Starting phenix.real_space_refine (version: dev) on Mon Feb 27 19:35:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pec_13352/02_2023/7pec_13352_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pec_13352/02_2023/7pec_13352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pec_13352/02_2023/7pec_13352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pec_13352/02_2023/7pec_13352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pec_13352/02_2023/7pec_13352_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pec_13352/02_2023/7pec_13352_updated.pdb" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 30911 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2192, 17454 Classifications: {'peptide': 2192} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 87, 'TRANS': 2104} Chain breaks: 20 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'UNK:plan-1': 56, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "E" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "I" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2580 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.37, per 1000 atoms: 0.56 Number of scatterers: 30911 At special positions: 0 Unit cell: (250.2, 167.912, 151.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 203 16.00 P 6 15.00 O 5616 8.00 N 5414 7.00 C 19672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.92 Conformation dependent library (CDL) restraints added in 4.7 seconds 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 162 helices and 28 sheets defined 57.4% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.34 Creating SS restraints... Processing helix chain 'A' and resid 20 through 29 removed outlier: 3.966A pdb=" N UNK A 24 " --> pdb=" O UNK A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.640A pdb=" N UNK A 52 " --> pdb=" O UNK A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 83 through 97 Processing helix chain 'A' and resid 101 through 116 removed outlier: 4.323A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 139 through 155 removed outlier: 3.596A pdb=" N ALA A 142 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 145 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 146 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 149 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 150 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 180 through 183 No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 197 removed outlier: 3.872A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.755A pdb=" N VAL A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.983A pdb=" N LEU A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.827A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 386 through 402 removed outlier: 3.669A pdb=" N THR A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) Proline residue: A 397 - end of helix removed outlier: 3.501A pdb=" N PHE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 removed outlier: 3.766A pdb=" N HIS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.893A pdb=" N GLN A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 465 removed outlier: 3.540A pdb=" N LEU A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Proline residue: A 453 - end of helix removed outlier: 4.041A pdb=" N LEU A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 457 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU A 463 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.571A pdb=" N THR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.502A pdb=" N LEU A 505 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 532 through 548 Processing helix chain 'A' and resid 580 through 591 Processing helix chain 'A' and resid 601 through 611 removed outlier: 4.037A pdb=" N ASP A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 629 removed outlier: 3.728A pdb=" N ARG A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 669 through 678 Processing helix chain 'A' and resid 681 through 687 removed outlier: 4.399A pdb=" N ALA A 685 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 687 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 701 removed outlier: 3.633A pdb=" N VAL A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 Processing helix chain 'A' and resid 723 through 743 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 747 through 763 Processing helix chain 'A' and resid 765 through 783 Proline residue: A 770 - end of helix removed outlier: 5.285A pdb=" N GLU A 773 " --> pdb=" O ARG A 769 " (cutoff:3.500A) Proline residue: A 774 - end of helix Processing helix chain 'A' and resid 792 through 809 removed outlier: 3.842A pdb=" N GLN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 828 removed outlier: 4.723A pdb=" N ASP A 818 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 821 " --> pdb=" O ASP A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'A' and resid 856 through 860 Processing helix chain 'A' and resid 862 through 874 removed outlier: 3.885A pdb=" N LEU A 865 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 868 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 869 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 871 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 890 Processing helix chain 'A' and resid 896 through 902 Processing helix chain 'A' and resid 934 through 940 Processing helix chain 'A' and resid 943 through 959 Proline residue: A 948 - end of helix removed outlier: 3.871A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 966 Processing helix chain 'A' and resid 968 through 982 removed outlier: 3.673A pdb=" N VAL A 972 " --> pdb=" O HIS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1003 Proline residue: A 991 - end of helix removed outlier: 4.571A pdb=" N MET A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Proline residue: A 995 - end of helix removed outlier: 3.627A pdb=" N LEU A 998 " --> pdb=" O PRO A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1041 removed outlier: 3.532A pdb=" N LEU A1016 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS A1024 " --> pdb=" O SER A1021 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N SER A1025 " --> pdb=" O PHE A1022 " (cutoff:3.500A) Proline residue: A1029 - end of helix removed outlier: 4.432A pdb=" N ASP A1032 " --> pdb=" O PRO A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1083 removed outlier: 3.555A pdb=" N VAL A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHE A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR A1070 " --> pdb=" O GLU A1066 " (cutoff:3.500A) Proline residue: A1072 - end of helix Proline residue: A1076 - end of helix Processing helix chain 'A' and resid 1088 through 1123 removed outlier: 3.699A pdb=" N ILE A1091 " --> pdb=" O PRO A1088 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL A1092 " --> pdb=" O GLY A1089 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A1095 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A1101 " --> pdb=" O ALA A1098 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A1104 " --> pdb=" O GLN A1101 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ALA A1105 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A1108 " --> pdb=" O ALA A1105 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A1109 " --> pdb=" O ASN A1106 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A1111 " --> pdb=" O ASP A1108 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N HIS A1112 " --> pdb=" O ASP A1109 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A1115 " --> pdb=" O HIS A1112 " (cutoff:3.500A) Proline residue: A1116 - end of helix removed outlier: 3.579A pdb=" N ASP A1123 " --> pdb=" O LYS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.726A pdb=" N SER A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1165 Proline residue: A1158 - end of helix removed outlier: 3.640A pdb=" N ASP A1164 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1202 removed outlier: 4.067A pdb=" N SER A1171 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A1173 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A1185 " --> pdb=" O PHE A1182 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS A1186 " --> pdb=" O GLN A1183 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Proline residue: A1193 - end of helix removed outlier: 3.744A pdb=" N VAL A1200 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1218 Processing helix chain 'A' and resid 1264 through 1269 Processing helix chain 'A' and resid 1277 through 1294 Processing helix chain 'A' and resid 1298 through 1309 removed outlier: 3.962A pdb=" N CYS A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP A1304 " --> pdb=" O LEU A1300 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ALA A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU A1306 " --> pdb=" O SER A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 Processing helix chain 'A' and resid 1318 through 1328 removed outlier: 3.549A pdb=" N GLU A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1346 Processing helix chain 'A' and resid 1351 through 1366 Processing helix chain 'A' and resid 1377 through 1389 removed outlier: 5.844A pdb=" N VAL A1381 " --> pdb=" O ASN A1378 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A1383 " --> pdb=" O ILE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1406 Processing helix chain 'A' and resid 1410 through 1422 Processing helix chain 'A' and resid 1426 through 1440 Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'A' and resid 1456 through 1469 Processing helix chain 'A' and resid 1474 through 1487 Processing helix chain 'A' and resid 1490 through 1499 Processing helix chain 'A' and resid 1506 through 1523 removed outlier: 4.469A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A1518 " --> pdb=" O ARG A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1535 removed outlier: 3.504A pdb=" N CYS A1534 " --> pdb=" O GLU A1530 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 Processing helix chain 'A' and resid 1557 through 1581 removed outlier: 3.506A pdb=" N GLN A1562 " --> pdb=" O SER A1558 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1607 removed outlier: 4.654A pdb=" N GLY A1588 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A1592 " --> pdb=" O GLY A1588 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A1603 " --> pdb=" O LEU A1599 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A1604 " --> pdb=" O GLU A1600 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A1605 " --> pdb=" O GLU A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1625 removed outlier: 3.522A pdb=" N ARG A1612 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU A1613 " --> pdb=" O GLU A1610 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A1616 " --> pdb=" O GLU A1613 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1624 " --> pdb=" O GLU A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1642 removed outlier: 3.610A pdb=" N LEU A1642 " --> pdb=" O MET A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1648 No H-bonds generated for 'chain 'A' and resid 1646 through 1648' Processing helix chain 'A' and resid 1650 through 1662 Processing helix chain 'A' and resid 1666 through 1677 Processing helix chain 'A' and resid 1694 through 1706 removed outlier: 3.578A pdb=" N LYS A1706 " --> pdb=" O LYS A1702 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1731 Processing helix chain 'A' and resid 1738 through 1761 Processing helix chain 'A' and resid 1766 through 1782 Proline residue: A1770 - end of helix Processing helix chain 'A' and resid 1787 through 1811 Processing helix chain 'A' and resid 1868 through 1895 removed outlier: 3.564A pdb=" N VAL A1882 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Proline residue: A1883 - end of helix removed outlier: 3.528A pdb=" N SER A1895 " --> pdb=" O SER A1891 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1913 Processing helix chain 'A' and resid 1917 through 1929 Processing helix chain 'A' and resid 1934 through 1945 removed outlier: 3.621A pdb=" N ILE A1939 " --> pdb=" O LEU A1936 " (cutoff:3.500A) Proline residue: A1940 - end of helix removed outlier: 3.531A pdb=" N ALA A1944 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1966 removed outlier: 3.582A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1971 No H-bonds generated for 'chain 'A' and resid 1969 through 1971' Processing helix chain 'A' and resid 1973 through 1980 Processing helix chain 'A' and resid 1985 through 2001 removed outlier: 3.926A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS A2001 " --> pdb=" O ASN A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2020 Processing helix chain 'A' and resid 2023 through 2038 Processing helix chain 'A' and resid 2044 through 2060 Proline residue: A2053 - end of helix removed outlier: 3.798A pdb=" N ARG A2060 " --> pdb=" O ALA A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2073 Processing helix chain 'A' and resid 2075 through 2091 removed outlier: 3.704A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2117 removed outlier: 3.747A pdb=" N GLN A2099 " --> pdb=" O LYS A2095 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Proline residue: A2116 - end of helix Processing helix chain 'A' and resid 2123 through 2126 No H-bonds generated for 'chain 'A' and resid 2123 through 2126' Processing helix chain 'A' and resid 2128 through 2132 Processing helix chain 'A' and resid 2193 through 2211 Processing helix chain 'A' and resid 2213 through 2218 Processing helix chain 'A' and resid 2246 through 2256 Processing helix chain 'A' and resid 2263 through 2271 Processing helix chain 'A' and resid 2275 through 2277 No H-bonds generated for 'chain 'A' and resid 2275 through 2277' Processing helix chain 'A' and resid 2280 through 2292 Processing helix chain 'A' and resid 2298 through 2306 Processing helix chain 'A' and resid 2310 through 2334 Processing helix chain 'A' and resid 2364 through 2367 No H-bonds generated for 'chain 'A' and resid 2364 through 2367' Processing helix chain 'A' and resid 2381 through 2386 Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2411 through 2423 removed outlier: 3.688A pdb=" N PHE A2421 " --> pdb=" O VAL A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2426 through 2434 removed outlier: 4.042A pdb=" N TRP A2429 " --> pdb=" O LEU A2426 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A2430 " --> pdb=" O LEU A2427 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2509 Processing helix chain 'A' and resid 2521 through 2533 Processing helix chain 'A' and resid 2535 through 2540 removed outlier: 3.747A pdb=" N GLN A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2543 through 2545 No H-bonds generated for 'chain 'A' and resid 2543 through 2545' Processing helix chain 'E' and resid 21 through 24 No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 33 through 36 No H-bonds generated for 'chain 'E' and resid 33 through 36' Processing helix chain 'E' and resid 95 through 113 removed outlier: 4.073A pdb=" N TRP E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 140 Processing helix chain 'E' and resid 179 through 185 Processing helix chain 'E' and resid 199 through 218 removed outlier: 3.678A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 268 Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 282 through 284 No H-bonds generated for 'chain 'E' and resid 282 through 284' Processing helix chain 'E' and resid 292 through 296 Processing helix chain 'E' and resid 308 through 327 Processing helix chain 'E' and resid 330 through 337 Processing helix chain 'E' and resid 341 through 360 removed outlier: 3.788A pdb=" N LEU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR E 360 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 391 removed outlier: 3.621A pdb=" N LEU E 390 " --> pdb=" O ASP E 387 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 391 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 397 Processing helix chain 'E' and resid 408 through 421 Processing helix chain 'E' and resid 431 through 441 Proline residue: E 434 - end of helix Processing helix chain 'E' and resid 446 through 459 removed outlier: 3.656A pdb=" N LEU E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'E' and resid 473 through 481 removed outlier: 3.561A pdb=" N LYS E 478 " --> pdb=" O PRO E 474 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 479 " --> pdb=" O TYR E 475 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E 480 " --> pdb=" O VAL E 476 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN E 481 " --> pdb=" O LEU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 501 Proline residue: E 489 - end of helix removed outlier: 3.582A pdb=" N VAL E 501 " --> pdb=" O LYS E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 511 removed outlier: 3.568A pdb=" N LEU E 509 " --> pdb=" O GLN E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 523 removed outlier: 3.579A pdb=" N PHE E 518 " --> pdb=" O GLY E 514 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 521 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 542 Processing helix chain 'E' and resid 547 through 555 Processing helix chain 'E' and resid 558 through 565 removed outlier: 3.548A pdb=" N GLN E 565 " --> pdb=" O ILE E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 584 Processing helix chain 'E' and resid 589 through 598 Processing helix chain 'E' and resid 600 through 609 removed outlier: 4.274A pdb=" N SER E 606 " --> pdb=" O GLU E 602 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU E 607 " --> pdb=" O LYS E 603 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 608 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER E 609 " --> pdb=" O TYR E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 613 through 629 removed outlier: 3.753A pdb=" N ASN E 629 " --> pdb=" O THR E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 648 Processing helix chain 'E' and resid 657 through 673 removed outlier: 3.521A pdb=" N GLU E 662 " --> pdb=" O MET E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 684 removed outlier: 3.604A pdb=" N THR E 680 " --> pdb=" O SER E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 819 removed outlier: 3.590A pdb=" N HIS E 817 " --> pdb=" O ARG E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 824 through 838 removed outlier: 3.596A pdb=" N ALA E 838 " --> pdb=" O LEU E 834 " (cutoff:3.500A) Processing helix chain 'E' and resid 959 through 968 removed outlier: 4.031A pdb=" N TYR E 966 " --> pdb=" O TRP E 962 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA E 968 " --> pdb=" O ALA E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 1007 Processing helix chain 'I' and resid 21 through 47 removed outlier: 3.804A pdb=" N ARG I 29 " --> pdb=" O ARG I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 76 removed outlier: 3.647A pdb=" N ILE I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 95 Processing helix chain 'I' and resid 128 through 144 Processing helix chain 'I' and resid 167 through 177 Processing helix chain 'I' and resid 183 through 196 Processing helix chain 'I' and resid 227 through 229 No H-bonds generated for 'chain 'I' and resid 227 through 229' Processing helix chain 'I' and resid 360 through 363 No H-bonds generated for 'chain 'I' and resid 360 through 363' Processing helix chain 'I' and resid 385 through 394 Processing sheet with id= A, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id= B, first strand: chain 'A' and resid 2181 through 2183 Processing sheet with id= C, first strand: chain 'A' and resid 2184 through 2187 Processing sheet with id= D, first strand: chain 'A' and resid 2243 through 2245 removed outlier: 3.623A pdb=" N ASP A2244 " --> pdb=" O LEU A2346 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.836A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 123 through 126 removed outlier: 3.759A pdb=" N ARG C 123 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY C 104 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG C 110 " --> pdb=" O THR C 102 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 153 through 156 removed outlier: 4.192A pdb=" N CYS C 133 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 215 through 217 removed outlier: 4.233A pdb=" N ASN C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 189 " --> pdb=" O ASN C 193 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 197 through 199 Processing sheet with id= J, first strand: chain 'C' and resid 223 through 228 removed outlier: 6.662A pdb=" N CYS C 238 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS C 226 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 236 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE C 228 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU C 234 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 239 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 258 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR C 256 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.546A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS C 298 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 304 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 17 through 19 removed outlier: 4.335A pdb=" N ALA C 18 " --> pdb=" O CYS C 317 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 118 through 123 removed outlier: 3.585A pdb=" N LEU E 62 " --> pdb=" O LYS E 120 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 163 through 167 Processing sheet with id= O, first strand: chain 'E' and resid 1019 through 1021 removed outlier: 3.542A pdb=" N ASN E1020 " --> pdb=" O ILE E1325 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 1028 through 1031 removed outlier: 4.342A pdb=" N VAL E1028 " --> pdb=" O ALA E1041 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E1041 " --> pdb=" O VAL E1028 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E1030 " --> pdb=" O ALA E1039 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E1039 " --> pdb=" O LYS E1030 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE E1046 " --> pdb=" O PHE E1060 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP E1058 " --> pdb=" O PHE E1048 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 1092 through 1094 Processing sheet with id= R, first strand: chain 'E' and resid 1181 through 1184 removed outlier: 3.535A pdb=" N ILE E1190 " --> pdb=" O TYR E1207 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR E1207 " --> pdb=" O ILE E1190 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET E1205 " --> pdb=" O VAL E1192 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 1227 through 1230 removed outlier: 3.762A pdb=" N SER E1229 " --> pdb=" O ARG E1237 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN E1248 " --> pdb=" O ILE E1238 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 1267 through 1269 Processing sheet with id= U, first strand: chain 'E' and resid 1070 through 1076 removed outlier: 3.641A pdb=" N THR E1071 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ALA E1087 " --> pdb=" O THR E1071 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N MET E1073 " --> pdb=" O LEU E1085 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU E1085 " --> pdb=" O MET E1073 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR E1075 " --> pdb=" O LEU E1083 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU E1083 " --> pdb=" O TYR E1075 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 1146 through 1151 removed outlier: 3.753A pdb=" N GLN E1159 " --> pdb=" O ILE E1149 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP E1151 " --> pdb=" O LYS E1157 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS E1157 " --> pdb=" O ASP E1151 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'I' and resid 98 through 100 Processing sheet with id= Y, first strand: chain 'I' and resid 154 through 156 Processing sheet with id= Z, first strand: chain 'I' and resid 199 through 201 Processing sheet with id= AA, first strand: chain 'I' and resid 329 through 333 Processing sheet with id= AB, first strand: chain 'I' and resid 342 through 344 1481 hydrogen bonds defined for protein. 3915 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: 15.31 Time building geometry restraints manager: 13.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10196 1.34 - 1.46: 6721 1.46 - 1.58: 14316 1.58 - 1.69: 6 1.69 - 1.81: 327 Bond restraints: 31566 Sorted by residual: bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.595 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.599 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" O15 IHP A2601 " pdb=" P5 IHP A2601 " ideal model delta sigma weight residual 1.675 1.617 0.058 2.00e-02 2.50e+03 8.52e+00 bond pdb=" C5 IHP A2601 " pdb=" O15 IHP A2601 " ideal model delta sigma weight residual 1.389 1.442 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" O16 IHP A2601 " pdb=" P6 IHP A2601 " ideal model delta sigma weight residual 1.672 1.620 0.052 2.00e-02 2.50e+03 6.82e+00 ... (remaining 31561 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.08: 1001 107.08 - 113.82: 18084 113.82 - 120.56: 12025 120.56 - 127.30: 11272 127.30 - 134.04: 424 Bond angle restraints: 42806 Sorted by residual: angle pdb=" CG ARG I 218 " pdb=" CD ARG I 218 " pdb=" NE ARG I 218 " ideal model delta sigma weight residual 112.00 119.62 -7.62 2.20e+00 2.07e-01 1.20e+01 angle pdb=" C GLU A 429 " pdb=" N ARG A 430 " pdb=" CA ARG A 430 " ideal model delta sigma weight residual 120.38 124.94 -4.56 1.46e+00 4.69e-01 9.77e+00 angle pdb=" CA PRO I 325 " pdb=" N PRO I 325 " pdb=" CD PRO I 325 " ideal model delta sigma weight residual 112.00 108.36 3.64 1.40e+00 5.10e-01 6.77e+00 angle pdb=" C4 IHP A2601 " pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 120.75 128.53 -7.78 3.00e+00 1.11e-01 6.72e+00 angle pdb=" C GLY I 323 " pdb=" N ALA I 324 " pdb=" CA ALA I 324 " ideal model delta sigma weight residual 121.80 128.12 -6.32 2.44e+00 1.68e-01 6.71e+00 ... (remaining 42801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 17139 17.25 - 34.50: 1432 34.50 - 51.75: 379 51.75 - 69.01: 99 69.01 - 86.26: 20 Dihedral angle restraints: 19069 sinusoidal: 7721 harmonic: 11348 Sorted by residual: dihedral pdb=" CA ALA I 324 " pdb=" C ALA I 324 " pdb=" N PRO I 325 " pdb=" CA PRO I 325 " ideal model delta harmonic sigma weight residual -180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PHE E1060 " pdb=" C PHE E1060 " pdb=" N HIS E1061 " pdb=" CA HIS E1061 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CG ARG I 218 " pdb=" CD ARG I 218 " pdb=" NE ARG I 218 " pdb=" CZ ARG I 218 " ideal model delta sinusoidal sigma weight residual -90.00 -26.73 -63.27 2 1.50e+01 4.44e-03 1.70e+01 ... (remaining 19066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4109 0.054 - 0.107: 653 0.107 - 0.161: 80 0.161 - 0.215: 2 0.215 - 0.268: 2 Chirality restraints: 4846 Sorted by residual: chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.58 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" O13 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.60 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C5 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O15 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.42 -2.59 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4843 not shown) Planarity restraints: 5459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E1105 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO E1106 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO E1106 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E1106 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 324 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO I 325 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO I 325 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 325 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A1157 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO A1158 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.029 5.00e-02 4.00e+02 ... (remaining 5456 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5427 2.77 - 3.30: 31051 3.30 - 3.84: 51150 3.84 - 4.37: 60652 4.37 - 4.90: 100949 Nonbonded interactions: 249229 Sorted by model distance: nonbonded pdb=" O GLY A2337 " pdb=" NH1 ARG A2339 " model vdw 2.238 2.520 nonbonded pdb=" O GLN I 152 " pdb=" OG1 THR I 164 " model vdw 2.253 2.440 nonbonded pdb=" O THR E1163 " pdb=" OH TYR E1193 " model vdw 2.266 2.440 nonbonded pdb=" NH1 ARG A2018 " pdb=" OE2 GLU A2067 " model vdw 2.270 2.520 nonbonded pdb=" OG SER A1658 " pdb=" O32 IHP A2601 " model vdw 2.275 2.440 ... (remaining 249224 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 203 5.16 5 C 19672 2.51 5 N 5414 2.21 5 O 5616 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 6.570 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: 0.030 Extract box with map and model: 25.660 Check model and map are aligned: 0.460 Process input model: 81.830 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.290 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.002 0.080 31566 Z= 0.147 Angle : 0.485 8.167 42806 Z= 0.252 Chirality : 0.039 0.268 4846 Planarity : 0.004 0.057 5459 Dihedral : 14.496 86.257 11673 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer Outliers : 4.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.13), residues: 3768 helix: -0.78 (0.10), residues: 2150 sheet: -3.17 (0.22), residues: 375 loop : -1.23 (0.17), residues: 1243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 671 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 167 outliers final: 24 residues processed: 802 average time/residue: 0.4735 time to fit residues: 591.4499 Evaluate side-chains 369 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 345 time to evaluate : 3.540 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3048 time to fit residues: 17.9348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 325 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 197 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 225 optimal weight: 0.0670 chunk 350 optimal weight: 0.5980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN ** A 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 GLN A2148 GLN A2277 HIS ** A2355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 87 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN I 99 HIS ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 31566 Z= 0.218 Angle : 0.634 11.694 42806 Z= 0.327 Chirality : 0.042 0.287 4846 Planarity : 0.005 0.059 5459 Dihedral : 4.428 51.788 4199 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 3768 helix: 0.67 (0.11), residues: 2173 sheet: -2.85 (0.23), residues: 366 loop : -1.10 (0.18), residues: 1229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 427 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 431 average time/residue: 0.4794 time to fit residues: 330.6084 Evaluate side-chains 289 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 287 time to evaluate : 3.727 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3092 time to fit residues: 6.5623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 194 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 291 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 351 optimal weight: 5.9990 chunk 379 optimal weight: 3.9990 chunk 312 optimal weight: 0.9990 chunk 348 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1424 GLN A1760 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1210 HIS ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 31566 Z= 0.224 Angle : 0.599 11.369 42806 Z= 0.306 Chirality : 0.041 0.331 4846 Planarity : 0.005 0.134 5459 Dihedral : 4.375 52.884 4199 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3768 helix: 0.98 (0.11), residues: 2181 sheet: -2.41 (0.24), residues: 367 loop : -1.00 (0.18), residues: 1220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 358 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 359 average time/residue: 0.4372 time to fit residues: 255.7604 Evaluate side-chains 268 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 3.828 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3286 time to fit residues: 5.8276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 346 optimal weight: 0.9990 chunk 264 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 352 optimal weight: 0.0370 chunk 373 optimal weight: 5.9990 chunk 184 optimal weight: 0.5980 chunk 334 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 GLN A1760 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 601 HIS ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 31566 Z= 0.158 Angle : 0.566 8.817 42806 Z= 0.284 Chirality : 0.040 0.228 4846 Planarity : 0.004 0.066 5459 Dihedral : 4.268 52.614 4199 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3768 helix: 1.14 (0.11), residues: 2172 sheet: -2.05 (0.25), residues: 367 loop : -0.93 (0.18), residues: 1229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 362 time to evaluate : 4.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 363 average time/residue: 0.4620 time to fit residues: 274.6030 Evaluate side-chains 268 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 3.862 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3365 time to fit residues: 5.6450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 310 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 190 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 chunk 94 optimal weight: 0.0870 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 HIS A1026 HIS ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1624 GLN A1760 ASN A1920 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 31566 Z= 0.296 Angle : 0.651 11.211 42806 Z= 0.331 Chirality : 0.041 0.206 4846 Planarity : 0.005 0.068 5459 Dihedral : 4.470 54.487 4199 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.50 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3768 helix: 1.02 (0.11), residues: 2163 sheet: -1.87 (0.25), residues: 373 loop : -0.78 (0.18), residues: 1232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 323 time to evaluate : 3.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 325 average time/residue: 0.4602 time to fit residues: 246.7798 Evaluate side-chains 261 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 259 time to evaluate : 4.127 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3290 time to fit residues: 6.6736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 125 optimal weight: 0.8980 chunk 336 optimal weight: 9.9990 chunk 73 optimal weight: 0.4980 chunk 219 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 373 optimal weight: 20.0000 chunk 310 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 196 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS A 899 HIS A1553 HIS A1670 HIS ** A1730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 31566 Z= 0.176 Angle : 0.570 10.088 42806 Z= 0.286 Chirality : 0.040 0.230 4846 Planarity : 0.004 0.068 5459 Dihedral : 4.307 54.742 4199 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.95 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3768 helix: 1.18 (0.11), residues: 2168 sheet: -1.87 (0.25), residues: 362 loop : -0.75 (0.18), residues: 1238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 321 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 322 average time/residue: 0.4427 time to fit residues: 235.1180 Evaluate side-chains 260 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 259 time to evaluate : 3.686 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3651 time to fit residues: 6.9210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 360 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 272 optimal weight: 7.9990 chunk 211 optimal weight: 0.6980 chunk 314 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 372 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS A 940 ASN ** A1730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 31566 Z= 0.200 Angle : 0.581 8.900 42806 Z= 0.293 Chirality : 0.040 0.222 4846 Planarity : 0.004 0.068 5459 Dihedral : 4.317 55.556 4199 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3768 helix: 1.14 (0.11), residues: 2159 sheet: -1.74 (0.25), residues: 367 loop : -0.69 (0.18), residues: 1242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.4554 time to fit residues: 238.6803 Evaluate side-chains 251 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 4.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 230 optimal weight: 0.0980 chunk 148 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 292 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A 878 GLN ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1311 ASN ** A1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 HIS ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 31566 Z= 0.161 Angle : 0.564 7.569 42806 Z= 0.285 Chirality : 0.040 0.231 4846 Planarity : 0.004 0.068 5459 Dihedral : 4.246 55.831 4199 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3768 helix: 1.21 (0.11), residues: 2137 sheet: -1.57 (0.26), residues: 367 loop : -0.63 (0.18), residues: 1264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 3.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.4604 time to fit residues: 247.2982 Evaluate side-chains 255 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 3.825 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 338 optimal weight: 6.9990 chunk 356 optimal weight: 2.9990 chunk 325 optimal weight: 6.9990 chunk 346 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 272 optimal weight: 6.9990 chunk 106 optimal weight: 0.0370 chunk 313 optimal weight: 3.9990 chunk 327 optimal weight: 4.9990 chunk 345 optimal weight: 0.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 31566 Z= 0.236 Angle : 0.612 10.048 42806 Z= 0.310 Chirality : 0.041 0.213 4846 Planarity : 0.004 0.069 5459 Dihedral : 4.352 58.285 4199 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3768 helix: 1.16 (0.11), residues: 2142 sheet: -1.55 (0.24), residues: 390 loop : -0.52 (0.19), residues: 1236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.4436 time to fit residues: 223.0272 Evaluate side-chains 252 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 3.514 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 227 optimal weight: 5.9990 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 254 optimal weight: 8.9990 chunk 384 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 236 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2282 GLN ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1022 ASN ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 31566 Z= 0.170 Angle : 0.588 10.138 42806 Z= 0.292 Chirality : 0.040 0.226 4846 Planarity : 0.004 0.069 5459 Dihedral : 4.299 58.981 4199 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3768 helix: 1.20 (0.11), residues: 2137 sheet: -1.50 (0.25), residues: 390 loop : -0.51 (0.19), residues: 1241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.4427 time to fit residues: 225.5594 Evaluate side-chains 251 residues out of total 3356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 3.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 243 optimal weight: 0.7980 chunk 326 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 282 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 306 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 314 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 ASN ** A2007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.081328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.060763 restraints weight = 179154.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.062384 restraints weight = 97468.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063458 restraints weight = 63679.129| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 31566 Z= 0.167 Angle : 0.573 11.568 42806 Z= 0.285 Chirality : 0.040 0.180 4846 Planarity : 0.004 0.069 5459 Dihedral : 4.248 59.627 4199 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3768 helix: 1.23 (0.11), residues: 2142 sheet: -1.40 (0.25), residues: 378 loop : -0.53 (0.19), residues: 1248 =============================================================================== Job complete usr+sys time: 6329.94 seconds wall clock time: 117 minutes 7.79 seconds (7027.79 seconds total)