Starting phenix.real_space_refine on Wed Mar 4 06:55:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tni_10534/03_2026/6tni_10534.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tni_10534/03_2026/6tni_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_10534/03_2026/6tni_10534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tni_10534/03_2026/6tni_10534.map" model { file = "/net/cci-nas-00/data/ceres_data/6tni_10534/03_2026/6tni_10534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tni_10534/03_2026/6tni_10534.cif" } 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 56, 'PHE:plan': 46, 'ASP:plan': 48, 'ASN:plan1': 33, 'ARG:plan': 31, 'GLN:plan1': 51, 'TRP:plan': 8, 'HIS:plan': 24, 'TYR:plan': 17} 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: {'GLU:plan': 56, 'PHE:plan': 46, 'ASP:plan': 48, 'ASN:plan1': 33, 'ARG:plan': 31, 'GLN:plan1': 51, 'TRP:plan': 8, 'HIS:plan': 25, 'TYR:plan': 17} Unresolved non-hydrogen planarities: 1418 Time building chain proxies: 3.02, per 1000 atoms: 0.26 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: 0.98 Conformation dependent library (CDL) restraints added in 863.5 milliseconds 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: 0.67 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: 2.13 Time building geometry restraints manager: 1.33 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: 8.120 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.160 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG A 533 TYR 0.018 0.003 TYR a 461 PHE 0.039 0.003 PHE a 424 TRP 0.004 0.001 TRP a 367 HIS 0.008 0.002 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00710 (11664) covalent geometry : angle 1.16793 (16152) hydrogen bonds : bond 0.18437 ( 845) hydrogen bonds : angle 8.07958 ( 2472) *********************** 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 : 0.278 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: 0.0870 time to fit residues: 23.4027 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 : 0.350 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.0010 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0980 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.178278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.150633 restraints weight = 30081.981| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 3.49 r_work: 0.4141 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11664 Z= 0.136 Angle : 0.635 12.016 16152 Z= 0.351 Chirality : 0.043 0.218 2194 Planarity : 0.003 0.044 2241 Dihedral : 7.639 57.675 2202 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.77 % Favored : 86.94 % Rotamer: Outliers : 9.73 % Allowed : 24.78 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.17), residues: 2106 helix: -1.13 (0.13), residues: 1314 sheet: None (None), residues: 0 loop : -4.09 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 533 TYR 0.013 0.002 TYR A 633 PHE 0.016 0.001 PHE A 435 TRP 0.002 0.000 TRP A 367 HIS 0.002 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00250 (11664) covalent geometry : angle 0.63455 (16152) hydrogen bonds : bond 0.03891 ( 845) hydrogen bonds : angle 5.27651 ( 2472) *********************** 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 155 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 THR cc_start: 0.8581 (p) cc_final: 0.8380 (p) REVERT: A 536 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: A 537 TYR cc_start: 0.8202 (t80) cc_final: 0.7847 (t80) REVERT: A 571 ASN cc_start: 0.6810 (t0) cc_final: 0.6542 (t0) REVERT: A 634 TYR cc_start: 0.7239 (m-80) cc_final: 0.6925 (m-80) REVERT: a 390 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7420 (tt) REVERT: a 462 LYS cc_start: 0.8667 (mttt) cc_final: 0.8463 (mtpt) REVERT: a 536 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.6560 (m-80) REVERT: a 537 TYR cc_start: 0.8225 (t80) cc_final: 0.7875 (t80) REVERT: a 571 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.6310 (p0) outliers start: 33 outliers final: 15 residues processed: 143 average time/residue: 0.0877 time to fit residues: 18.4361 Evaluate side-chains 132 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 382 VAL 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 520 ILE 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 483 HIS Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 571 ASN Chi-restraints excluded: chain a residue 572 HIS 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 205 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 186 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.175672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.149995 restraints weight = 30126.177| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 3.85 r_work: 0.4088 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11664 Z= 0.203 Angle : 0.666 11.907 16152 Z= 0.371 Chirality : 0.044 0.226 2194 Planarity : 0.003 0.039 2241 Dihedral : 6.973 57.566 2169 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.53 % Favored : 85.23 % Rotamer: Outliers : 10.91 % Allowed : 24.78 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.18), residues: 2106 helix: -0.49 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -3.88 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 533 TYR 0.011 0.002 TYR a 461 PHE 0.018 0.002 PHE a 435 TRP 0.002 0.000 TRP a 367 HIS 0.005 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00418 (11664) covalent geometry : angle 0.66613 (16152) hydrogen bonds : bond 0.04236 ( 845) hydrogen bonds : angle 5.28295 ( 2472) *********************** 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 150 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.402 Fit side-chains REVERT: A 390 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7126 (tt) REVERT: A 533 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7523 (ttm110) REVERT: A 536 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: A 537 TYR cc_start: 0.8280 (t80) cc_final: 0.7868 (t80) REVERT: A 575 MET cc_start: 0.7761 (mpp) cc_final: 0.7541 (mpp) REVERT: a 390 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7510 (tt) REVERT: a 536 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: a 537 TYR cc_start: 0.8291 (t80) cc_final: 0.7969 (t80) outliers start: 37 outliers final: 24 residues processed: 138 average time/residue: 0.0859 time to fit residues: 17.9734 Evaluate side-chains 136 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 572 HIS Chi-restraints excluded: chain A residue 617 ASP 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 617 ASP Chi-restraints excluded: chain a residue 653 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 104 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 14 optimal weight: 0.0670 chunk 193 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.176429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.150110 restraints weight = 30154.300| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 4.19 r_work: 0.4083 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11664 Z= 0.177 Angle : 0.637 12.845 16152 Z= 0.351 Chirality : 0.043 0.217 2194 Planarity : 0.003 0.041 2241 Dihedral : 6.546 59.338 2165 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.82 % Favored : 85.99 % Rotamer: Outliers : 9.73 % Allowed : 27.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.19), residues: 2106 helix: -0.08 (0.14), residues: 1298 sheet: None (None), residues: 0 loop : -3.80 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 399 TYR 0.010 0.002 TYR A 471 PHE 0.015 0.001 PHE a 435 TRP 0.002 0.000 TRP A 367 HIS 0.005 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00363 (11664) covalent geometry : angle 0.63700 (16152) hydrogen bonds : bond 0.03837 ( 845) hydrogen bonds : angle 5.01627 ( 2472) *********************** 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 152 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.380 Fit side-chains REVERT: A 533 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7621 (ttm110) REVERT: A 536 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: A 537 TYR cc_start: 0.8340 (t80) cc_final: 0.7948 (t80) REVERT: A 575 MET cc_start: 0.7978 (mpp) cc_final: 0.7725 (mpp) REVERT: A 635 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: a 390 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7436 (tt) REVERT: a 533 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7421 (ttm110) REVERT: a 536 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: a 537 TYR cc_start: 0.8320 (t80) cc_final: 0.7949 (t80) REVERT: a 571 ASN cc_start: 0.7151 (t0) cc_final: 0.6947 (t0) REVERT: a 635 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7874 (m-30) outliers start: 33 outliers final: 20 residues processed: 141 average time/residue: 0.0833 time to fit residues: 17.8693 Evaluate side-chains 142 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 47 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 115 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.4585 r_free = 0.4585 target = 0.177421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.151373 restraints weight = 30309.121| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 4.11 r_work: 0.4103 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11664 Z= 0.147 Angle : 0.607 12.869 16152 Z= 0.333 Chirality : 0.043 0.204 2194 Planarity : 0.003 0.038 2241 Dihedral : 6.131 58.487 2162 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.96 % Favored : 85.90 % Rotamer: Outliers : 7.96 % Allowed : 28.02 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.19), residues: 2106 helix: 0.26 (0.15), residues: 1308 sheet: None (None), residues: 0 loop : -3.81 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 533 TYR 0.010 0.001 TYR a 634 PHE 0.015 0.001 PHE a 435 TRP 0.001 0.000 TRP A 367 HIS 0.004 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00303 (11664) covalent geometry : angle 0.60665 (16152) hydrogen bonds : bond 0.03555 ( 845) hydrogen bonds : angle 4.75232 ( 2472) *********************** 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 144 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.433 Fit side-chains REVERT: A 388 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6185 (mm) REVERT: A 390 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7116 (tt) REVERT: A 533 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7668 (ttm110) REVERT: A 536 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.6484 (m-80) REVERT: A 537 TYR cc_start: 0.8278 (t80) cc_final: 0.7822 (t80) REVERT: A 635 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: a 533 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7388 (ttm110) REVERT: a 536 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.6606 (m-80) REVERT: a 537 TYR cc_start: 0.8228 (t80) cc_final: 0.7786 (t80) REVERT: a 571 ASN cc_start: 0.7168 (t0) cc_final: 0.6886 (t0) outliers start: 27 outliers final: 15 residues processed: 135 average time/residue: 0.0842 time to fit residues: 17.1955 Evaluate side-chains 136 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 461 TYR 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 635 ASP Chi-restraints excluded: chain a residue 372 GLU Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 453 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 635 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 113 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 201 optimal weight: 0.4980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.4595 r_free = 0.4595 target = 0.178506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.152557 restraints weight = 30174.687| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 4.56 r_work: 0.4107 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2462 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= 0.135 Angle : 0.586 12.992 16152 Z= 0.322 Chirality : 0.042 0.279 2194 Planarity : 0.003 0.037 2241 Dihedral : 5.799 57.572 2157 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.15 % Favored : 86.70 % Rotamer: Outliers : 7.67 % Allowed : 30.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.19), residues: 2106 helix: 0.51 (0.15), residues: 1324 sheet: None (None), residues: 0 loop : -3.85 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 533 TYR 0.010 0.001 TYR A 634 PHE 0.015 0.001 PHE A 435 TRP 0.002 0.000 TRP A 367 HIS 0.004 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00275 (11664) covalent geometry : angle 0.58580 (16152) hydrogen bonds : bond 0.03398 ( 845) hydrogen bonds : angle 4.52522 ( 2472) *********************** 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 149 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.370 Fit side-chains REVERT: A 390 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7185 (tt) REVERT: A 533 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7701 (ttm110) REVERT: A 536 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.6432 (m-80) REVERT: A 537 TYR cc_start: 0.8405 (t80) cc_final: 0.7928 (t80) REVERT: A 635 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: a 390 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7426 (tt) REVERT: a 533 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7467 (ttm110) REVERT: a 536 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: a 537 TYR cc_start: 0.8298 (t80) cc_final: 0.7830 (t80) REVERT: a 571 ASN cc_start: 0.7148 (t0) cc_final: 0.6858 (t0) REVERT: a 634 TYR cc_start: 0.7120 (m-80) cc_final: 0.6871 (m-80) REVERT: a 635 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7895 (m-30) outliers start: 26 outliers final: 16 residues processed: 143 average time/residue: 0.0863 time to fit residues: 18.7115 Evaluate side-chains 140 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 572 HIS Chi-restraints excluded: chain A residue 635 ASP 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 453 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 197 optimal weight: 0.5980 chunk 29 optimal weight: 0.0970 chunk 100 optimal weight: 0.0970 chunk 45 optimal weight: 5.9990 chunk 193 optimal weight: 0.4980 overall best weight: 0.8578 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.177055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.150874 restraints weight = 29582.343| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 3.94 r_work: 0.4107 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11664 Z= 0.168 Angle : 0.623 13.220 16152 Z= 0.342 Chirality : 0.044 0.305 2194 Planarity : 0.003 0.038 2241 Dihedral : 5.871 54.808 2153 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.87 % Favored : 85.99 % Rotamer: Outliers : 8.85 % Allowed : 30.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.19), residues: 2106 helix: 0.55 (0.15), residues: 1306 sheet: None (None), residues: 0 loop : -3.76 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 533 TYR 0.010 0.001 TYR A 471 PHE 0.013 0.001 PHE A 435 TRP 0.005 0.001 TRP a 367 HIS 0.004 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00350 (11664) covalent geometry : angle 0.62340 (16152) hydrogen bonds : bond 0.03637 ( 845) hydrogen bonds : angle 4.71319 ( 2472) *********************** 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 146 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6158 (mm) REVERT: A 390 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7101 (tt) REVERT: A 533 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7691 (ttm110) REVERT: A 536 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: A 537 TYR cc_start: 0.8379 (t80) cc_final: 0.7908 (t80) REVERT: a 390 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7418 (tt) REVERT: a 533 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7489 (ttm110) REVERT: a 536 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: a 537 TYR cc_start: 0.8279 (t80) cc_final: 0.7861 (t80) REVERT: a 571 ASN cc_start: 0.7063 (t0) cc_final: 0.6814 (t0) REVERT: a 617 ASP cc_start: 0.9196 (t0) cc_final: 0.8623 (m-30) REVERT: a 635 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7855 (m-30) outliers start: 30 outliers final: 21 residues processed: 139 average time/residue: 0.0798 time to fit residues: 16.8333 Evaluate side-chains 143 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 572 HIS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 39 optimal weight: 0.1980 chunk 117 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 25 optimal weight: 0.0000 chunk 109 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 170 optimal weight: 0.0170 chunk 2 optimal weight: 6.9990 chunk 71 optimal weight: 0.0970 overall best weight: 0.2620 ------------------------------------------------------------------------------- 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 = 0.4617 r_free = 0.4617 target = 0.180456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.153434 restraints weight = 30163.247| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 3.77 r_work: 0.4162 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 11664 Z= 0.104 Angle : 0.557 12.459 16152 Z= 0.306 Chirality : 0.042 0.312 2194 Planarity : 0.002 0.034 2241 Dihedral : 5.379 54.932 2153 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.49 % Favored : 88.37 % Rotamer: Outliers : 7.37 % Allowed : 32.45 % Favored : 60.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.19), residues: 2106 helix: 0.91 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -3.84 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 533 TYR 0.011 0.001 TYR a 634 PHE 0.018 0.001 PHE A 435 TRP 0.004 0.000 TRP A 367 HIS 0.004 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00209 (11664) covalent geometry : angle 0.55723 (16152) hydrogen bonds : bond 0.03041 ( 845) hydrogen bonds : angle 4.19986 ( 2472) *********************** 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 148 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.318 Fit side-chains REVERT: A 388 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6091 (mm) REVERT: A 390 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7334 (tt) REVERT: A 536 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: A 537 TYR cc_start: 0.8301 (t80) cc_final: 0.7970 (t80) REVERT: A 634 TYR cc_start: 0.7111 (m-80) cc_final: 0.6815 (m-80) REVERT: a 536 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: a 617 ASP cc_start: 0.9174 (t0) cc_final: 0.8646 (m-30) REVERT: a 634 TYR cc_start: 0.7030 (m-80) cc_final: 0.6818 (m-80) outliers start: 25 outliers final: 16 residues processed: 142 average time/residue: 0.0784 time to fit residues: 17.4592 Evaluate side-chains 138 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 520 ILE Chi-restraints excluded: chain A residue 536 PHE 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 483 HIS Chi-restraints excluded: chain a residue 520 ILE Chi-restraints excluded: chain a residue 536 PHE Chi-restraints excluded: chain a residue 635 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 164 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 91 optimal weight: 0.0040 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 34 optimal weight: 0.0570 overall best weight: 0.6290 ------------------------------------------------------------------------------- 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 426 ASN a 447 HIS a 483 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.177491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.149894 restraints weight = 30028.365| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 3.66 r_work: 0.4132 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11664 Z= 0.136 Angle : 0.585 14.050 16152 Z= 0.321 Chirality : 0.044 0.300 2194 Planarity : 0.003 0.034 2241 Dihedral : 5.238 53.603 2151 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.01 % Favored : 86.85 % Rotamer: Outliers : 7.08 % Allowed : 33.33 % Favored : 59.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 2106 helix: 0.99 (0.15), residues: 1308 sheet: None (None), residues: 0 loop : -3.56 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 533 TYR 0.012 0.001 TYR a 634 PHE 0.015 0.001 PHE A 435 TRP 0.003 0.000 TRP a 367 HIS 0.003 0.001 HIS a 483 Details of bonding type rmsd covalent geometry : bond 0.00285 (11664) covalent geometry : angle 0.58519 (16152) hydrogen bonds : bond 0.03256 ( 845) hydrogen bonds : angle 4.30142 ( 2472) *********************** 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 140 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6109 (mm) REVERT: A 390 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7275 (tt) REVERT: A 536 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.6415 (m-80) REVERT: A 537 TYR cc_start: 0.8399 (t80) cc_final: 0.7951 (t80) REVERT: A 660 LEU cc_start: 0.6795 (mt) cc_final: 0.6502 (mt) REVERT: a 390 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7399 (tt) REVERT: a 536 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.6570 (m-80) REVERT: a 617 ASP cc_start: 0.9174 (t0) cc_final: 0.8614 (m-30) REVERT: a 634 TYR cc_start: 0.7162 (m-80) cc_final: 0.6933 (m-80) outliers start: 24 outliers final: 18 residues processed: 134 average time/residue: 0.0685 time to fit residues: 14.6663 Evaluate side-chains 138 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 520 ILE 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 382 VAL Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 390 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 97 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4555 r_free = 0.4555 target = 0.175015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.147130 restraints weight = 30067.493| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 3.69 r_work: 0.4092 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 11664 Z= 0.202 Angle : 0.655 13.909 16152 Z= 0.364 Chirality : 0.045 0.354 2194 Planarity : 0.003 0.035 2241 Dihedral : 5.709 54.171 2151 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.77 % Favored : 86.09 % Rotamer: Outliers : 7.08 % Allowed : 33.92 % Favored : 59.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.19), residues: 2106 helix: 0.72 (0.15), residues: 1308 sheet: None (None), residues: 0 loop : -3.55 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 512 TYR 0.012 0.002 TYR a 634 PHE 0.014 0.001 PHE a 536 TRP 0.002 0.001 TRP A 367 HIS 0.008 0.002 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00428 (11664) covalent geometry : angle 0.65512 (16152) hydrogen bonds : bond 0.03799 ( 845) hydrogen bonds : angle 4.78424 ( 2472) ********************** 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 141 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.398 Fit side-chains REVERT: A 388 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6162 (mm) REVERT: A 390 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7153 (tt) REVERT: A 536 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: A 537 TYR cc_start: 0.8404 (t80) cc_final: 0.7931 (t80) REVERT: A 660 LEU cc_start: 0.6987 (mt) cc_final: 0.6686 (mt) REVERT: a 390 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7480 (tt) REVERT: a 536 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6549 (m-80) REVERT: a 537 TYR cc_start: 0.8289 (t80) cc_final: 0.7868 (t80) REVERT: a 617 ASP cc_start: 0.9230 (t0) cc_final: 0.8618 (m-30) REVERT: a 634 TYR cc_start: 0.7169 (m-80) cc_final: 0.6888 (m-80) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 0.0714 time to fit residues: 15.3022 Evaluate side-chains 133 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 461 TYR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 520 ILE 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 382 VAL Chi-restraints excluded: chain a residue 388 LEU Chi-restraints excluded: chain a residue 390 LEU Chi-restraints excluded: chain a residue 511 LEU Chi-restraints excluded: chain a residue 520 ILE Chi-restraints excluded: chain a residue 536 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 91 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 129 optimal weight: 0.3980 chunk 30 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 185 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.4592 r_free = 0.4592 target = 0.178198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.151445 restraints weight = 30409.998| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.65 r_work: 0.4145 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3068 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= 0.116 Angle : 0.578 13.788 16152 Z= 0.318 Chirality : 0.043 0.335 2194 Planarity : 0.002 0.038 2241 Dihedral : 5.190 54.095 2151 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.73 % Favored : 88.13 % Rotamer: Outliers : 5.90 % Allowed : 34.51 % Favored : 59.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 2106 helix: 1.11 (0.15), residues: 1304 sheet: None (None), residues: 0 loop : -3.51 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.010 0.001 TYR a 634 PHE 0.017 0.001 PHE A 435 TRP 0.004 0.000 TRP a 367 HIS 0.004 0.001 HIS a 572 Details of bonding type rmsd covalent geometry : bond 0.00243 (11664) covalent geometry : angle 0.57758 (16152) hydrogen bonds : bond 0.03119 ( 845) hydrogen bonds : angle 4.27035 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2762.15 seconds wall clock time: 47 minutes 41.86 seconds (2861.86 seconds total)