make -k und/T0086-1sesA-local.index und/1sesA-T0086-local.index make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t86' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/T0086-1sesA-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/T0086-1sesA-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1sesA/T0086-1sesA-local.pw.a2m.gz \ -target T0086 -template 1sesA \ -out T0086-1sesA-local -outdir und Debugging on ! Reading sequence file Reading input structure 77 residues read Measuring phi and psi Getting chi values PRO 1 2 ASP 4 5 PRO 5 2 GLN 6 12 LEU 8 3 ASP 9 4 TRP 10 5 LEU 11 3 LEU 12 3 LEU 13 3 GLU 14 15 ASP 15 6 SER 16 2 MET 17 11 THR 18 2 PHE 21 3 GLU 22 12 GLN 23 11 GLN 24 14 LYS 26 31 THR 27 2 VAL 28 3 SER 29 3 VAL 30 1 THR 31 2 MET 32 10 ARG 34 30 GLU 35 12 PHE 37 3 VAL 38 1 GLU 39 15 GLN 40 11 ASN 41 4 ILE 43 4 PRO 44 2 GLU 45 12 LEU 49 3 PRO 50 2 LEU 52 3 PRO 53 2 SER 56 3 TRP 59 7 ARG 61 28 GLU 62 15 ILE 63 4 CYS 66 2 ASP 68 6 GLU 70 14 LEU 73 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 6 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 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 F 22 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 14 rotamers of residue Q 25 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 2 rotamers of residue P 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 2 rotamers of residue P 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. All 2 rotamers of residue P 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 7 rotamers of residue W 60 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 11 15 56.2055 keepclash 11 40 17.4101 keepclash 11 44 75.5881 keepclash 15 44 33.4660 keepclash 18 21 25.1096 keepclash 21 25 34.9264 keepclash 25 33 14.1139 Cluster 1 = 11 15 18 21 25 33 40 44 8 clashing residues after turn Residue clashes: 11-15 11-40 11-44 15-40 15-44 18-21 18-33 18-40 21-25 25-33 cluster 1 has 8 members and 0.000e+00 combinations: 21 44 11 25 33 40 18 15 Energy 569.9982 Searching cluster 11 Combinations for 8 members in cluster 1 OK: 0.000e+00 - Sending to search 225.211319 < 569.998169: keeping 169.611664 < 538.987000: keeping 168.081436 < 483.495148: keeping 167.148148 < 482.459229: keeping 166.217789 < 481.563599: keeping 164.687561 < 480.439209: keeping 163.754272 < 479.403259: keeping 144.502045 < 478.507660: keeping 142.971817 < 459.032196: keeping 142.038528 < 457.996277: keeping 138.436371 < 457.100647: keeping 136.906143 < 456.338348: keeping 135.972855 < 455.302429: keeping 135.918549 < 454.406799: keeping 134.388321 < 454.129272: keeping 133.455032 < 453.093323: keeping 130.388168 < 452.197754: keeping 128.857941 < 445.661865: keeping 127.924652 < 444.625946: keeping 124.322510 < 443.730347: keeping 122.792282 < 442.968048: keeping 121.858994 < 441.932129: keeping 121.804687 < 441.036499: keeping 120.274460 < 440.758972: keeping 119.341171 < 439.723022: keeping 121.226913 < 438.827454: keeping 119.696686 < 431.842651: keeping 118.763397 < 430.806702: keeping 115.161247 < 429.911102: keeping 113.631020 < 429.148804: keeping 112.697731 < 428.112854: keeping 112.643425 < 427.217255: keeping 111.113197 < 426.939728: keeping 110.179909 < 425.903778: keeping 121.770599 < 425.008179: keeping 120.240372 < 415.667114: keeping 119.307083 < 414.631165: keeping 115.704941 < 413.735596: keeping 114.174713 < 412.973267: keeping 113.241425 < 411.937347: keeping 113.187119 < 411.041748: keeping 111.656891 < 410.764221: keeping 110.723602 < 409.728271: keeping 125.938309 < 408.832672: keeping 125.005020 < 408.507202: keeping 126.422699 < 407.611633: keeping 124.892471 < 406.608673: keeping 123.959183 < 405.572754: keeping 120.357033 < 404.677124: keeping 118.826805 < 403.914825: keeping 117.893517 < 402.878906: keeping 117.839211 < 401.983307: keeping 116.308983 < 401.705750: keeping 115.375694 < 400.669830: keeping 123.590347 < 399.774231: keeping 122.060120 < 392.705933: keeping 121.126831 < 391.669983: keeping 117.524689 < 390.774384: keeping 115.994461 < 390.012085: keeping 115.061172 < 388.976135: keeping 115.006866 < 388.080566: keeping 113.476639 < 387.803009: keeping 112.543350 < 386.767090: keeping 115.647240 < 385.871460: keeping 114.713951 < 385.691925: keeping 95.461731 < 384.796326: keeping 93.931503 < 365.320862: keeping 92.998215 < 364.284912: keeping 89.396065 < 363.389343: keeping 87.865837 < 362.627014: keeping 86.932549 < 361.591095: keeping 86.878242 < 360.695496: keeping 85.348015 < 360.417938: keeping 84.414726 < 359.382019: keeping 107.615906 < 358.486420: keeping 98.540298 < 227.620056: keeping 76.613449 < 219.141510: keeping 75.083221 < 197.322479: keeping 74.149933 < 196.286545: keeping 73.219566 < 195.390961: keeping 71.689339 < 194.266525: keeping 70.756050 < 193.230591: keeping 51.503830 < 192.334991: keeping 49.973602 < 172.859512: keeping 49.040314 < 171.823578: keeping 37.389961 < 170.927979: keeping 35.859734 < 159.489227: keeping 34.926445 < 158.453278: keeping 28.228703 < 157.557693: keeping 26.698471 < 145.669983: keeping 25.765184 < 144.634048: keeping 28.772394 < 143.738464: keeping 27.242163 < 129.494446: keeping 26.308876 < 128.458496: keeping 41.523582 < 127.562912: keeping 40.590294 < 127.237457: keeping 33.424484 < 126.341866: keeping 31.894255 < 120.435989: keeping 30.960968 < 119.400055: keeping 30.592138 < 118.504463: keeping 29.061907 < 106.533241: keeping 28.128620 < 105.497299: keeping 24.179255 < 104.601715: keeping 22.649023 < 100.555206: keeping 21.715736 < 99.519272: keeping 2.463517 < 98.623680: keeping 0.933287 < 79.148193: keeping 0.000000 < 78.112259: keeping 2.463517 < 77.216667: keeping 0.933287 < 70.067772: keeping 0.000000 < 69.031837: keeping Solved cluster 1: residual clashing 68.14 Still clashes at these sidechain pairs: ires= 11 irot= 5 jres= 43 jrot= 1 56.4431 ires= 25 irot= 12 jres= 29 jrot= 1 16.3403 Residual clashes = 77.08944 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/1sesA-T0086-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/1sesA-T0086-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1sesA/1sesA-T0086-local.pw.a2m.gz \ -target T0086 -template 1sesA \ -out 1sesA-T0086-local -outdir und Debugging on ! Reading sequence file Reading input structure 143 residues read Measuring phi and psi Getting chi values TYR 1 2 CYS 2 2 LYS 3 26 GLU 4 15 ILE 5 2 PRO 6 2 PRO 10 2 GLN 11 12 LEU 12 3 LEU 13 3 ASP 14 4 TRP 15 6 LEU 16 3 LEU 17 3 LEU 18 3 GLU 19 12 ASP 20 5 SER 21 3 MET 22 10 THR 23 2 LYS 24 25 ARG 25 32 PHE 26 4 GLU 27 12 GLN 29 14 THR 32 3 SER 34 3 ILE 37 2 ARG 38 27 GLU 39 12 PHE 41 2 VAL 42 1 GLU 43 12 GLN 44 12 ASN 45 4 GLU 46 12 ILE 47 5 PRO 48 2 LEU 51 3 PRO 52 2 LEU 53 3 PRO 55 2 LYS 56 25 GLU 57 12 SER 58 3 TYR 60 3 TRP 61 6 LEU 62 3 ARG 63 25 GLU 64 15 ILE 65 3 LEU 66 3 LEU 67 3 CYS 68 2 ASP 70 4 GLU 72 13 TRP 74 5 LEU 75 3 ARG 79 32 THR 80 1 VAL 81 2 VAL 82 1 SER 85 2 LEU 88 2 SER 89 2 PRO 91 2 GLU 92 13 LEU 93 3 LEU 95 3 GLN 96 11 LYS 97 31 LEU 98 3 LYS 100 21 THR 101 2 LEU 103 3 SER 106 3 THR 108 2 LEU 109 3 THR 110 3 ARG 111 29 PHE 113 2 ILE 114 2 GLU 115 15 ILE 116 3 ARG 118 26 ASP 119 4 LEU 122 2 ARG 125 32 SER 128 2 ARG 131 32 LEU 132 3 ARG 133 22 LEU 134 2 LYS 137 31 PRO 138 2 LEU 139 3 LEU 141 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 7 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 2 rotamers of residue P 11 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 6 rotamers of residue W 16 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 2 rotamers of residue P 49 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 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. All 2 rotamers of residue P 56 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 D 71 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 76 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 S 86 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 89 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 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. All 3 rotamers of residue L 104 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 107 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 32 rotamers of residue R 126 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 S 129 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 69 1 10.2090 ssdist 3 1 69 2 7.7788 ssdist 3 2 69 1 11.4512 ssdist 3 2 69 2 9.3625 Found 0 disulfide bonds. Residue clashes: keepclash 13 66 25.6137 keepclash 16 58 52.8783 keepclash 16 62 51.1766 keepclash 86 92 19.9396 Cluster 1 = 13 66 Cluster 2 = 16 58 62 Cluster 3 = 86 92 7 clashing residues after turn Residue clashes: 13-66 16-58 16-62 58-62 86-92 cluster 1 has 2 members and 3.000e+00 combinations: 66 13 Energy 29.2383 Searching cluster 13 Combinations for 2 members in cluster 1 OK: 3.000e+00 - Sending to search 0.000000 < 29.238342: keeping Solved cluster 1: residual clashing 3.03 cluster 2 has 3 members and 6.000e+01 combinations: 62 16 58 Energy 117.0680 Searching cluster 16 Combinations for 3 members in cluster 2 OK: 6.000e+01 - Sending to search 97.830093 < 117.067986: keeping 51.176643 < 111.440178: keeping Solved cluster 2: residual clashing 64.95 cluster 3 has 2 members and 4.000e+00 combinations: 92 86 Energy 155.9476 Searching cluster 86 Combinations for 2 members in cluster 3 OK: 4.000e+00 - Sending to search 2.211390 < 155.947647: keeping 10.897968 < 122.132614: keeping Solved cluster 3: residual clashing 108.72 Still clashes at these sidechain pairs: ires= 16 irot= 1 jres= 62 jrot= 2 51.1766 ires= 86 irot= 2 jres= 92 jrot= 2 10.8980 Residual clashes = 109.29519 Printing make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86'