Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 05:52:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tni_10534/04_2023/6tni_10534.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tni_10534/04_2023/6tni_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tni_10534/04_2023/6tni_10534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tni_10534/04_2023/6tni_10534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tni_10534/04_2023/6tni_10534.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tni_10534/04_2023/6tni_10534.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "a GLU 628": "OE1" <-> "OE2" Residue "a GLU 636": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 7.14, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 5.19 Conformation dependent library (CDL) restraints added in 2.6 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: 0.93 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: 4.05 Time building geometry restraints manager: 5.54 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: 100.79 - 107.43: 237 107.43 - 114.06: 6679 114.06 - 120.69: 5266 120.69 - 127.32: 3921 127.32 - 133.96: 49 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 2.440 nonbonded pdb=" O ILE a 578 " pdb=" OG1 THR a 582 " model vdw 2.149 2.440 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 2.440 nonbonded pdb=" O TYR A 537 " pdb=" OG1 THR A 541 " model vdw 2.225 2.440 ... (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 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: 8.930 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: 19.400 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.340 Find NCS groups from input model: 0.760 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.680 ------------------------------------------------------------------------------- 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= 0.490 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 % 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 *********************** 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 fitting. rotamer outliers: 53 poor density : 142 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 33 residues processed: 181 average time/residue: 0.2117 time to fit residues: 56.8948 Evaluate side-chains 149 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1205 time to fit residues: 8.8420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 54 optimal weight: 0.0040 chunk 108 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 101 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 overall best weight: 2.0996 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.086 11664 Z= 0.493 Angle : 0.852 13.267 16152 Z= 0.480 Chirality : 0.049 0.280 2194 Planarity : 0.005 0.051 2241 Dihedral : 7.317 29.372 2142 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 17.81 % Favored : 81.81 % Rotamer Outliers : 7.96 % 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: -4.02 (0.16), residues: 2106 helix: -1.77 (0.12), residues: 1270 sheet: None (None), residues: 0 loop : -4.12 (0.21), residues: 836 *********************** 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 141 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.313 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 134 average time/residue: 0.2108 time to fit residues: 42.9916 Evaluate side-chains 125 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1648 time to fit residues: 5.5806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 154 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 483 HIS a 651 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11664 Z= 0.199 Angle : 0.621 8.849 16152 Z= 0.344 Chirality : 0.042 0.225 2194 Planarity : 0.003 0.038 2241 Dihedral : 5.969 26.143 2142 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.30 % Favored : 86.42 % Rotamer Outliers : 5.01 % 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: -2.67 (0.18), residues: 2106 helix: -0.56 (0.14), residues: 1294 sheet: None (None), residues: 0 loop : -3.89 (0.21), residues: 812 *********************** 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 138 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.291 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 132 average time/residue: 0.1899 time to fit residues: 39.3493 Evaluate side-chains 121 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1642 time to fit residues: 4.8440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 100 optimal weight: 0.0050 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 425 GLN ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 11664 Z= 0.210 Angle : 0.616 12.795 16152 Z= 0.337 Chirality : 0.043 0.220 2194 Planarity : 0.003 0.040 2241 Dihedral : 5.626 25.460 2142 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.05 % Favored : 84.81 % Rotamer Outliers : 4.42 % 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: -2.11 (0.18), residues: 2106 helix: -0.01 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -3.88 (0.20), residues: 806 *********************** 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 133 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.443 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 127 average time/residue: 0.1905 time to fit residues: 37.6754 Evaluate side-chains 120 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1048 time to fit residues: 3.3174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 152 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11664 Z= 0.217 Angle : 0.611 12.260 16152 Z= 0.337 Chirality : 0.043 0.223 2194 Planarity : 0.003 0.038 2241 Dihedral : 5.490 25.622 2142 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.29 % Favored : 85.57 % Rotamer Outliers : 3.83 % 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: -1.76 (0.19), residues: 2106 helix: 0.29 (0.15), residues: 1296 sheet: None (None), residues: 0 loop : -3.75 (0.21), residues: 810 *********************** 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 126 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.251 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.1801 time to fit residues: 34.8270 Evaluate side-chains 119 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0997 time to fit residues: 3.7105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 170 optimal weight: 0.0070 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 398 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11664 Z= 0.174 Angle : 0.569 12.458 16152 Z= 0.314 Chirality : 0.042 0.206 2194 Planarity : 0.003 0.036 2241 Dihedral : 5.092 25.043 2142 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.91 % Favored : 85.94 % Rotamer Outliers : 3.54 % 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: -1.38 (0.19), residues: 2106 helix: 0.64 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -3.74 (0.21), residues: 804 *********************** 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 130 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.423 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 125 average time/residue: 0.2128 time to fit residues: 40.5926 Evaluate side-chains 117 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1070 time to fit residues: 3.0948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 0.1980 chunk 172 optimal weight: 0.4980 chunk 114 optimal weight: 0.1980 chunk 204 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 124 optimal weight: 0.1980 chunk 94 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 11664 Z= 0.155 Angle : 0.569 13.138 16152 Z= 0.313 Chirality : 0.043 0.294 2194 Planarity : 0.003 0.035 2241 Dihedral : 4.848 24.721 2142 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.35 % Favored : 87.51 % Rotamer Outliers : 1.47 % 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: -1.15 (0.19), residues: 2106 helix: 0.82 (0.15), residues: 1322 sheet: None (None), residues: 0 loop : -3.74 (0.21), residues: 784 *********************** 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 126 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.429 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 123 average time/residue: 0.1897 time to fit residues: 36.9519 Evaluate side-chains 115 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1011 time to fit residues: 2.4229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.0030 chunk 122 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 139 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 160 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 11664 Z= 0.174 Angle : 0.580 13.492 16152 Z= 0.319 Chirality : 0.043 0.267 2194 Planarity : 0.003 0.032 2241 Dihedral : 4.781 24.022 2142 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.34 % Favored : 86.51 % Rotamer Outliers : 2.06 % 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: -1.04 (0.19), residues: 2106 helix: 0.91 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -3.70 (0.20), residues: 786 *********************** 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 122 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.291 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 118 average time/residue: 0.1772 time to fit residues: 34.0184 Evaluate side-chains 116 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1052 time to fit residues: 2.7516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 149 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 11664 Z= 0.323 Angle : 0.673 13.133 16152 Z= 0.375 Chirality : 0.047 0.361 2194 Planarity : 0.004 0.036 2241 Dihedral : 5.478 25.511 2142 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.77 % Favored : 85.04 % Rotamer Outliers : 2.36 % 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: -1.42 (0.19), residues: 2106 helix: 0.53 (0.15), residues: 1304 sheet: None (None), residues: 0 loop : -3.62 (0.20), residues: 802 *********************** 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 123 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.414 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 118 average time/residue: 0.1880 time to fit residues: 35.4441 Evaluate side-chains 115 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1159 time to fit residues: 3.3368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.8980 chunk 122 optimal weight: 0.0010 chunk 95 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 211 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 129 optimal weight: 0.0770 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.4944 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 11664 Z= 0.191 Angle : 0.602 12.835 16152 Z= 0.335 Chirality : 0.045 0.283 2194 Planarity : 0.003 0.035 2241 Dihedral : 4.976 25.246 2142 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.30 % Favored : 87.56 % Rotamer Outliers : 0.29 % 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: -1.05 (0.19), residues: 2106 helix: 0.87 (0.15), residues: 1290 sheet: None (None), residues: 0 loop : -3.48 (0.21), residues: 816 ********************** 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 119 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.265 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.1926 time to fit residues: 36.0363 Evaluate side-chains 115 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1037 time to fit residues: 2.1300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 51 optimal weight: 0.0170 chunk 155 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 0.0370 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 172 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.0170 chunk 147 optimal weight: 1.9990 overall best weight: 0.1872 ------------------------------------------------------------------------------- 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 425 GLN A 463 GLN a 392 HIS a 426 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.180527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.153605 restraints weight = 29939.945| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 3.86 r_work: 0.4188 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.067 11664 Z= 0.147 Angle : 0.553 12.422 16152 Z= 0.306 Chirality : 0.042 0.261 2194 Planarity : 0.003 0.036 2241 Dihedral : 4.413 24.376 2142 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.92 % Favored : 87.99 % Rotamer Outliers : 0.59 % 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: -0.58 (0.20), residues: 2106 helix: 1.45 (0.15), residues: 1288 sheet: None (None), residues: 0 loop : -3.67 (0.20), residues: 818 =============================================================================== Job complete usr+sys time: 2318.09 seconds wall clock time: 42 minutes 39.23 seconds (2559.23 seconds total)