mkdir tmp mkdir und /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 2oneA/T0111-2oneA-karplus.a2m \ -target T0111 -template 2oneA \ -out T011-2oneA-karplus -outdir und Debugging on ! Reading sequence file Reading input structure 434 residues read Measuring phi and psi Getting chi values LYS 0 30 ILE 1 2 VAL 2 2 ILE 4 4 ILE 5 4 GLU 8 14 ILE 9 2 ILE 10 5 VAL 22 1 HIS 23 3 LEU 24 4 PHE 29 3 MET 32 11 SER 43 3 ARG 44 20 LEU 49 3 ARG 56 19 PHE 57 2 LEU 58 2 THR 63 2 LYS 64 25 PRO 72 2 GLN 75 12 LEU 77 3 ILE 78 5 LYS 82 25 ILE 90 2 LYS 92 25 ILE 93 2 MET 94 10 ASP 96 5 GLU 101 16 PHE 106 3 ASN 118 7 LYS 120 25 MET 128 9 GLU 132 13 ILE 134 4 GLU 136 12 ASN 138 5 THR 140 2 PRO 141 2 LYS 145 19 SER 147 3 MET 148 10 MET 152 10 MET 153 10 ILE 155 3 ILE 156 2 GLU 160 15 ASP 163 7 ASN 164 6 ASN 165 4 VAL 166 1 ASP 167 6 ILE 168 4 GLN 174 12 VAL 176 3 VAL 181 2 LYS 182 26 ILE 185 4 MET 187 12 PHE 192 3 HIS 194 3 LYS 197 24 VAL 198 3 LEU 199 3 LYS 202 29 MET 204 10 ASN 205 4 THR 206 2 TYR 216 3 LEU 220 3 SER 222 3 ASN 223 4 VAL 229 1 GLU 232 15 VAL 234 1 LYS 241 26 ASP 242 4 ILE 243 4 THR 244 1 LEU 245 3 MET 247 12 TYR 255 3 VAL 261 1 PHE 267 3 SER 269 3 GLU 270 12 GLU 271 12 PHE 272 3 THR 273 1 HIS 274 3 PHE 275 3 LEU 276 3 GLU 277 15 GLU 278 12 THR 280 2 GLN 282 15 LEU 292 5 ASP 293 6 SER 295 2 ASP 298 5 PHE 300 2 TYR 302 2 GLN 303 11 THR 304 2 VAL 306 3 LEU 307 3 LEU 313 3 PHE 319 1 THR 323 2 ILE 325 4 LEU 326 3 LYS 327 26 GLU 328 12 ILE 334 4 ASN 336 6 SER 337 3 ILE 338 3 ILE 340 3 PHE 342 3 SER 347 3 THR 349 2 THR 351 2 LEU 352 3 ILE 355 2 LYS 356 30 MET 357 10 LYS 359 26 ASP 360 4 TYR 363 3 THR 364 1 VAL 366 1 ILE 367 4 THR 378 1 THR 386 1 SER 395 2 MET 396 8 SER 397 2 ASP 400 4 VAL 402 3 TYR 405 4 ILE 409 2 GLU 417 14 LYS 418 26 PRO 420 2 TYR 421 3 ASN 422 4 ARG 424 27 LYS 425 20 GLU 426 12 ILE 427 4 LYS 428 22 GLN 432 10 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 73 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 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 3 rotamers of residue L 200 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 217 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 273 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 281 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 L 293 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 301 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 320 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 T 365 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 423 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 57 58 20.3181 keepclash 83 94 16.7224 keepclash 107 112 26.5132 keepclash 113 343 20.0000 keepclash 127 137 16.6057 keepclash 133 147 20.0000 keepclash 147 421 13.1284 keepclash 154 397 13.7909 keepclash 169 224 23.8025 keepclash 175 427 12.2817 keepclash 301 335 44.5069 turnclash 133 4 129 0 31.6447 turnclash 154 8 406 0 36.6465 Cluster 1 = 57 58 Cluster 2 = 83 94 Cluster 3 = 107 112 Cluster 4 = 113 343 Cluster 5 = 127 137 Cluster 6 = 129 133 147 421 Cluster 7 = 154 397 406 Cluster 8 = 169 224 Cluster 9 = 175 427 Cluster 10 = 301 335 23 clashing residues after turn Residue clashes: 57-58 83-94 107-112 113-343 127-137 133-147 133-129 147-421 154-397 154-406 169-224 175-427 301-335 397-406 cluster 1 has 2 members and 1.700e+01 combinations: 58 57 Energy 20.3181 Searching cluster 57 Combinations for 2 members in cluster 1 OK: 1.700e+01 - Sending to search 18.044254 < 20.318068: keeping 0.000000 < 18.250044: keeping Solved cluster 1: residual clashing 2.81 cluster 2 has 2 members and 3.000e+01 combinations: 94 83 Energy 17.8727 Searching cluster 83 Combinations for 2 members in cluster 2 OK: 3.000e+01 - Sending to search 0.000000 < 17.872654: keeping 0.000000 < 2.735135: keeping Solved cluster 2: residual clashing 2.45 cluster 3 has 2 members and 0.000e+00 combinations: 112 107 Energy 114.5293 Searching cluster 107 Combinations for 2 members in cluster 3 OK: 0.000e+00 - Sending to search 4.524684 < 114.529312: keeping 0.000000 < 67.462990: keeping Solved cluster 3: residual clashing 29.50 cluster 4 has 2 members and 0.000e+00 combinations: 113 343 Energy 23.8905 Searching cluster 113 Combinations for 2 members in cluster 4 OK: 0.000e+00 - Sending to search Solved cluster 4: residual clashing 23.89 cluster 5 has 2 members and 0.000e+00 combinations: 127 137 Energy 16.6057 Searching cluster 127 Combinations for 2 members in cluster 5 OK: 0.000e+00 - Sending to search 14.252064 < 16.605652: keeping 8.086180 < 14.849133: keeping 0.000000 < 8.733774: keeping Solved cluster 5: residual clashing 0.76 cluster 6 has 4 members and 0.000e+00 combinations: 129 147 421 133 Energy 38.8820 Searching cluster 129 Combinations for 4 members in cluster 6 OK: 0.000e+00 - Sending to search 33.128399 < 38.881973: keeping 30.000000 < 38.881969: keeping 13.128399 < 33.201267: keeping 10.000000 < 19.231804: keeping Solved cluster 6: residual clashing 13.55 cluster 7 has 3 members and 2.400e+01 combinations: 406 397 154 Energy 23.0467 Searching cluster 154 Combinations for 3 members in cluster 7 OK: 2.400e+01 - Sending to search 13.790913 < 23.046680: keeping 3.044824 < 23.046679: keeping 0.000000 < 8.351469: keeping Solved cluster 7: residual clashing 5.65 cluster 8 has 2 members and 6.000e+00 combinations: 224 169 Energy 23.8025 Searching cluster 169 Combinations for 2 members in cluster 8 OK: 6.000e+00 - Sending to search 0.000000 < 23.802479: keeping Solved cluster 8: residual clashing 1.30 cluster 9 has 2 members and 1.800e+01 combinations: 427 175 Energy 14.7138 Searching cluster 175 Combinations for 2 members in cluster 9 OK: 1.800e+01 - Sending to search 9.902499 < 14.713779: keeping 1.565932 < 12.489964: keeping 0.000000 < 4.204974: keeping Solved cluster 9: residual clashing 0.83 cluster 10 has 2 members and 2.000e+00 combinations: 301 335 Energy 271.5952 Searching cluster 301 Combinations for 2 members in cluster 10 OK: 2.000e+00 - Sending to search 0.000000 < 271.595184: keeping Solved cluster 10: residual clashing 7.97 Still clashes at these sidechain pairs: ires= 98 irot= 1 jres= 107 jrot= 3 22.6573 ires= 113 irot= 1 jres= 343 jrot= 3 20.0000 Residual clashes = 241.88612 Printing