make -k und/T0124-1reqA-local.index \ und/T0124-1reqA-2track-l.index \ und/1reqA-T0124-local.index \ und/1reqA-T0124-fssp-global.index make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t124' mkdir tmp mkdir und /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1reqA/T0124-1reqA-local.pw.a2m.gz \ -target T0124 -template 1reqA \ -out T0124-1reqA-local -outdir und partial PDB gets fragment 406 through 427 extending start extending end Debugging on ! Reading sequence file Reading input structure 24 residues read Measuring phi and psi Getting chi values ASN 1 4 ILE 2 2 LYS 3 24 ASP 4 4 ILE 5 3 LYS 6 24 LYS 7 26 LYS 8 24 GLU 10 12 ARG 13 32 LEU 14 3 ASP 15 4 ARG 16 27 VAL 19 2 MET 20 10 MET 21 10 ARG 22 27 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/T0124-1reqA-2track-l.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/T0124-1reqA-2track-l.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1reqA/T0124-1reqA-2track-local.pw.a2m.gz \ -target T0124 -template 1reqA \ -out T0124-1reqA-2track-l -outdir und partial PDB gets fragment 93 through 110 extending start extending end partial PDB gets fragment 398 through 457 extending start extending end Debugging on ! Reading sequence file Reading input structure 82 residues read Measuring phi and psi Getting chi values SER 1 3 ARG 3 28 ARG 4 26 GLU 5 15 GLU 6 12 LEU 7 3 LEU 8 3 GLN 9 12 LYS 10 26 TYR 11 2 SER 12 3 VAL 13 3 LEU 14 2 PHE 15 3 LEU 16 3 GLU 17 12 PRO 18 2 VAL 21 1 TYR 22 3 ARG 24 29 LEU 26 3 ASP 27 5 SER 28 3 GLN 29 11 VAL 31 1 LYS 34 23 GLU 35 12 ARG 36 26 GLU 38 12 MET 39 10 GLU 40 12 LEU 41 3 ILE 42 3 HIS 43 4 LEU 44 3 GLU 46 12 GLU 47 13 TYR 48 2 HIS 49 4 ASP 50 4 ILE 52 4 ARG 53 31 ARG 54 32 ARG 55 27 GLU 57 13 GLN 58 12 HIS 59 4 THR 61 1 GLU 62 12 GLN 63 12 THR 64 2 LYS 66 24 THR 68 2 LEU 70 4 ARG 72 26 GLU 73 12 LYS 74 24 ILE 76 2 GLU 78 12 LEU 79 3 LYS 80 29 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 12 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 2 rotamers of residue Y 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 4 rotamers of residue I 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 12 17 104.0422 keepclash 49 55 30.8277 keepclash 49 58 14.8310 turnclash 55 16 64 0 21.4940 Cluster 1 = 12 17 Cluster 2 = 49 55 58 64 6 clashing residues after turn Residue clashes: 12-17 49-55 49-58 49-64 55-64 58-64 cluster 1 has 2 members and 2.000e+00 combinations: 12 17 Energy 142.9362 Searching cluster 12 Combinations for 2 members in cluster 1 OK: 2.000e+00 - Sending to search 0.000000 < 142.936234: keeping Solved cluster 1: residual clashing 11.15 cluster 2 has 4 members and 4.464e+03 combinations: 64 49 58 55 Energy 219.6709 Searching cluster 49 Combinations for 4 members in cluster 2 OK: 4.464e+03 - Sending to search 14.831014 < 219.670914: keeping 9.555314 < 189.644196: keeping 5.029006 < 184.862778: keeping 0.000000 < 180.374191: keeping 52.611469 < 175.959122: keeping 0.000000 < 65.416260: keeping 0.000000 < 17.110050: keeping Solved cluster 2: residual clashing 13.95 Still clashes at these sidechain pairs: ires= 8 irot= 1 jres= 12 jrot= 2 32.5226 Residual clashes = 47.29462 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[1]: [und/1reqA-T0124-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/1reqA-T0124-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1reqA/1reqA-T0124-local.pw.a2m.gz \ -target T0124 -template 1reqA \ -out 1reqA-T0124-local -outdir und Sequence named T0124 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[1]: [und/1reqA-T0124-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/1reqA-T0124-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1reqA/1reqA-T0124-fssp-global.pw.a2m.gz \ -target T0124 -template 1reqA \ -out 1reqA-T0124-fssp-global -outdir und partial PDB gets fragment 97 through 99 extending start extending end partial PDB gets fragment 122 through 124 extending start extending end partial PDB gets fragment 172 through 178 extending start extending end partial PDB gets fragment 212 through 225 extending start extending end partial PDB gets fragment 258 through 268 extending start extending end partial PDB gets fragment 296 through 307 extending start extending end partial PDB gets fragment 324 through 330 extending start extending end partial PDB gets fragment 354 through 363 extending start extending end partial PDB gets fragment 384 through 392 extending start extending end partial PDB gets fragment 469 through 514 extending start extending end partial PDB gets fragment 661 through 698 extending start extending end Debugging on ! Reading sequence file Reading input structure 182 residues read Measuring phi and psi Getting chi values THR 1 2 GLN 2 11 LEU 3 3 PRO 6 2 GLU 7 14 PRO 8 2 GLN 11 11 THR 12 2 SER 14 3 LEU 15 3 GLU 17 12 LEU 20 3 GLN 22 15 MET 23 10 LYS 24 26 LEU 25 3 PHE 26 3 LEU 27 3 LYS 28 30 LEU 29 3 LEU 30 3 LYS 31 24 LYS 32 26 GLN 33 11 GLU 36 12 LYS 37 26 GLU 38 12 LEU 39 3 LYS 40 24 GLU 41 12 LEU 42 3 GLU 43 12 LYS 45 25 SER 49 3 LYS 50 30 ARG 51 26 ARG 52 27 GLU 53 12 GLU 54 12 LEU 55 3 LEU 56 3 GLN 57 12 LYS 58 26 TYR 59 3 SER 60 3 VAL 63 1 LEU 64 5 PHE 65 3 LEU 66 5 GLU 67 15 PRO 68 2 VAL 69 1 TYR 72 4 PRO 73 2 ARG 74 20 LEU 76 3 ASP 77 4 GLN 79 13 VAL 80 2 VAL 81 1 GLU 84 12 LEU 85 3 LYS 86 26 GLU 87 12 ARG 88 27 LEU 89 3 GLU 90 12 MET 91 10 GLU 92 15 ILE 95 5 HIS 96 3 LEU 97 3 GLU 100 16 TYR 101 2 HIS 102 3 ASP 103 5 ILE 105 3 ARG 106 27 ARG 107 29 ARG 108 26 LYS 109 24 GLU 110 14 GLN 111 13 HIS 112 3 THR 114 1 THR 117 2 ILE 120 4 THR 121 1 GLU 122 12 ARG 125 25 GLU 126 15 LYS 127 22 GLN 128 12 ILE 129 3 GLU 131 15 LEU 132 3 LEU 135 3 LYS 136 24 GLU 137 12 SER 138 3 SER 139 3 GLU 140 12 SER 143 3 ASN 144 4 ILE 145 2 LYS 146 26 ASP 147 4 ILE 148 2 LYS 149 25 LYS 150 30 LYS 151 26 GLU 153 13 LYS 155 22 ARG 156 24 LEU 157 3 ASP 158 4 ARG 159 32 GLN 161 16 VAL 162 2 MET 163 7 MET 164 11 ARG 165 24 SER 166 3 THR 167 1 SER 168 2 ASP 169 6 LYS 170 30 GLN 173 12 GLU 174 12 ARG 175 25 LYS 177 23 LYS 178 30 GLU 179 13 ILE 180 4 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 L 67 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 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 3 rotamers of residue L 77 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 181 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 40 60 20.3540 keepclash 53 67 31.1333 keepclash 53 75 15.3118 keepclash 67 77 74.4057 keepclash 73 80 53.2358 keepclash 73 86 25.7289 keepclash 129 132 13.2454 keepclash 146 165 15.2041 keepclash 146 181 13.6836 keepclash 147 180 20.7252 keepclash 150 181 20.0000 turnclash 150 16 154 0 29.7548 turnclash 180 5 177 0 27.1674 Cluster 1 = 40 60 Cluster 2 = 53 67 73 75 77 80 86 Cluster 3 = 129 132 Cluster 4 = 146 147 150 154 165 177 180 181 19 clashing residues after turn Residue clashes: 40-60 53-67 53-75 53-77 67-75 67-77 67-80 73-80 73-86 75-77 80-86 129-132 146-165 146-181 147-180 150-181 150-154 165-177 180-177 cluster 1 has 2 members and 6.000e+00 combinations: 60 40 Energy 20.3540 Searching cluster 40 Combinations for 2 members in cluster 1 OK: 6.000e+00 - Sending to search 0.000000 < 20.353970: keeping Solved cluster 1: residual clashing 0.44 cluster 2 has 7 members and 1.440e+04 combinations: 77 67 75 86 73 53 80 Energy 233.3904 Searching cluster 53 Combinations for 7 members in cluster 2 OK: 1.440e+04 - Sending to search 200.812973 < 233.390350: keeping 196.838821 < 233.390335: keeping 174.836960 < 229.470901: keeping 147.577209 < 207.960709: keeping 145.339905 < 180.766769: keeping 116.973450 < 178.738663: keeping 91.244568 < 151.557556: keeping 91.171158 < 126.105072: keeping 65.442276 < 120.883865: keeping Solved cluster 2: residual clashing 95.43 cluster 3 has 2 members and 1.320e+02 combinations: 132 129 Energy 13.2454 Searching cluster 129 Combinations for 2 members in cluster 3 OK: 1.320e+02 - Sending to search 0.000000 < 13.245422: keeping Solved cluster 3: residual clashing 0.07 cluster 4 has 8 members and 0.000e+00 combinations: 177 154 146 181 150 180 165 147 Energy 106.2537 Searching cluster 146 Combinations for 8 members in cluster 4 OK: 0.000e+00 - Sending to search 58.887753 < 106.253738: keeping 53.683613 < 82.925484: keeping 43.683613 < 78.204697: keeping 39.750614 < 68.943062: keeping 34.546474 < 54.016827: keeping 24.546474 < 49.296043: keeping 14.546474 < 40.034405: keeping 14.587247 < 30.592419: keeping Solved cluster 4: residual clashing 30.56 Still clashes at these sidechain pairs: ires= 53 irot= 15 jres= 75 jrot= 15 15.3118 ires= 67 irot= 2 jres= 75 jrot= 15 25.1377 ires= 67 irot= 2 jres= 77 jrot= 1 23.9954 Residual clashes = 121.95114 Printing make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t124'