make -k und/T0086-1ctt-local.index und/1ctt-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/T0086-1ctt-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/T0086-1ctt-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1ctt/T0086-1ctt-local.pw.a2m.gz \ -target T0086 -template 1ctt \ -out T0086-1ctt-local -outdir und Sequence named 1ctt has all gap columns. It will be included anyway. Sequence named 1ctt 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/1ctt-T0086-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[1]: [und/1ctt-T0086-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1ctt/1ctt-T0086-local.pw.a2m.gz \ -target T0086 -template 1ctt \ -out 1ctt-T0086-local -outdir und Debugging on ! Reading sequence file Reading input structure 75 residues read Measuring phi and psi Getting chi values GLN 1 11 GLN 2 11 LYS 4 26 THR 5 2 VAL 6 1 SER 7 3 VAL 8 3 THR 9 2 MET 10 10 ILE 11 5 ARG 12 32 GLU 13 12 PHE 15 3 VAL 16 2 GLU 17 15 GLN 18 12 ASN 19 5 GLU 20 7 ILE 21 2 GLU 23 14 GLU 24 15 LEU 25 3 PRO 26 2 LEU 28 3 PRO 29 2 GLU 31 12 SER 32 2 TYR 34 3 TRP 35 5 LEU 36 3 ARG 37 31 GLU 38 15 ILE 39 4 LEU 40 3 LEU 41 2 CYS 42 3 ASP 44 3 GLU 46 13 TRP 48 5 ARG 54 28 THR 55 2 VAL 56 2 VAL 57 2 VAL 59 2 SER 60 3 THR 61 2 LEU 62 3 SER 63 3 PRO 65 2 GLU 66 12 LEU 67 3 GLN 70 14 LYS 71 30 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 10 rotamers of residue M 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 5 rotamers of residue I 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 I 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 15 rotamers of residue E 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 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 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 3 rotamers of residue L 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 2 rotamers of residue L 42 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 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 V 58 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 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 7 35 32.6237 keepclash 7 37 30.8635 keepclash 8 27 20.0000 keepclash 11 25 30.0000 keepclash 11 39 23.3740 keepclash 16 41 13.7412 keepclash 19 49 12.9247 keepclash 22 58 30.0000 keepclash 22 60 10.2132 keepclash 24 62 20.0000 keepclash 27 35 14.1714 keepclash 30 34 25.2458 keepclash 35 37 94.9645 keepclash 42 49 42.5348 Cluster 1 = 7 8 11 25 27 35 37 39 Cluster 2 = 16 41 Cluster 3 = 19 42 49 Cluster 4 = 22 58 60 Cluster 5 = 24 62 Cluster 6 = 30 34 20 clashing residues after turn Residue clashes: 7-35 7-37 8-27 11-25 11-27 11-37 11-39 16-41 19-49 22-58 22-60 24-62 25-37 27-35 27-37 30-34 35-37 42-49 cluster 1 has 8 members and 4.050e+04 combinations: 7 37 27 11 35 25 8 39 Energy 650.0379 Searching cluster 7 Combinations for 8 members in cluster 1 OK: 4.050e+04 - Sending to search 232.623199 < 650.037903: keeping 214.723221 < 625.306885: keeping 202.623199 < 607.858826: keeping 184.723221 < 592.083313: keeping 184.723221 < 574.635254: keeping 202.623199 < 562.243530: keeping 184.723221 < 558.470581: keeping 225.997208 < 541.022522: keeping 202.623199 < 518.579468: keeping 184.723221 < 493.848419: keeping 114.237534 < 476.400391: keeping 90.863525 < 432.155518: keeping 72.963547 < 407.424469: keeping 60.863525 < 389.976440: keeping 42.963543 < 374.200897: keeping 42.963543 < 356.752838: keeping 60.863525 < 344.361115: keeping 42.963543 < 340.588104: keeping 84.237534 < 323.140045: keeping 60.863525 < 300.697083: keeping 42.963543 < 275.966003: keeping 60.863525 < 258.517975: keeping 52.107788 < 252.326035: keeping 42.963543 < 245.379272: keeping 42.963543 < 234.877991: keeping 38.220856 < 222.151337: keeping 38.220856 < 211.928223: keeping 34.375778 < 199.201569: keeping 34.375778 < 198.187210: keeping 35.195091 < 185.460556: keeping 35.195091 < 180.799438: keeping Solved cluster 1: residual clashing 168.07 cluster 2 has 2 members and 6.000e+00 combinations: 41 16 Energy 14.3835 Searching cluster 16 Combinations for 2 members in cluster 2 OK: 6.000e+00 - Sending to search 0.000000 < 14.383501: keeping Solved cluster 2: residual clashing 1.05 cluster 3 has 3 members and 1.200e+02 combinations: 42 49 19 Energy 370.2259 Searching cluster 19 Combinations for 3 members in cluster 3 OK: 1.200e+02 - Sending to search 42.534836 < 370.225891: keeping 29.949835 < 357.415649: keeping 19.998507 < 115.194580: keeping 18.123589 < 105.468140: keeping 6.083693 < 103.482803: keeping Solved cluster 3: residual clashing 87.87 cluster 4 has 3 members and 8.000e+00 combinations: 22 58 60 Energy 89.8739 Searching cluster 22 Combinations for 3 members in cluster 4 OK: 8.000e+00 - Sending to search 30.000000 < 89.873924: keeping 13.765386 < 79.990097: keeping 3.552160 < 64.114616: keeping Solved cluster 4: residual clashing 54.23 cluster 5 has 2 members and 6.000e+00 combinations: 62 24 Energy 20.0000 Searching cluster 24 Combinations for 2 members in cluster 5 OK: 6.000e+00 - Sending to search 4.659104 < 20.000000: keeping 0.000000 < 7.051795: keeping Solved cluster 5: residual clashing 2.99 cluster 6 has 2 members and 0.000e+00 combinations: 34 30 Energy 26.9802 Searching cluster 30 Combinations for 2 members in cluster 6 OK: 0.000e+00 - Sending to search 18.222588 < 26.980234: keeping Solved cluster 6: residual clashing 19.71 Still clashes at these sidechain pairs: ires= 7 irot= 1 jres= 37 jrot= 2 32.2758 ires= 12 irot= 1 jres= 25 jrot= 7 79.5344 ires= 29 irot= 1 jres= 35 jrot= 2 65.2834 ires= 30 irot= 2 jres= 34 jrot= 1 18.2226 ires= 40 irot= 3 jres= 49 jrot= 4 38.5311 ires= 62 irot= 2 jres= 66 jrot= 1 11.9098 Residual clashes = 259.93515 Printing make[1]: Leaving directory `/export/projects/compbio/experiments/casp4/t86'