Starting phenix.real_space_refine on Tue Jul 29 20:45:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tni_10534/07_2025/6tni_10534.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tni_10534/07_2025/6tni_10534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tni_10534/07_2025/6tni_10534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tni_10534/07_2025/6tni_10534.map" model { file = "/net/cci-nas-00/data/ceres_data/6tni_10534/07_2025/6tni_10534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tni_10534/07_2025/6tni_10534.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 7083 2.51 5 N 2234 2.21 5 O 2286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11625 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 5815 Classifications: {'peptide': 1067} Incomplete info: {'truncation_to_alanine': 800} Link IDs: {'PTRANS': 45, 'TRANS': 1021} Chain breaks: 6 Unresolved chain link angles: 39 Unresolved non-hydrogen bonds: 2782 Unresolved non-hydrogen angles: 3545 Unresolved non-hydrogen dihedrals: 2305 Unresolved non-hydrogen chiralities: 274 Planarities with less than four sites: {'GLN:plan1': 51, 'HIS:plan': 24, 'TYR:plan': 17, 'ASN:plan1': 33, 'TRP:plan': 8, 'ASP:plan': 48, 'PHE:plan': 46, 'GLU:plan': 56, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1413 Chain: "a" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 5810 Classifications: {'peptide': 1067} Incomplete info: {'truncation_to_alanine': 801} Link IDs: {'PTRANS': 45, 'TRANS': 1021} Chain breaks: 6 Unresolved chain link angles: 39 Unresolved non-hydrogen bonds: 2788 Unresolved non-hydrogen angles: 3553 Unresolved non-hydrogen dihedrals: 2311 Unresolved non-hydrogen chiralities: 274 Planarities with less than four sites: {'GLN:plan1': 51, 'HIS:plan': 25, 'TYR:plan': 17, 'ASN:plan1': 33, 'TRP:plan': 8, 'ASP:plan': 48, 'PHE:plan': 46, 'GLU:plan': 56, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1418 Time building chain proxies: 9.97, per 1000 atoms: 0.86 Number of scatterers: 11625 At special positions: 0 Unit cell: (111.3, 168.54, 100.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 2286 8.00 N 2234 7.00 C 7083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 2.1 seconds 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 0 sheets defined 69.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 162 through 166 removed outlier: 4.120A pdb=" N PHE A 165 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 166 " --> pdb=" O PHE A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 166' Processing helix chain 'A' and resid 168 through 173 removed outlier: 4.473A pdb=" N THR A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.199A pdb=" N LEU A 178 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 207 through 214 removed outlier: 3.604A pdb=" N ILE A 214 " --> pdb=" O ILE A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.832A pdb=" N GLU A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 234' Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.681A pdb=" N ILE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 3.976A pdb=" N ASP A 256 " --> pdb=" O SER A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.985A pdb=" N THR A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 removed outlier: 4.423A pdb=" N PHE A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.815A pdb=" N ILE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 removed outlier: 4.504A pdb=" N LEU A 383 " --> pdb=" O HIS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 395 removed outlier: 3.605A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 411 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.546A pdb=" N MET A 420 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.556A pdb=" N PHE A 435 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 444 Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.734A pdb=" N CYS A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 486 Processing helix chain 'A' and resid 489 through 505 removed outlier: 4.399A pdb=" N ASP A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.788A pdb=" N LEU A 510 " --> pdb=" O HIS A 506 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 506 through 511' Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 517 through 524 removed outlier: 3.622A pdb=" N ILE A 520 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 521 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 545 removed outlier: 3.917A pdb=" N LYS A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 568 removed outlier: 3.567A pdb=" N ILE A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 563 " --> pdb=" O MET A 559 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 removed outlier: 3.516A pdb=" N VAL A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 625 removed outlier: 4.214A pdb=" N GLN A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 644 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.591A pdb=" N LEU A 653 " --> pdb=" O ASP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.664A pdb=" N ASP A 663 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 removed outlier: 4.122A pdb=" N GLN A 709 " --> pdb=" O PRO A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 746 removed outlier: 3.651A pdb=" N LEU A 738 " --> pdb=" O PRO A 734 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 741 " --> pdb=" O ARG A 737 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 744 " --> pdb=" O ARG A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 803 removed outlier: 4.649A pdb=" N CYS A 785 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU A 787 " --> pdb=" O PHE A 783 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 835 Processing helix chain 'A' and resid 840 through 845 Processing helix chain 'A' and resid 920 through 925 removed outlier: 3.790A pdb=" N PHE A 924 " --> pdb=" O ARG A 921 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG A 925 " --> pdb=" O PRO A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 940 removed outlier: 4.222A pdb=" N CYS A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 940 " --> pdb=" O HIS A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 980 removed outlier: 4.601A pdb=" N HIS A 977 " --> pdb=" O TRP A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1017 Processing helix chain 'A' and resid 1019 through 1035 removed outlier: 3.675A pdb=" N CYS A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1072 removed outlier: 3.834A pdb=" N TYR A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A1054 " --> pdb=" O ILE A1050 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A1060 " --> pdb=" O MET A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1093 removed outlier: 4.138A pdb=" N GLN A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A1091 " --> pdb=" O SER A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1121 removed outlier: 3.821A pdb=" N PHE A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A1115 " --> pdb=" O SER A1111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A1121 " --> pdb=" O LEU A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1134 Processing helix chain 'A' and resid 1134 through 1141 Processing helix chain 'A' and resid 1146 through 1167 removed outlier: 3.708A pdb=" N ARG A1150 " --> pdb=" O THR A1146 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A1151 " --> pdb=" O GLY A1147 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER A1164 " --> pdb=" O PHE A1160 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TRP A1165 " --> pdb=" O LEU A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1176 removed outlier: 4.252A pdb=" N GLY A1175 " --> pdb=" O ASP A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 4.970A pdb=" N LEU A1182 " --> pdb=" O PHE A1178 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A1183 " --> pdb=" O ASN A1179 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1208 Processing helix chain 'A' and resid 1218 through 1222 removed outlier: 3.749A pdb=" N SER A1221 " --> pdb=" O GLY A1218 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A1222 " --> pdb=" O CYS A1219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1218 through 1222' Processing helix chain 'A' and resid 1225 through 1228 Processing helix chain 'A' and resid 1229 through 1246 removed outlier: 3.547A pdb=" N VAL A1237 " --> pdb=" O VAL A1233 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1240 " --> pdb=" O ARG A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1260 through 1284 removed outlier: 3.711A pdb=" N LYS A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN A1280 " --> pdb=" O HIS A1276 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A1281 " --> pdb=" O ILE A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1309 removed outlier: 4.150A pdb=" N SER A1292 " --> pdb=" O ARG A1288 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A1296 " --> pdb=" O SER A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1314 Processing helix chain 'A' and resid 1315 through 1317 No H-bonds generated for 'chain 'A' and resid 1315 through 1317' Processing helix chain 'A' and resid 1320 through 1323 Processing helix chain 'A' and resid 1324 through 1341 removed outlier: 3.813A pdb=" N THR A1330 " --> pdb=" O SER A1326 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU A1331 " --> pdb=" O LEU A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1375 removed outlier: 3.567A pdb=" N LEU A1360 " --> pdb=" O HIS A1356 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A1363 " --> pdb=" O LEU A1359 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) Processing helix chain 'a' and resid 162 through 167 removed outlier: 4.034A pdb=" N PHE a 165 " --> pdb=" O GLU a 162 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL a 167 " --> pdb=" O PHE a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 174 through 181 Processing helix chain 'a' and resid 182 through 187 removed outlier: 7.085A pdb=" N TRP a 185 " --> pdb=" O GLN a 182 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 201 Processing helix chain 'a' and resid 207 through 215 Processing helix chain 'a' and resid 223 through 228 removed outlier: 4.469A pdb=" N GLN a 227 " --> pdb=" O GLU a 223 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN a 228 " --> pdb=" O ASP a 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 223 through 228' Processing helix chain 'a' and resid 229 through 234 removed outlier: 3.762A pdb=" N GLU a 233 " --> pdb=" O GLU a 229 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU a 234 " --> pdb=" O VAL a 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 229 through 234' Processing helix chain 'a' and resid 244 through 251 removed outlier: 3.518A pdb=" N LEU a 249 " --> pdb=" O THR a 245 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA a 251 " --> pdb=" O PRO a 247 " (cutoff:3.500A) Processing helix chain 'a' and resid 253 through 256 removed outlier: 4.085A pdb=" N ASP a 256 " --> pdb=" O SER a 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 253 through 256' Processing helix chain 'a' and resid 257 through 273 removed outlier: 3.958A pdb=" N THR a 271 " --> pdb=" O GLN a 267 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE a 272 " --> pdb=" O SER a 268 " (cutoff:3.500A) Processing helix chain 'a' and resid 280 through 292 removed outlier: 4.407A pdb=" N PHE a 287 " --> pdb=" O VAL a 283 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE a 288 " --> pdb=" O VAL a 284 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL a 292 " --> pdb=" O ILE a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 297 through 309 Processing helix chain 'a' and resid 345 through 358 removed outlier: 3.768A pdb=" N ILE a 353 " --> pdb=" O LEU a 349 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA a 356 " --> pdb=" O VAL a 352 " (cutoff:3.500A) Processing helix chain 'a' and resid 359 through 361 No H-bonds generated for 'chain 'a' and resid 359 through 361' Processing helix chain 'a' and resid 363 through 370 Processing helix chain 'a' and resid 381 through 395 removed outlier: 3.537A pdb=" N LEU a 385 " --> pdb=" O LYS a 381 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL a 387 " --> pdb=" O LEU a 383 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 411 Processing helix chain 'a' and resid 416 through 424 Processing helix chain 'a' and resid 427 through 432 Processing helix chain 'a' and resid 437 through 446 Processing helix chain 'a' and resid 453 through 468 removed outlier: 3.778A pdb=" N CYS a 459 " --> pdb=" O SER a 455 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA a 466 " --> pdb=" O LYS a 462 " (cutoff:3.500A) Processing helix chain 'a' and resid 469 through 485 Processing helix chain 'a' and resid 489 through 505 removed outlier: 4.359A pdb=" N ASP a 493 " --> pdb=" O GLU a 489 " (cutoff:3.500A) Processing helix chain 'a' and resid 510 through 514 removed outlier: 4.100A pdb=" N ALA a 514 " --> pdb=" O LEU a 511 " (cutoff:3.500A) Processing helix chain 'a' and resid 519 through 524 Processing helix chain 'a' and resid 530 through 545 removed outlier: 3.892A pdb=" N LYS a 534 " --> pdb=" O CYS a 530 " (cutoff:3.500A) Processing helix chain 'a' and resid 549 through 568 removed outlier: 3.757A pdb=" N ILE a 553 " --> pdb=" O GLU a 549 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN a 554 " --> pdb=" O GLY a 550 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS a 563 " --> pdb=" O MET a 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER a 568 " --> pdb=" O TRP a 564 " (cutoff:3.500A) Processing helix chain 'a' and resid 573 through 587 removed outlier: 3.669A pdb=" N VAL a 587 " --> pdb=" O MET a 583 " (cutoff:3.500A) Processing helix chain 'a' and resid 607 through 625 removed outlier: 3.636A pdb=" N LEU a 615 " --> pdb=" O GLN a 611 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU a 618 " --> pdb=" O THR a 614 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL a 619 " --> pdb=" O LEU a 615 " (cutoff:3.500A) Processing helix chain 'a' and resid 628 through 644 Processing helix chain 'a' and resid 649 through 657 removed outlier: 3.516A pdb=" N LEU a 653 " --> pdb=" O ASP a 649 " (cutoff:3.500A) Processing helix chain 'a' and resid 732 through 746 removed outlier: 3.694A pdb=" N LEU a 738 " --> pdb=" O PRO a 734 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU a 741 " --> pdb=" O ARG a 737 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY a 744 " --> pdb=" O ARG a 740 " (cutoff:3.500A) Processing helix chain 'a' and resid 781 through 786 removed outlier: 4.546A pdb=" N CYS a 785 " --> pdb=" O ARG a 781 " (cutoff:3.500A) Processing helix chain 'a' and resid 787 through 803 removed outlier: 3.924A pdb=" N ALA a 791 " --> pdb=" O LEU a 787 " (cutoff:3.500A) Processing helix chain 'a' and resid 809 through 835 removed outlier: 3.618A pdb=" N LYS a 813 " --> pdb=" O GLU a 809 " (cutoff:3.500A) Processing helix chain 'a' and resid 840 through 845 Processing helix chain 'a' and resid 920 through 925 removed outlier: 3.703A pdb=" N PHE a 924 " --> pdb=" O ARG a 921 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG a 925 " --> pdb=" O PRO a 922 " (cutoff:3.500A) Processing helix chain 'a' and resid 929 through 940 removed outlier: 3.550A pdb=" N SER a 933 " --> pdb=" O LEU a 929 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU a 940 " --> pdb=" O HIS a 936 " (cutoff:3.500A) Processing helix chain 'a' and resid 960 through 980 removed outlier: 4.521A pdb=" N HIS a 977 " --> pdb=" O TRP a 973 " (cutoff:3.500A) Processing helix chain 'a' and resid 1007 through 1016 Processing helix chain 'a' and resid 1019 through 1035 removed outlier: 3.654A pdb=" N CYS a1023 " --> pdb=" O LEU a1019 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET a1026 " --> pdb=" O LEU a1022 " (cutoff:3.500A) Processing helix chain 'a' and resid 1049 through 1072 removed outlier: 3.807A pdb=" N TYR a1053 " --> pdb=" O ASN a1049 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN a1054 " --> pdb=" O ILE a1050 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU a1055 " --> pdb=" O GLN a1051 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR a1060 " --> pdb=" O MET a1056 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE a1071 " --> pdb=" O PHE a1067 " (cutoff:3.500A) Processing helix chain 'a' and resid 1081 through 1093 removed outlier: 4.243A pdb=" N GLN a1090 " --> pdb=" O ARG a1086 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL a1091 " --> pdb=" O SER a1087 " (cutoff:3.500A) Processing helix chain 'a' and resid 1107 through 1121 removed outlier: 3.723A pdb=" N PHE a1114 " --> pdb=" O ILE a1110 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN a1121 " --> pdb=" O LEU a1117 " (cutoff:3.500A) Processing helix chain 'a' and resid 1129 through 1134 Processing helix chain 'a' and resid 1136 through 1141 Processing helix chain 'a' and resid 1147 through 1167 removed outlier: 4.010A pdb=" N GLU a1151 " --> pdb=" O GLY a1147 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N SER a1164 " --> pdb=" O PHE a1160 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N TRP a1165 " --> pdb=" O LEU a1161 " (cutoff:3.500A) Processing helix chain 'a' and resid 1176 through 1189 removed outlier: 4.646A pdb=" N LEU a1182 " --> pdb=" O PHE a1178 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU a1186 " --> pdb=" O LEU a1182 " (cutoff:3.500A) Processing helix chain 'a' and resid 1195 through 1208 Processing helix chain 'a' and resid 1218 through 1222 removed outlier: 3.842A pdb=" N SER a1221 " --> pdb=" O GLY a1218 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR a1222 " --> pdb=" O CYS a1219 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1218 through 1222' Processing helix chain 'a' and resid 1225 through 1228 Processing helix chain 'a' and resid 1229 through 1246 removed outlier: 3.518A pdb=" N ALA a1240 " --> pdb=" O ARG a1236 " (cutoff:3.500A) Processing helix chain 'a' and resid 1255 through 1258 Processing helix chain 'a' and resid 1259 through 1284 removed outlier: 4.105A pdb=" N GLU a1263 " --> pdb=" O GLU a1259 " (cutoff:3.500A) Processing helix chain 'a' and resid 1288 through 1309 removed outlier: 4.295A pdb=" N SER a1292 " --> pdb=" O ARG a1288 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS a1296 " --> pdb=" O SER a1292 " (cutoff:3.500A) Processing helix chain 'a' and resid 1309 through 1314 Processing helix chain 'a' and resid 1315 through 1317 No H-bonds generated for 'chain 'a' and resid 1315 through 1317' Processing helix chain 'a' and resid 1323 through 1342 removed outlier: 3.765A pdb=" N LEU a1327 " --> pdb=" O ASP a1323 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU a1331 " --> pdb=" O LEU a1327 " (cutoff:3.500A) Processing helix chain 'a' and resid 1355 through 1375 removed outlier: 4.056A pdb=" N SER a1363 " --> pdb=" O LEU a1359 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU a1364 " --> pdb=" O LEU a1360 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2695 1.33 - 1.45: 2143 1.45 - 1.57: 6796 1.57 - 1.69: 0 1.69 - 1.82: 30 Bond restraints: 11664 Sorted by residual: bond pdb=" C ARG A 921 " pdb=" N PRO A 922 " ideal model delta sigma weight residual 1.335 1.232 0.103 9.40e-03 1.13e+04 1.19e+02 bond pdb=" C ARG a 921 " pdb=" N PRO a 922 " ideal model delta sigma weight residual 1.337 1.233 0.104 1.06e-02 8.90e+03 9.56e+01 bond pdb=" C PHE A 664 " pdb=" N PRO A 665 " ideal model delta sigma weight residual 1.334 1.370 -0.036 8.40e-03 1.42e+04 1.85e+01 bond pdb=" C PHE a 664 " pdb=" N PRO a 665 " ideal model delta sigma weight residual 1.334 1.369 -0.035 8.40e-03 1.42e+04 1.74e+01 bond pdb=" CA SER A 919 " pdb=" CB SER A 919 " ideal model delta sigma weight residual 1.537 1.485 0.052 1.41e-02 5.03e+03 1.35e+01 ... (remaining 11659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 15052 2.05 - 4.11: 903 4.11 - 6.16: 132 6.16 - 8.22: 51 8.22 - 10.27: 14 Bond angle restraints: 16152 Sorted by residual: angle pdb=" N MET A 559 " pdb=" CA MET A 559 " pdb=" C MET A 559 " ideal model delta sigma weight residual 111.36 102.52 8.84 1.09e+00 8.42e-01 6.58e+01 angle pdb=" N VAL a 560 " pdb=" CA VAL a 560 " pdb=" C VAL a 560 " ideal model delta sigma weight residual 111.05 101.44 9.61 1.25e+00 6.40e-01 5.91e+01 angle pdb=" N LYS a 658 " pdb=" CA LYS a 658 " pdb=" C LYS a 658 " ideal model delta sigma weight residual 114.75 105.53 9.22 1.26e+00 6.30e-01 5.36e+01 angle pdb=" N LYS A 658 " pdb=" CA LYS A 658 " pdb=" C LYS A 658 " ideal model delta sigma weight residual 114.75 105.91 8.84 1.26e+00 6.30e-01 4.92e+01 angle pdb=" N TYR A 920 " pdb=" CA TYR A 920 " pdb=" C TYR A 920 " ideal model delta sigma weight residual 110.70 100.79 9.91 1.55e+00 4.16e-01 4.08e+01 ... (remaining 16147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.87: 6440 14.87 - 29.75: 340 29.75 - 44.62: 87 44.62 - 59.50: 35 59.50 - 74.37: 6 Dihedral angle restraints: 6908 sinusoidal: 674 harmonic: 6234 Sorted by residual: dihedral pdb=" N GLN a 425 " pdb=" C GLN a 425 " pdb=" CA GLN a 425 " pdb=" CB GLN a 425 " ideal model delta harmonic sigma weight residual 122.80 139.26 -16.46 0 2.50e+00 1.60e-01 4.34e+01 dihedral pdb=" N TYR A 461 " pdb=" C TYR A 461 " pdb=" CA TYR A 461 " pdb=" CB TYR A 461 " ideal model delta harmonic sigma weight residual 122.80 138.41 -15.61 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" C TYR A 461 " pdb=" N TYR A 461 " pdb=" CA TYR A 461 " pdb=" CB TYR A 461 " ideal model delta harmonic sigma weight residual -122.60 -137.61 15.01 0 2.50e+00 1.60e-01 3.61e+01 ... (remaining 6905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 2104 0.133 - 0.265: 77 0.265 - 0.398: 8 0.398 - 0.531: 2 0.531 - 0.664: 3 Chirality restraints: 2194 Sorted by residual: chirality pdb=" CA TYR A 461 " pdb=" N TYR A 461 " pdb=" C TYR A 461 " pdb=" CB TYR A 461 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA GLN a 425 " pdb=" N GLN a 425 " pdb=" C GLN a 425 " pdb=" CB GLN a 425 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.81e+00 chirality pdb=" CA PRO a 436 " pdb=" N PRO a 436 " pdb=" C PRO a 436 " pdb=" CB PRO a 436 " both_signs ideal model delta sigma weight residual False 2.72 2.15 0.57 2.00e-01 2.50e+01 8.10e+00 ... (remaining 2191 not shown) Planarity restraints: 2241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE a 424 " 0.024 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C PHE a 424 " -0.087 2.00e-02 2.50e+03 pdb=" O PHE a 424 " 0.032 2.00e-02 2.50e+03 pdb=" N GLN a 425 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE a 435 " -0.025 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C PHE a 435 " 0.084 2.00e-02 2.50e+03 pdb=" O PHE a 435 " -0.030 2.00e-02 2.50e+03 pdb=" N PRO a 436 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN a 916 " 0.021 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C GLN a 916 " -0.076 2.00e-02 2.50e+03 pdb=" O GLN a 916 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU a 917 " 0.027 2.00e-02 2.50e+03 ... (remaining 2238 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 330 2.69 - 3.24: 12539 3.24 - 3.80: 17777 3.80 - 4.35: 21278 4.35 - 4.90: 33005 Nonbonded interactions: 84929 Sorted by model distance: nonbonded pdb=" O ILE A 578 " pdb=" OG1 THR A 582 " model vdw 2.140 3.040 nonbonded pdb=" O ILE a 578 " pdb=" OG1 THR a 582 " model vdw 2.149 3.040 nonbonded pdb=" O GLN a 421 " pdb=" O PHE a 424 " model vdw 2.184 3.040 nonbonded pdb=" O TYR a 537 " pdb=" OG1 THR a 541 " model vdw 2.218 3.040 nonbonded pdb=" O TYR A 537 " pdb=" OG1 THR A 541 " model vdw 2.225 3.040 ... (remaining 84924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 151 through 426 or (resid 427 and (name N or name CA or na \ me C or name O or name CB )) or resid 428 through 1375)) selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.480 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 11664 Z= 0.447 Angle : 1.168 10.274 16152 Z= 0.764 Chirality : 0.066 0.664 2194 Planarity : 0.006 0.050 2241 Dihedral : 13.104 74.370 2804 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.47 % Allowed : 15.19 % Favored : 84.33 % Rotamer: Outliers : 15.63 % Allowed : 22.71 % Favored : 61.65 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.14 (0.14), residues: 2106 helix: -2.93 (0.10), residues: 1220 sheet: None (None), residues: 0 loop : -4.08 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP a 367 HIS 0.008 0.002 HIS A 447 PHE 0.039 0.003 PHE a 424 TYR 0.018 0.003 TYR a 461 ARG 0.007 0.001 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.18437 ( 845) hydrogen bonds : angle 8.07958 ( 2472) covalent geometry : bond 0.00710 (11664) covalent geometry : angle 1.16793 (16152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 142 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 536 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.6822 (m-80) REVERT: A 537 TYR cc_start: 0.8028 (t80) cc_final: 0.7762 (t80) REVERT: A 571 ASN cc_start: 0.6976 (t0) cc_final: 0.6563 (t0) REVERT: A 572 HIS cc_start: 0.6566 (OUTLIER) cc_final: 0.5517 (m-70) REVERT: A 635 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: a 536 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: a 537 TYR cc_start: 0.8013 (t80) cc_final: 0.7745 (t80) REVERT: a 567 SER cc_start: 0.5715 (t) cc_final: 0.5422 (m) REVERT: a 571 ASN cc_start: 0.7009 (t0) cc_final: 0.5634 (t0) REVERT: a 635 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7866 (m-30) outliers start: 53 outliers final: 33 residues processed: 181 average time/residue: 0.2012 time to fit residues: 54.0815 Evaluate side-chains 151 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 382 VAL Chi-restraints excluded: chain a residue 386 ILE Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 421 GLN Chi-restraints excluded: chain a residue 453 VAL Chi-restraints excluded: chain a residue 458 SER Chi-restraints excluded: chain a residue 472 CYS Chi-restraints excluded: chain a residue 484 VAL Chi-restraints excluded: chain a residue 493 ASP Chi-restraints excluded: chain a residue 498 VAL Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 512 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 541 THR Chi-restraints excluded: chain a residue 572 HIS Chi-restraints excluded: chain a residue 619 VAL Chi-restraints excluded: chain a residue 635 ASP Chi-restraints excluded: chain a residue 653 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 6.9990 chunk 160 optimal weight: 0.1980 chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN A 425 GLN ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 483 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.172136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.145611 restraints weight = 29396.434| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 4.13 r_work: 0.4036 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11664 Z= 0.273 Angle : 0.772 12.662 16152 Z= 0.433 Chirality : 0.047 0.259 2194 Planarity : 0.004 0.047 2241 Dihedral : 8.741 59.765 2202 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 15.86 % Favored : 83.81 % Rotamer: Outliers : 13.57 % Allowed : 24.78 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.17), residues: 2106 helix: -1.58 (0.12), residues: 1296 sheet: None (None), residues: 0 loop : -4.06 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP a 367 HIS 0.005 0.001 HIS A 572 PHE 0.017 0.002 PHE a 536 TYR 0.015 0.002 TYR a 461 ARG 0.004 0.001 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.05005 ( 845) hydrogen bonds : angle 6.06844 ( 2472) covalent geometry : bond 0.00544 (11664) covalent geometry : angle 0.77227 (16152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 1.351 Fit side-chains REVERT: A 482 THR cc_start: 0.8705 (p) cc_final: 0.8471 (p) REVERT: A 536 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.6690 (m-80) REVERT: a 390 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7569 (tt) REVERT: a 536 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6632 (m-80) outliers start: 46 outliers final: 29 residues processed: 147 average time/residue: 0.1955 time to fit residues: 43.7161 Evaluate side-chains 143 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 382 VAL Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 453 VAL Chi-restraints excluded: chain a residue 458 SER Chi-restraints excluded: chain a residue 472 CYS Chi-restraints excluded: chain a residue 483 HIS Chi-restraints excluded: chain a residue 498 VAL Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 533 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 572 HIS Chi-restraints excluded: chain a residue 648 LEU Chi-restraints excluded: chain a residue 653 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.176321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.150340 restraints weight = 29936.629| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 4.11 r_work: 0.4090 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11664 Z= 0.154 Angle : 0.639 12.453 16152 Z= 0.354 Chirality : 0.043 0.217 2194 Planarity : 0.003 0.039 2241 Dihedral : 7.406 59.093 2179 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.58 % Favored : 86.18 % Rotamer: Outliers : 10.62 % Allowed : 26.55 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.18), residues: 2106 helix: -0.59 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -3.94 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP a 367 HIS 0.020 0.002 HIS a 483 PHE 0.016 0.001 PHE a 435 TYR 0.011 0.002 TYR a 634 ARG 0.003 0.001 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 845) hydrogen bonds : angle 5.24120 ( 2472) covalent geometry : bond 0.00307 (11664) covalent geometry : angle 0.63918 (16152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 2.017 Fit side-chains REVERT: A 390 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7229 (tt) REVERT: A 536 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: A 537 TYR cc_start: 0.8337 (t80) cc_final: 0.7990 (t80) REVERT: a 390 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7445 (tt) REVERT: a 462 LYS cc_start: 0.8723 (mttt) cc_final: 0.8507 (mtpt) REVERT: a 533 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7796 (ttm110) REVERT: a 536 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: a 537 TYR cc_start: 0.8317 (t80) cc_final: 0.8004 (t80) REVERT: a 617 ASP cc_start: 0.9200 (t0) cc_final: 0.8680 (m-30) outliers start: 36 outliers final: 25 residues processed: 145 average time/residue: 0.2574 time to fit residues: 56.8853 Evaluate side-chains 140 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain a residue 372 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 378 SER Chi-restraints excluded: chain a residue 382 VAL Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 453 VAL Chi-restraints excluded: chain a residue 483 HIS Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 520 ILE Chi-restraints excluded: chain a residue 533 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 635 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 123 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 124 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 425 GLN a 447 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.177286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.151394 restraints weight = 30031.212| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 4.03 r_work: 0.4110 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11664 Z= 0.150 Angle : 0.615 12.298 16152 Z= 0.339 Chirality : 0.043 0.207 2194 Planarity : 0.003 0.039 2241 Dihedral : 6.684 58.943 2169 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.91 % Favored : 85.85 % Rotamer: Outliers : 10.03 % Allowed : 28.02 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.19), residues: 2106 helix: -0.00 (0.14), residues: 1310 sheet: None (None), residues: 0 loop : -3.85 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 367 HIS 0.006 0.001 HIS a 483 PHE 0.017 0.001 PHE a 435 TYR 0.009 0.002 TYR A 471 ARG 0.003 0.001 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 845) hydrogen bonds : angle 4.88924 ( 2472) covalent geometry : bond 0.00308 (11664) covalent geometry : angle 0.61505 (16152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.351 Fit side-chains REVERT: A 388 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6103 (mm) REVERT: A 390 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7163 (tt) REVERT: A 533 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7573 (ttm110) REVERT: A 536 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.6574 (m-80) REVERT: A 537 TYR cc_start: 0.8360 (t80) cc_final: 0.8024 (t80) REVERT: a 462 LYS cc_start: 0.8862 (mttt) cc_final: 0.8599 (mtpt) REVERT: a 536 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.6688 (m-80) REVERT: a 537 TYR cc_start: 0.8368 (t80) cc_final: 0.7991 (t80) outliers start: 34 outliers final: 23 residues processed: 144 average time/residue: 0.3103 time to fit residues: 70.7487 Evaluate side-chains 138 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain a residue 372 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 378 SER Chi-restraints excluded: chain a residue 382 VAL Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 483 HIS Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 520 ILE Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 619 VAL Chi-restraints excluded: chain a residue 635 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 109 optimal weight: 0.0770 chunk 199 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 98 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.179553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.153842 restraints weight = 30209.020| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 4.49 r_work: 0.4138 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11664 Z= 0.114 Angle : 0.575 12.928 16152 Z= 0.314 Chirality : 0.042 0.187 2194 Planarity : 0.003 0.037 2241 Dihedral : 6.179 59.941 2165 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.30 % Favored : 87.56 % Rotamer: Outliers : 8.55 % Allowed : 30.97 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.19), residues: 2106 helix: 0.47 (0.15), residues: 1310 sheet: None (None), residues: 0 loop : -3.84 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP a 367 HIS 0.003 0.001 HIS A 427 PHE 0.017 0.001 PHE A 435 TYR 0.011 0.001 TYR a 634 ARG 0.003 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 845) hydrogen bonds : angle 4.48718 ( 2472) covalent geometry : bond 0.00226 (11664) covalent geometry : angle 0.57509 (16152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.286 Fit side-chains REVERT: A 390 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7303 (tt) REVERT: A 536 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: A 537 TYR cc_start: 0.8311 (t80) cc_final: 0.7886 (t80) REVERT: A 634 TYR cc_start: 0.7092 (m-80) cc_final: 0.6872 (m-80) REVERT: a 390 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7548 (tt) REVERT: a 536 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6598 (m-80) REVERT: a 537 TYR cc_start: 0.8274 (t80) cc_final: 0.7854 (t80) outliers start: 29 outliers final: 19 residues processed: 143 average time/residue: 0.1740 time to fit residues: 39.3472 Evaluate side-chains 135 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain a residue 378 SER Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 520 ILE Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 619 VAL Chi-restraints excluded: chain a residue 635 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 153 optimal weight: 0.0570 chunk 76 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.177879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.152359 restraints weight = 30261.281| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 3.98 r_work: 0.4121 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11664 Z= 0.144 Angle : 0.595 13.049 16152 Z= 0.327 Chirality : 0.043 0.277 2194 Planarity : 0.003 0.038 2241 Dihedral : 5.858 55.440 2157 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.68 % Favored : 86.18 % Rotamer: Outliers : 8.85 % Allowed : 31.27 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 2106 helix: 0.58 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -3.88 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 367 HIS 0.003 0.001 HIS A 483 PHE 0.014 0.001 PHE a 435 TYR 0.010 0.002 TYR A 471 ARG 0.002 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 845) hydrogen bonds : angle 4.53848 ( 2472) covalent geometry : bond 0.00296 (11664) covalent geometry : angle 0.59463 (16152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 1.565 Fit side-chains REVERT: A 388 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6099 (mm) REVERT: A 390 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7155 (tt) REVERT: A 536 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6405 (m-80) REVERT: A 537 TYR cc_start: 0.8312 (t80) cc_final: 0.7933 (t80) REVERT: A 635 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: a 390 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7413 (tt) REVERT: a 533 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7422 (ttm110) REVERT: a 536 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6583 (m-80) REVERT: a 537 TYR cc_start: 0.8285 (t80) cc_final: 0.7927 (t80) REVERT: a 634 TYR cc_start: 0.7122 (m-80) cc_final: 0.6864 (m-80) REVERT: a 635 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7878 (m-30) outliers start: 30 outliers final: 20 residues processed: 139 average time/residue: 0.2088 time to fit residues: 45.4310 Evaluate side-chains 141 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain A residue 617 ASP Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain a residue 372 GLU Chi-restraints excluded: chain a residue 378 SER Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 453 VAL Chi-restraints excluded: chain a residue 483 HIS Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 520 ILE Chi-restraints excluded: chain a residue 533 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 619 VAL Chi-restraints excluded: chain a residue 635 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 421 GLN a 426 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.171582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.145306 restraints weight = 29360.762| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 3.77 r_work: 0.4029 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 11664 Z= 0.357 Angle : 0.836 12.808 16152 Z= 0.469 Chirality : 0.051 0.332 2194 Planarity : 0.005 0.051 2241 Dihedral : 7.251 57.712 2156 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.71 % Favored : 83.10 % Rotamer: Outliers : 10.03 % Allowed : 31.56 % Favored : 58.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.18), residues: 2106 helix: -0.47 (0.14), residues: 1312 sheet: None (None), residues: 0 loop : -3.74 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 367 HIS 0.011 0.003 HIS a 572 PHE 0.020 0.002 PHE a 536 TYR 0.013 0.002 TYR A 471 ARG 0.006 0.001 ARG a 358 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 845) hydrogen bonds : angle 6.02051 ( 2472) covalent geometry : bond 0.00739 (11664) covalent geometry : angle 0.83637 (16152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.236 Fit side-chains REVERT: A 388 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6293 (mm) REVERT: A 390 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7194 (tt) REVERT: A 533 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7588 (ttm110) REVERT: A 536 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: A 571 ASN cc_start: 0.7006 (t0) cc_final: 0.6365 (t0) REVERT: a 390 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7611 (tt) REVERT: a 533 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7351 (ttm110) REVERT: a 536 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.6508 (m-80) outliers start: 34 outliers final: 23 residues processed: 144 average time/residue: 0.2269 time to fit residues: 48.8558 Evaluate side-chains 136 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain a residue 372 GLU Chi-restraints excluded: chain a residue 378 SER Chi-restraints excluded: chain a residue 382 VAL Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 453 VAL Chi-restraints excluded: chain a residue 498 VAL Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 520 ILE Chi-restraints excluded: chain a residue 533 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 619 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 131 optimal weight: 0.6980 chunk 170 optimal weight: 0.0060 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.176896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.151326 restraints weight = 29846.906| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 4.36 r_work: 0.4104 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11664 Z= 0.138 Angle : 0.627 13.526 16152 Z= 0.344 Chirality : 0.044 0.333 2194 Planarity : 0.003 0.039 2241 Dihedral : 5.984 55.910 2154 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.35 % Favored : 87.51 % Rotamer: Outliers : 8.85 % Allowed : 33.92 % Favored : 57.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.19), residues: 2106 helix: 0.25 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -3.60 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP a 367 HIS 0.004 0.001 HIS a 572 PHE 0.016 0.001 PHE A 536 TYR 0.022 0.002 TYR a 537 ARG 0.001 0.000 ARG a 533 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 845) hydrogen bonds : angle 4.87278 ( 2472) covalent geometry : bond 0.00279 (11664) covalent geometry : angle 0.62706 (16152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.250 Fit side-chains REVERT: A 388 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6174 (mm) REVERT: A 390 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7102 (tt) REVERT: A 482 THR cc_start: 0.8642 (p) cc_final: 0.8435 (p) REVERT: A 533 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7740 (ttm110) REVERT: A 536 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: A 537 TYR cc_start: 0.8128 (t80) cc_final: 0.7794 (t80) REVERT: A 634 TYR cc_start: 0.7094 (m-80) cc_final: 0.6815 (m-80) REVERT: a 390 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7389 (tt) REVERT: a 533 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7585 (ttm110) REVERT: a 536 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: a 537 TYR cc_start: 0.8159 (t80) cc_final: 0.7816 (t80) REVERT: a 634 TYR cc_start: 0.7053 (m-80) cc_final: 0.6764 (m-80) outliers start: 30 outliers final: 18 residues processed: 135 average time/residue: 0.1930 time to fit residues: 39.7091 Evaluate side-chains 133 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 378 SER Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 458 SER Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 520 ILE Chi-restraints excluded: chain a residue 533 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 619 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 95 optimal weight: 0.6980 chunk 198 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 173 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.176393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.150599 restraints weight = 29850.820| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 3.84 r_work: 0.4109 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 11664 Z= 0.167 Angle : 0.641 14.408 16152 Z= 0.354 Chirality : 0.044 0.290 2194 Planarity : 0.003 0.040 2241 Dihedral : 5.875 55.687 2152 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.53 % Favored : 85.33 % Rotamer: Outliers : 8.26 % Allowed : 33.04 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.19), residues: 2106 helix: 0.44 (0.15), residues: 1312 sheet: None (None), residues: 0 loop : -3.53 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP a 367 HIS 0.008 0.001 HIS A 572 PHE 0.013 0.001 PHE a 536 TYR 0.024 0.002 TYR a 537 ARG 0.002 0.000 ARG a 533 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 845) hydrogen bonds : angle 4.81649 ( 2472) covalent geometry : bond 0.00351 (11664) covalent geometry : angle 0.64117 (16152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 1.404 Fit side-chains REVERT: A 388 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6212 (mm) REVERT: A 390 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7069 (tt) REVERT: A 482 THR cc_start: 0.8673 (p) cc_final: 0.8436 (p) REVERT: A 512 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7059 (mmp80) REVERT: A 533 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7819 (ttm110) REVERT: A 536 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6599 (m-80) REVERT: A 537 TYR cc_start: 0.8168 (t80) cc_final: 0.7875 (t80) REVERT: A 634 TYR cc_start: 0.7078 (m-80) cc_final: 0.6812 (m-80) REVERT: a 390 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7396 (tt) REVERT: a 533 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7565 (ttm110) REVERT: a 536 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: a 537 TYR cc_start: 0.8183 (t80) cc_final: 0.7877 (t80) REVERT: a 634 TYR cc_start: 0.7147 (m-80) cc_final: 0.6898 (m-80) outliers start: 28 outliers final: 19 residues processed: 132 average time/residue: 0.2041 time to fit residues: 41.0855 Evaluate side-chains 135 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain a residue 372 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 378 SER Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 458 SER Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 520 ILE Chi-restraints excluded: chain a residue 533 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 619 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 194 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.177882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.152513 restraints weight = 29842.292| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 3.95 r_work: 0.4121 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11664 Z= 0.137 Angle : 0.607 14.082 16152 Z= 0.334 Chirality : 0.044 0.263 2194 Planarity : 0.003 0.038 2241 Dihedral : 5.557 54.766 2152 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.58 % Favored : 87.27 % Rotamer: Outliers : 8.55 % Allowed : 32.74 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.19), residues: 2106 helix: 0.74 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -3.56 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP a 367 HIS 0.003 0.001 HIS a 572 PHE 0.014 0.001 PHE A 435 TYR 0.021 0.002 TYR A 537 ARG 0.002 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 845) hydrogen bonds : angle 4.54123 ( 2472) covalent geometry : bond 0.00288 (11664) covalent geometry : angle 0.60733 (16152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4212 Ramachandran restraints generated. 2106 Oldfield, 0 Emsley, 2106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 1.291 Fit side-chains REVERT: A 388 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6153 (mm) REVERT: A 390 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7130 (tt) REVERT: A 482 THR cc_start: 0.8664 (p) cc_final: 0.8436 (p) REVERT: A 512 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6972 (mmp80) REVERT: A 533 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7826 (ttm110) REVERT: A 536 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: A 537 TYR cc_start: 0.8183 (t80) cc_final: 0.7855 (t80) REVERT: A 634 TYR cc_start: 0.7082 (m-80) cc_final: 0.6782 (m-80) REVERT: a 390 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7395 (tt) REVERT: a 533 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7682 (ttm110) REVERT: a 536 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.6708 (m-80) REVERT: a 537 TYR cc_start: 0.8190 (t80) cc_final: 0.7853 (t80) REVERT: a 634 TYR cc_start: 0.7092 (m-80) cc_final: 0.6856 (m-80) REVERT: a 635 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7831 (m-30) outliers start: 29 outliers final: 19 residues processed: 134 average time/residue: 0.1920 time to fit residues: 39.5309 Evaluate side-chains 138 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain a residue 372 GLU Chi-restraints excluded: chain a residue 375 THR Chi-restraints excluded: chain a residue 378 SER Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 458 SER Chi-restraints excluded: chain a residue 483 HIS Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 520 ILE Chi-restraints excluded: chain a residue 533 ARG Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 619 VAL Chi-restraints excluded: chain a residue 635 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 191 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 39 optimal weight: 0.0980 chunk 19 optimal weight: 0.0670 chunk 201 optimal weight: 0.8980 chunk 32 optimal weight: 0.0030 chunk 159 optimal weight: 0.5980 chunk 156 optimal weight: 8.9990 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.180029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.154717 restraints weight = 29986.306| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 4.27 r_work: 0.4152 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 11664 Z= 0.112 Angle : 0.580 14.185 16152 Z= 0.319 Chirality : 0.043 0.254 2194 Planarity : 0.003 0.038 2241 Dihedral : 5.177 53.841 2151 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.73 % Favored : 87.13 % Rotamer: Outliers : 6.78 % Allowed : 34.81 % Favored : 58.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 2106 helix: 1.13 (0.15), residues: 1298 sheet: None (None), residues: 0 loop : -3.56 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP a 367 HIS 0.005 0.001 HIS a 483 PHE 0.018 0.001 PHE A 435 TYR 0.020 0.002 TYR A 537 ARG 0.002 0.000 ARG A 533 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 845) hydrogen bonds : angle 4.22319 ( 2472) covalent geometry : bond 0.00227 (11664) covalent geometry : angle 0.57971 (16152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5895.42 seconds wall clock time: 104 minutes 44.14 seconds (6284.14 seconds total)