ASN 74 5 HIS 79 3 GLU 80 16 ILE 81 4 LEU 82 3 SER 83 3 ILE 84 2 ARG 85 27 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 Y 8 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 1 rotamers of residue V 32 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 3 rotamers of residue Y 36 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 54 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 3 rotamers of residue S 57 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 13 rotamers of residue E 62 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 19 39 11.6688 keepclash 24 62 43.1728 keepclash 32 58 18.4332 keepclash 53 54 36.5530 turnclash 58 4 36 0 106.3106 Cluster 1 = 19 39 Cluster 2 = 24 62 Cluster 3 = 32 36 58 Cluster 4 = 53 54 9 clashing residues after turn Residue clashes: 19-39 24-62 32-58 53-54 58-36 cluster 1 has 2 members and 5.000e+00 combinations: 19 39 Energy 11.8173 Searching cluster 19 Combinations for 2 members in cluster 1 OK: 5.000e+00 - Sending to search 8.063236 < 11.817266: keeping 1.059031 < 8.447630: keeping 0.000000 < 1.917754: keeping Solved cluster 1: residual clashing 1.02 cluster 2 has 2 members and 2.600e+01 combinations: 62 24 Energy 127.4174 Searching cluster 24 Combinations for 2 members in cluster 2 OK: 2.600e+01 - Sending to search 0.000000 < 127.417412: keeping 0.000000 < 84.436546: keeping 0.000000 < 22.643856: keeping Solved cluster 2: residual clashing 16.74 cluster 3 has 3 members and 9.000e+00 combinations: 36 32 58 Energy 63.2348 Searching cluster 32 Combinations for 3 members in cluster 3 OK: 9.000e+00 - Sending to search 18.433186 < 63.234798: keeping 3.955117 < 44.269325: keeping Solved cluster 3: residual clashing 30.33 cluster 4 has 2 members and 3.300e+01 combinations: 53 54 Energy 46.5530 Searching cluster 53 Combinations for 2 members in cluster 4 OK: 3.300e+01 - Sending to search 11.800226 < 46.552998: keeping 11.908936 < 24.056683: keeping 0.000000 < 23.471901: keeping 0.000000 < 14.093376: keeping Solved cluster 4: residual clashing 10.26 Still clashes at these sidechain pairs: Residual clashes = 32.16319 Printing make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1qhfA-local.index und/1qhfA-T0114-local.index \ und/1qhfA-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/T0114-1qhfA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0114-1qhfA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qhfA/T0114-1qhfA-local.pw.a2m.gz \ -target T0114 -template 1qhfA \ -out T0114-1qhfA-local -outdir und Couldn't open file 1qhfA/T0114-1qhfA-local.pw.a2m.gz or 1qhfA/T0114-1qhfA-local.pw.a2m.gz.gz for input Can't open A2M file 1qhfA/T0114-1qhfA-local.pw.a2m.gz for input /projects/kestrel/users/karplus/burial/slicer/slicer: Error while reading the input a2m file. /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR read_input_alignment failed. make[2]: *** [und/T0114-1qhfA-local.index] Error 1 mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1qhfA-T0114-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1qhfA-T0114-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qhfA/1qhfA-T0114-local.pw.a2m.gz \ -target T0114 -template 1qhfA \ -out 1qhfA-T0114-local -outdir und Couldn't open file 1qhfA/1qhfA-T0114-local.pw.a2m.gz or 1qhfA/1qhfA-T0114-local.pw.a2m.gz.gz for input Can't open A2M file 1qhfA/1qhfA-T0114-local.pw.a2m.gz for input /projects/kestrel/users/karplus/burial/slicer/slicer: Error while reading the input a2m file. /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR read_input_alignment failed. make[2]: *** [und/1qhfA-T0114-local.index] Error 1 mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1qhfA-T0114-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1qhfA-T0114-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qhfA/1qhfA-T0114-fssp-global.pw.a2m.gz \ -target T0114 -template 1qhfA \ -out 1qhfA-T0114-fssp-global -outdir und Couldn't open file 1qhfA/1qhfA-T0114-fssp-global.pw.a2m.gz or 1qhfA/1qhfA-T0114-fssp-global.pw.a2m.gz.gz for input Can't open A2M file 1qhfA/1qhfA-T0114-fssp-global.pw.a2m.gz for input /projects/kestrel/users/karplus/burial/slicer/slicer: Error while reading the input a2m file. /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR read_input_alignment failed. make[2]: *** [und/1qhfA-T0114-fssp-global.index] Error 1 make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make[1]: *** [1qhfA.indexes] Error 2 make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make: *** [indexes] Error 2 make -k 1qh7A.indexes \ 1qtsA.indexes \ 1axkA.indexes \ 1qfhA.indexes make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1qh7A-local.index und/1qh7A-T0114-local.index \ und/1qh7A-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' make[2]: `und/T0114-1qh7A-local.index' is up to date. make[2]: `und/1qh7A-T0114-local.index' is up to date. mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1qh7A-T0114-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1qh7A-T0114-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz \ -target T0114 -template 1qh7A \ -out 1qh7A-T0114-fssp-global -outdir und Couldn't open file 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz or 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz.gz for input Can't open A2M file 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz for input /projects/kestrel/users/karplus/burial/slicer/slicer: Error while reading the input a2m file. /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR read_input_alignment failed. make[2]: *** [und/1qh7A-T0114-fssp-global.index] Error 1 make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make[1]: *** [1qh7A.indexes] Error 2 make -k und/T0114-1qtsA-local.index und/1qtsA-T0114-local.index \ und/1qtsA-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/T0114-1qtsA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0114-1qtsA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qtsA/T0114-1qtsA-local.pw.a2m.gz \ -target T0114 -template 1qtsA \ -out T0114-1qtsA-local -outdir und Sequence named 1qtsA has all gap columns. It will be included anyway. Sequence named 1qtsA has all gap columns. It will be included anyway. /projects/kestrel/users/karplus/burial/slicer/slicer: no segments found make[2]: `und/1qtsA-T0114-local.index' is up to date. make[2]: `und/1qtsA-T0114-fssp-global.index' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1axkA-local.index und/1axkA-T0114-local.index \ und/1axkA-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' make[2]: `und/T0114-1axkA-local.index' is up to date. make[2]: `und/1axkA-T0114-local.index' is up to date. make[2]: `und/1axkA-T0114-fssp-global.index' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1qfhA-local.index und/1qfhA-T0114-local.index \ und/1qfhA-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/T0114-1qfhA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0114-1qfhA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qfhA/T0114-1qfhA-local.pw.a2m.gz \ -target T0114 -template 1qfhA \ -out T0114-1qfhA-local -outdir und Sequence named 1qfhA has all gap columns. It will be included anyway. Sequence named 1qfhA has all gap columns. It will be included anyway. /projects/kestrel/users/karplus/burial/slicer/slicer: no segments found mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1qfhA-T0114-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1qfhA-T0114-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qfhA/1qfhA-T0114-local.pw.a2m.gz \ -target T0114 -template 1qfhA \ -out 1qfhA-T0114-local -outdir und partial PDB gets fragment 111 through 144 extending start extending end partial PDB gets fragment 151 through 163 extending start extending end Debugging on ! Reading sequence file Reading input structure 51 residues read Measuring phi and psi Getting chi values CYS 1 2 ASN 2 5 GLU 3 13 ASN 4 4 SER 5 3 TYR 6 2 LEU 7 5 GLU 8 14 ILE 9 3 HIS 10 3 ASN 11 5 ASN 12 5 GLU 13 13 ARG 15 22 ASP 16 4 THR 17 2 LEU 18 3 CYS 19 2 PHE 20 2 ASN 22 5 THR 25 1 MET 26 10 PRO 27 2 TYR 31 2 VAL 33 2 ASN 34 5 TRP 37 5 VAL 38 1 GLU 39 12 SER 40 2 ASN 42 5 ASN 43 5 VAL 44 2 VAL 45 3 LEU 47 3 GLN 48 13 PHE 49 1 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 5 rotamers of residue W 38 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 5 rotamers of residue N 44 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 3 rotamers of residue L 48 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 1 rotamers of residue F 50 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. ssdist 2 1 20 1 35.5236 ssdist 2 1 20 2 33.0353 ssdist 2 2 20 1 37.3511 ssdist 2 2 20 2 34.9618 Found 0 disulfide bonds. Residue clashes: keepclash 6 50 44.7778 keepclash 29 38 37.0332 Cluster 1 = 6 50 Cluster 2 = 29 38 4 clashing residues after turn Residue clashes: 6-50 29-38 cluster 1 has 2 members and 3.000e+00 combinations: 50 6 Energy 54.5242 Searching cluster 6 Combinations for 2 members in cluster 1 OK: 3.000e+00 - Sending to search 3.730414 < 54.524200: keeping 0.000000 < 13.728938: keeping Solved cluster 1: residual clashing 10.30 cluster 2 has 2 members and 0.000e+00 combinations: 29 38 Energy 255.2579 Searching cluster 29 Combinations for 2 members in cluster 2 OK: 0.000e+00 - Sending to search 0.000000 < 255.257935: keeping Solved cluster 2: residual clashing 131.65 Still clashes at these sidechain pairs: ires= 27 irot= 1 jres= 38 jrot= 2 12.0562 Residual clashes = 48.48854 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1qfhA-T0114-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1qfhA-T0114-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qfhA/1qfhA-T0114-fssp-global.pw.a2m.gz \ -target T0114 -template 1qfhA \ -out 1qfhA-T0114-fssp-global -outdir und partial PDB gets fragment 14 through 34 extending start extending end partial PDB gets fragment 43 through 56 extending start extending end partial PDB gets fragment 68 through 73 extending start extending end partial PDB gets fragment 76 through 99 extending start extending end partial PDB gets fragment 146 through 156 extending start extending end partial PDB gets fragment 206 through 211 extending start Debugging on ! Reading sequence file Reading input structure 93 residues read Measuring phi and psi Getting chi values MET 1 11 ILE 2 2 ASN 3 5 ARG 4 32 THR 5 3 ASP 6 6 CYS 7 2 GLU 9 13 ASN 10 5 SER 11 2 TYR 12 3 LEU 13 4 GLU 14 15 HIS 16 3 ASN 17 5 ASN 18 5 GLU 19 14 ARG 21 28 THR 25 2 LEU 26 3 CYS 27 2 PHE 28 3 ASN 30 5 THR 33 2 MET 34 6 PRO 35 2 VAL 36 3 ILE 40 4 ASN 44 5 TRP 45 6 VAL 48 3 GLU 49 13 SER 50 3 ASN 53 5 VAL 54 1 THR 56 1 LEU 57 3 GLN 58 11 PHE 59 3 GLN 60 7 ARG 61 28 LEU 63 4 SER 64 2 ASP 65 5 PRO 66 2 ARG 67 29 LEU 68 2 GLU 69 15 THR 70 2 ILE 71 4 THR 74 3 LEU 75 4 GLN 76 14 LYS 77 31 TRP 78 5 SER 80 2 TRP 81 5 PRO 83 2 LEU 87 3 SER 88 3 ILE 89 5 ARG 90 32 ILE 91 4 TYR 92 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 11 rotamers of residue M 2 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 3 rotamers of residue F 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. All 2 rotamers of residue L 69 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 4 rotamers of residue I 72 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 84 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 4 rotamers of residue I 92 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. ssdist 8 1 28 1 25.6450 ssdist 8 1 28 2 23.1953 ssdist 8 2 28 1 27.7227 ssdist 8 2 28 2 25.3617 Found 0 disulfide bonds. Residue clashes: keepclash 2 12 16.7017 keepclash 13 45 52.0171 keepclash 16 29 30.0000 keepclash 17 19 11.6397 keepclash 18 25 12.4604 keepclash 27 60 92.2250 keepclash 29 58 37.9510 keepclash 31 54 42.7188 keepclash 57 69 50.0000 keepclash 83 84 26.6846 Cluster 1 = 2 12 13 45 Cluster 2 = 16 29 31 54 58 Cluster 3 = 17 19 Cluster 4 = 18 25 Cluster 5 = 27 60 Cluster 6 = 57 69 Cluster 7 = 83 84 19 clashing residues after turn Residue clashes: 2-12 2-13 13-45 16-29 17-19 18-25 27-60 29-31 29-58 31-54 57-69 83-84 cluster 1 has 4 members and 1.650e+02 combinations: 2 12 13 45 Energy 221.2143 Searching cluster 2 Combinations for 4 members in cluster 1 OK: 1.650e+02 - Sending to search 46.312141 < 221.214310: keeping 29.180119 < 199.435455: keeping 20.551611 < 182.555664: keeping 16.701664 < 174.677750: keeping 29.610477 < 171.455597: keeping 12.478455 < 168.720062: keeping 3.849946 < 151.840271: keeping 0.000000 < 143.962357: keeping 12.478455 < 140.740204: keeping 4.546114 < 132.407898: keeping 0.696168 < 125.226166: keeping 52.017124 < 122.004013: keeping 29.610477 < 107.919342: keeping 12.478455 < 86.140488: keeping 3.849946 < 69.260696: keeping 0.000000 < 61.382786: keeping 12.478455 < 58.160637: keeping 3.849946 < 42.986954: keeping 0.000000 < 35.109047: keeping Solved cluster 1: residual clashing 31.89 cluster 2 has 5 members and 0.000e+00 combinations: 16 58 29 54 31 Energy 128.7360 Searching cluster 16 Combinations for 5 members in cluster 2 OK: 0.000e+00 - Sending to search 69.743843 < 128.736008: keeping 44.511639 < 86.418793: keeping 37.287235 < 63.818871: keeping 1.792843 < 57.271774: keeping Solved cluster 2: residual clashing 22.03 cluster 3 has 2 members and 1.500e+01 combinations: 17 19 Energy 11.6397 Searching cluster 17 Combinations for 2 members in cluster 3 OK: 1.500e+01 - Sending to search 0.000000 < 11.639745: keeping Solved cluster 3: residual clashing 0.72 cluster 4 has 2 members and 0.000e+00 combinations: 25 18 Energy 14.1860 Searching cluster 18 Combinations for 2 members in cluster 4 OK: 0.000e+00 - Sending to search 3.138708 < 14.186013: keeping 0.000000 < 3.201785: keeping Solved cluster 4: residual clashing 0.68 cluster 5 has 2 members and 4.000e+00 combinations: 27 60 Energy 93.7412 Searching cluster 27 Combinations for 2 members in cluster 5 OK: 4.000e+00 - Sending to search 0.000000 < 93.741188: keeping Solved cluster 5: residual clashing 1.35 cluster 6 has 2 members and 2.000e+00 combinations: 57 69 Energy 93.1590 Searching cluster 57 Combinations for 2 members in cluster 6 OK: 2.000e+00 - Sending to search 40.000000 < 93.159004: keeping Solved cluster 6: residual clashing 56.36 cluster 7 has 2 members and 0.000e+00 combinations: 83 84 Energy 38.4118 Searching cluster 83 Combinations for 2 members in cluster 7 OK: 0.000e+00 - Sending to search Solved cluster 7: residual clashing 38.41 Still clashes at these sidechain pairs: ires= 2 irot= 9 jres= 14 jrot= 1 14.5303 ires= 18 irot= 4 jres= 42 jrot= 1 19.4636 ires= 29 irot= 2 jres= 46 jrot= 2 11.1020 ires= 57 irot= 1 jres= 69 jrot= 2 40.0000 ires= 64 irot= 1 jres= 69 jrot= 2 25.6314 ires= 83 irot= 1 jres= 84 jrot= 1 26.6846 Residual clashes = 151.03705 Printing make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make: *** [indexes] Error 2 make -k 1qh7A.indexes \ 1qtsA.indexes \ 1axkA.indexes \ 1qfhA.indexes \ 1hoe.indexes make[1]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1qh7A-local.index und/1qh7A-T0114-local.index \ und/1qh7A-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' make[2]: `und/T0114-1qh7A-local.index' is up to date. make[2]: `und/1qh7A-T0114-local.index' is up to date. mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1qh7A-T0114-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1qh7A-T0114-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz \ -target T0114 -template 1qh7A \ -out 1qh7A-T0114-fssp-global -outdir und Couldn't open file 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz or 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz.gz for input Can't open A2M file 1qh7A/1qh7A-T0114-fssp-global.pw.a2m.gz for input /projects/kestrel/users/karplus/burial/slicer/slicer: Error while reading the input a2m file. /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR read_input_alignment failed. make[2]: *** [und/1qh7A-T0114-fssp-global.index] Error 1 make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make[1]: *** [1qh7A.indexes] Error 2 make -k und/T0114-1qtsA-local.index und/1qtsA-T0114-local.index \ und/1qtsA-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/T0114-1qtsA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0114-1qtsA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qtsA/T0114-1qtsA-local.pw.a2m.gz \ -target T0114 -template 1qtsA \ -out T0114-1qtsA-local -outdir und Sequence named 1qtsA has all gap columns. It will be included anyway. Sequence named 1qtsA has all gap columns. It will be included anyway. /projects/kestrel/users/karplus/burial/slicer/slicer: no segments found make[2]: `und/1qtsA-T0114-local.index' is up to date. make[2]: `und/1qtsA-T0114-fssp-global.index' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1axkA-local.index und/1axkA-T0114-local.index \ und/1axkA-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' make[2]: `und/T0114-1axkA-local.index' is up to date. make[2]: `und/1axkA-T0114-local.index' is up to date. make[2]: `und/1axkA-T0114-fssp-global.index' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1qfhA-local.index und/1qfhA-T0114-local.index \ und/1qfhA-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/T0114-1qfhA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0114-1qfhA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1qfhA/T0114-1qfhA-local.pw.a2m.gz \ -target T0114 -template 1qfhA \ -out T0114-1qfhA-local -outdir und Sequence named 1qfhA has all gap columns. It will be included anyway. Sequence named 1qfhA has all gap columns. It will be included anyway. /projects/kestrel/users/karplus/burial/slicer/slicer: no segments found make[2]: `und/1qfhA-T0114-local.index' is up to date. make[2]: `und/1qfhA-T0114-fssp-global.index' is up to date. make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make -k und/T0114-1hoe-local.index und/1hoe-T0114-local.index \ und/1hoe-T0114-fssp-global.index make[2]: Entering directory `/auto/projects/compbio/experiments/casp4/t114' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/T0114-1hoe-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0114-1hoe-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1hoe/T0114-1hoe-local.pw.a2m.gz \ -target T0114 -template 1hoe \ -out T0114-1hoe-local -outdir und partial PDB gets fragment 24 through 49 extending start extending end Debugging on ! Reading sequence file Reading input structure 28 residues read Measuring phi and psi Getting chi values THR 1 1 ASP 2 4 ASN 4 5 ASN 6 4 SER 7 3 TYR 8 3 LEU 9 2 GLU 10 16 ILE 11 4 HIS 12 3 ASN 13 6 ASN 14 4 GLU 15 14 ARG 17 27 ASP 18 7 THR 19 2 PHE 22 3 ASN 24 4 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 Y 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. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: keepclash 2 25 18.7325 keepclash 13 19 29.0213 Cluster 1 = 2 25 Cluster 2 = 13 19 4 clashing residues after turn Residue clashes: 2-25 13-19 cluster 1 has 2 members and 2.000e+00 combinations: 2 25 Energy 18.7325 Searching cluster 2 Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search 0.000000 < 18.732483: keeping Solved cluster 1: residual clashing 1.19 cluster 2 has 2 members and 1.500e+01 combinations: 13 19 Energy 29.0213 Searching cluster 13 Combinations for 2 members in cluster 2 OK: 1.500e+01 - Sending to search 28.016319 < 29.021317: keeping 0.000000 < 28.836824: keeping Solved cluster 2: residual clashing 1.32 Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1hoe-T0114-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1hoe-T0114-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1hoe/1hoe-T0114-local.pw.a2m.gz \ -target T0114 -template 1hoe \ -out 1hoe-T0114-local -outdir und partial PDB gets fragment 24 through 47 extending start extending end Debugging on ! Reading sequence file Reading input structure 26 residues read Measuring phi and psi Getting chi values THR 1 1 ASP 2 4 ASN 4 5 ASN 6 4 SER 7 3 TYR 8 3 LEU 9 2 GLU 10 16 ILE 11 4 HIS 12 3 ASN 13 6 ASN 14 4 GLU 15 14 ARG 17 27 ASP 18 7 THR 19 2 PHE 22 3 ASN 24 4 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 Y 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. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: keepclash 2 25 18.7325 keepclash 13 19 29.0213 Cluster 1 = 2 25 Cluster 2 = 13 19 4 clashing residues after turn Residue clashes: 2-25 13-19 cluster 1 has 2 members and 2.000e+00 combinations: 2 25 Energy 18.7325 Searching cluster 2 Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search 0.000000 < 18.732483: keeping Solved cluster 1: residual clashing 1.19 cluster 2 has 2 members and 1.500e+01 combinations: 13 19 Energy 29.0213 Searching cluster 13 Combinations for 2 members in cluster 2 OK: 1.500e+01 - Sending to search 28.016319 < 29.021317: keeping 0.000000 < 28.836824: keeping Solved cluster 2: residual clashing 1.32 Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1hoe-T0114-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1hoe-T0114-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1hoe/1hoe-T0114-fssp-global.pw.a2m.gz \ -target T0114 -template 1hoe \ -out 1hoe-T0114-fssp-global -outdir und partial PDB gets fragment 0 through 7 extending end partial PDB gets fragment 8 through 42 extending start extending end partial PDB gets fragment 43 through 62 extending start extending end partial PDB gets fragment 63 through 73 extending start Debugging on ! Reading sequence file Reading input structure 80 residues read Measuring phi and psi Getting chi values MET 0 10 ILE 1 3 ASN 2 4 ARG 3 32 THR 4 2 ASP 5 4 CYS 6 3 ASN 7 6 ASN 10 5 TYR 12 2 LEU 13 3 GLU 14 15 ILE 15 3 HIS 16 3 ASN 17 4 ASN 18 4 GLU 19 15 ARG 21 29 ASP 22 4 THR 23 3 LEU 24 3 CYS 25 2 PHE 26 3 ASN 28 6 MET 32 12 PRO 33 2 ILE 36 4 TYR 37 3 VAL 39 2 ASN 40 6 TRP 41 5 VAL 42 3 SER 44 3 PHE 47 3 GLN 48 13 ARG 49 30 ASN 50 5 LEU 51 3 SER 52 3 ASP 53 5 PRO 54 2 ARG 55 30 LEU 56 3 GLU 57 15 ILE 59 3 THR 60 2 LEU 61 3 GLN 62 13 LYS 63 29 TRP 64 5 ILE 70 3 GLU 72 15 ILE 73 2 LEU 74 4 SER 75 3 ILE 76 5 ILE 78 4 TYR 79 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 6 rotamers of residue N 8 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 5 rotamers of residue N 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 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. All 3 rotamers of residue L 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 3 rotamers of residue F 27 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 3 rotamers of residue Y 38 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 3 rotamers of residue S 45 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 3 rotamers of residue F 48 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 5 rotamers of residue D 54 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 T 61 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 13 rotamers of residue Q 63 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 5 rotamers of residue W 65 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. ssdist 7 1 26 1 17.4388 ssdist 7 1 26 2 17.0836 ssdist 7 2 26 1 16.8712 ssdist 7 2 26 2 17.0061 ssdist 7 3 26 1 14.9397 ssdist 7 3 26 2 14.7461 Found 0 disulfide bonds. Residue clashes: keepclash 5 38 56.4344 keepclash 14 27 13.6058 keepclash 16 73 13.0334 keepclash 20 65 41.4577 keepclash 23 37 23.9458 keepclash 23 61 20.0000 keepclash 23 73 47.5326 keepclash 24 57 15.4380 keepclash 25 60 28.8270 keepclash 27 52 93.5384 keepclash 37 73 45.2670 keepclash 38 44 12.2871 keepclash 38 77 104.2505 keepclash 41 43 17.9201 keepclash 49 79 24.8670 keepclash 50 59 21.6267 keepclash 52 58 10.7311 keepclash 64 72 20.0000 turnclash 58 7 56 6 27.3538 Cluster 1 = 5 38 44 77 Cluster 2 = 14 16 23 25 27 37 50 52 56 58 59 60 61 73 Cluster 3 = 20 64 65 72 Cluster 4 = 24 57 Cluster 5 = 41 43 Cluster 6 = 49 79 28 clashing residues after turn Residue clashes: 5-38 14-25 14-27 16-73 20-64 20-65 23-37 23-61 23-73 24-57 25-27 25-52 25-60 27-52 37-60 37-73 38-44 38-77 41-43 49-79 50-58 50-59 50-60 52-58 58-56 64-72 cluster 1 has 4 members and 0.000e+00 combinations: 44 38 5 77 Energy 274.3542 Searching cluster 5 Combinations for 4 members in cluster 1 OK: 0.000e+00 - Sending to search 144.257339 < 274.354187: keeping 8.072715 < 240.029343: keeping Solved cluster 1: residual clashing 40.91 cluster 2 has 14 members and 0.000e+00 combinations: 56 59 27 52 37 61 16 23 14 60 25 73 58 50 Energy 420.3185 Searching cluster 14 Combinations for 14 members in cluster 2 OK: 0.000e+00 - Sending to search 331.885223 < 420.318512: keeping 309.255951 < 420.318390: keeping 309.255951 < 396.673584: keeping 298.524902 < 396.585175: keeping 298.524902 < 386.494171: keeping 252.323349 < 386.405762: keeping 229.694077 < 344.151184: keeping 229.694077 < 320.506378: keeping 218.963013 < 320.417938: keeping 218.963013 < 310.326935: keeping 217.640778 < 310.238525: keeping 217.640778 < 307.638428: keeping 210.100937 < 307.549988: keeping 204.862808 < 304.031464: keeping 199.369873 < 298.704926: keeping 194.131744 < 293.852051: keeping 192.809509 < 288.525482: keeping 188.803879 < 285.836975: keeping 183.310944 < 284.574615: keeping 178.072815 < 279.721741: keeping 176.750580 < 274.395172: keeping 168.812775 < 271.706665: keeping 163.574646 < 267.276123: keeping 162.643433 < 261.949554: keeping 145.179123 < 259.652069: keeping 122.549850 < 250.188507: keeping 122.549850 < 226.543701: keeping 111.818794 < 226.455292: keeping 111.818794 < 216.364288: keeping 110.496544 < 216.275864: keeping 110.496544 < 213.675751: keeping 102.956726 < 213.587341: keeping 97.718597 < 210.068817: keeping 92.225662 < 204.742279: keeping 86.987534 < 199.889404: keeping 85.665283 < 194.562836: keeping 81.097633 < 191.874313: keeping 77.727486 < 189.235291: keeping 72.489357 < 187.443756: keeping 71.558136 < 182.117218: keeping 67.921707 < 179.819702: keeping 66.990486 < 179.478180: keeping Solved cluster 2: residual clashing 177.18 cluster 3 has 4 members and 0.000e+00 combinations: 72 65 64 20 Energy 111.2341 Searching cluster 20 Combinations for 4 members in cluster 3 OK: 0.000e+00 - Sending to search 36.271526 < 111.234100: keeping 32.865986 < 86.806808: keeping 18.113106 < 84.297646: keeping 12.865986 < 69.507645: keeping 33.780155 < 65.156898: keeping 13.780154 < 62.424667: keeping 0.000000 < 43.283920: keeping Solved cluster 3: residual clashing 24.35 cluster 4 has 2 members and 4.000e+00 combinations: 24 57 Energy 15.8646 Searching cluster 24 Combinations for 2 members in cluster 4 OK: 4.000e+00 - Sending to search 0.000000 < 15.864566: keeping Solved cluster 4: residual clashing 3.60 cluster 5 has 2 members and 1.500e+01 combinations: 43 41 Energy 17.9201 Searching cluster 41 Combinations for 2 members in cluster 5 OK: 1.500e+01 - Sending to search 0.000000 < 17.920139: keeping Solved cluster 5: residual clashing 0.07 cluster 6 has 2 members and 1.000e+00 combinations: 79 49 Energy 31.1094 Searching cluster 49 Combinations for 2 members in cluster 6 OK: 1.000e+00 - Sending to search Solved cluster 6: residual clashing 31.11 Still clashes at these sidechain pairs: ires= 23 irot= 3 jres= 37 jrot= 2 11.3562 ires= 27 irot= 2 jres= 54 jrot= 1 43.4393 ires= 37 irot= 2 jres= 73 jrot= 10 23.6411 ires= 49 irot= 10 jres= 79 jrot= 2 24.8670 Residual clashes = 164.00330 Printing make[2]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make[1]: Leaving directory `/auto/projects/compbio/experiments/casp4/t114' make: *** [indexes] Error 2