Starting phenix.real_space_refine (version: dev) on Mon Feb 27 01:53:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2023/7peb_13351_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2023/7peb_13351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2023/7peb_13351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2023/7peb_13351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2023/7peb_13351_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2023/7peb_13351_updated.pdb" } resolution = 3.67 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29140 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2192, 17468 Classifications: {'peptide': 2192} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 87, 'TRANS': 2104} Chain breaks: 20 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 2, 'UNK:plan-1': 56} Unresolved non-hydrogen planarities: 64 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: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} 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: 16.63, per 1000 atoms: 0.57 Number of scatterers: 29140 At special positions: 0 Unit cell: (247.976, 169.024, 152.344, 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 193 16.00 P 6 15.00 O 5301 8.00 N 5084 7.00 C 18556 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: 12.72 Conformation dependent library (CDL) restraints added in 4.2 seconds 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 24 sheets defined 58.1% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.02 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.789A 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 removed outlier: 3.600A pdb=" N SER A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 4.216A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (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: 3.591A pdb=" N ALA A 142 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 145 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 146 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 149 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 150 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 151 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.506A 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 186 removed outlier: 3.518A pdb=" N GLN A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 removed outlier: 3.731A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.683A pdb=" N VAL A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.643A 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: 3.632A pdb=" N LEU A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 removed outlier: 3.966A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 372 through 375 No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 387 through 402 Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 410 through 425 removed outlier: 3.849A pdb=" N HIS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.690A pdb=" N GLN A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.592A pdb=" N VAL A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Proline residue: A 453 - end of helix removed outlier: 3.917A pdb=" N LEU A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 457 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.716A pdb=" N THR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 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 579 through 591 Processing helix chain 'A' and resid 601 through 611 removed outlier: 3.722A pdb=" N ASP A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 629 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: 4.579A pdb=" N ALA A 685 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 687 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 701 removed outlier: 3.583A pdb=" N VAL A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 3.900A 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: 5.316A 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: 3.903A pdb=" N GLN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 828 removed outlier: 4.468A pdb=" N ASP A 818 " --> pdb=" O LYS A 815 " (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: 3.810A pdb=" N LEU A 865 " --> pdb=" O PRO A 862 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 868 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 869 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 871 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 890 removed outlier: 3.582A pdb=" N LEU A 888 " --> pdb=" O ALA A 884 " (cutoff:3.500A) 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: 3.843A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 982 removed outlier: 7.232A pdb=" N THR A 969 " --> pdb=" O SER A 965 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET A 970 " --> pdb=" O HIS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1003 Proline residue: A 991 - end of helix removed outlier: 4.600A pdb=" N MET A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Proline residue: A 995 - end of helix removed outlier: 3.586A pdb=" N LEU A 998 " --> pdb=" O PRO A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1041 removed outlier: 3.553A pdb=" N LEU A1016 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1023 " --> pdb=" O VAL A1020 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS A1024 " --> pdb=" O SER A1021 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER A1025 " --> pdb=" O PHE A1022 " (cutoff:3.500A) Proline residue: A1029 - end of helix removed outlier: 4.398A pdb=" N ASP A1032 " --> pdb=" O PRO A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1069 removed outlier: 6.992A pdb=" N GLY A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLU A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N PHE A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1083 Proline residue: A1076 - end of helix Processing helix chain 'A' and resid 1088 through 1123 removed outlier: 3.733A pdb=" N ILE A1091 " --> pdb=" O PRO A1088 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL A1092 " --> pdb=" O GLY A1089 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A1094 " --> pdb=" O ILE A1091 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A1095 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A1101 " --> pdb=" O ALA A1098 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A1104 " --> pdb=" O GLN A1101 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA A1105 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A1108 " --> pdb=" O ALA A1105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP A1109 " --> pdb=" O ASN A1106 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A1111 " --> pdb=" O ASP A1108 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N HIS A1112 " --> pdb=" O ASP A1109 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A1115 " --> pdb=" O HIS A1112 " (cutoff:3.500A) Proline residue: A1116 - end of helix removed outlier: 3.693A pdb=" N ASP A1123 " --> pdb=" O LYS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.611A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) removed outlier: 3.801A 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 Processing helix chain 'A' and resid 1170 through 1202 removed outlier: 6.964A pdb=" N LYS A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS A1187 " --> pdb=" O GLN A1183 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TYR A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN A1189 " --> pdb=" O GLY A1185 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE A1190 " --> pdb=" O LYS A1186 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE A1191 " --> pdb=" O LYS A1187 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A1192 " --> pdb=" O TYR A1188 " (cutoff:3.500A) Proline residue: A1193 - end of helix removed outlier: 3.629A pdb=" N HIS A1202 " --> pdb=" O VAL A1198 " (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: 3.991A pdb=" N CYS A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP A1304 " --> pdb=" O LEU A1300 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU A1306 " --> pdb=" O SER A1302 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 Processing helix chain 'A' and resid 1318 through 1328 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 1379 No H-bonds generated for 'chain 'A' and resid 1377 through 1379' Processing helix chain 'A' and resid 1382 through 1389 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: 4.480A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A1518 " --> pdb=" O ARG A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1535 removed outlier: 3.600A 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: 4.506A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1607 removed outlier: 4.644A pdb=" N GLY A1588 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A1603 " --> pdb=" O LEU A1599 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A1605 " --> pdb=" O GLU A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1625 removed outlier: 3.614A pdb=" N ARG A1612 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU A1613 " --> pdb=" O GLU A1610 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A1616 " --> pdb=" O GLU A1613 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A1624 " --> pdb=" O GLU A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1642 removed outlier: 3.790A 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: 3.555A 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 removed outlier: 3.569A pdb=" N ARG A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) 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: 3.540A pdb=" N VAL A1882 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Proline residue: A1883 - end of helix removed outlier: 3.502A 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 1932 through 1945 removed outlier: 3.632A pdb=" N ILE A1939 " --> pdb=" O LEU A1936 " (cutoff:3.500A) Proline residue: A1940 - end of helix removed outlier: 3.581A pdb=" N ALA A1944 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1966 removed outlier: 3.792A 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: 3.558A pdb=" N ASN A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) removed outlier: 4.230A 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: 3.768A 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 2090 removed outlier: 3.645A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2117 removed outlier: 3.735A pdb=" N GLN A2099 " --> pdb=" O LYS A2095 " (cutoff:3.500A) removed outlier: 3.568A 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 removed outlier: 3.557A pdb=" N ASP A2315 " --> pdb=" O GLU A2311 " (cutoff:3.500A) 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: 3.588A pdb=" N PHE A2421 " --> pdb=" O VAL A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2426 through 2434 removed outlier: 4.088A pdb=" N TRP A2429 " --> pdb=" O LEU A2426 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.688A 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 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 95 through 113 removed outlier: 4.029A 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: 3.714A 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: 3.857A pdb=" N LEU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR E 360 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 391 removed outlier: 3.592A pdb=" N ALA E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 397 Processing helix chain 'E' and resid 408 through 422 removed outlier: 4.030A pdb=" N MET E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) 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: 3.622A 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: 3.759A pdb=" N LEU E 480 " --> pdb=" O VAL E 476 " (cutoff:3.500A) removed outlier: 4.328A 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 Processing helix chain 'E' and resid 503 through 511 removed outlier: 3.607A pdb=" N LEU E 509 " --> pdb=" O GLN E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 522 removed outlier: 3.515A pdb=" N PHE E 518 " --> pdb=" O GLY E 514 " (cutoff:3.500A) removed outlier: 3.508A 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 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: 4.337A pdb=" N SER E 606 " --> pdb=" O GLU E 602 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 607 " --> pdb=" O LYS E 603 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 608 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER E 609 " --> pdb=" O TYR E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 613 through 629 removed outlier: 4.001A 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: 3.563A pdb=" N LEU E 670 " --> pdb=" O ALA E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 684 removed outlier: 3.720A pdb=" N THR E 680 " --> pdb=" O SER E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 819 Processing helix chain 'E' and resid 824 through 838 removed outlier: 3.548A pdb=" N ILE E 837 " --> pdb=" O VAL E 833 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 838 " --> pdb=" O LEU E 834 " (cutoff:3.500A) Processing helix chain 'E' and resid 959 through 968 removed outlier: 4.008A pdb=" N TYR E 966 " --> pdb=" O TRP E 962 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) removed outlier: 3.845A 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 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 Processing sheet with id= E, first strand: chain 'C' and resid 24 through 27 removed outlier: 4.195A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA C 18 " --> pdb=" O CYS C 317 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 47 through 50 Processing sheet with id= G, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.733A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 124 through 126 removed outlier: 4.945A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY C 104 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 110 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 102 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 134 through 136 Processing sheet with id= J, first strand: chain 'C' and resid 215 through 217 removed outlier: 4.188A pdb=" N ASN C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 189 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 175 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 197 through 199 Processing sheet with id= L, first strand: chain 'C' and resid 223 through 228 removed outlier: 6.626A pdb=" N CYS C 238 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS C 226 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA C 236 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE C 228 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU C 234 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 239 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 256 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 284 through 288 removed outlier: 3.730A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS C 298 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 304 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 118 through 123 removed outlier: 3.542A pdb=" N LEU E 62 " --> pdb=" O LYS E 120 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 163 through 167 Processing sheet with id= P, first strand: chain 'E' and resid 1019 through 1021 removed outlier: 3.632A pdb=" N ASN E1020 " --> pdb=" O ILE E1325 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER E1326 " --> pdb=" O VAL E1318 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL E1318 " --> pdb=" O SER E1326 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 1028 through 1031 removed outlier: 4.318A pdb=" N VAL E1028 " --> pdb=" O ALA E1041 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS E1030 " --> pdb=" O ALA E1039 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E1039 " --> pdb=" O LYS E1030 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE E1046 " --> pdb=" O PHE E1060 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE E1048 " --> pdb=" O ASP E1058 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP E1058 " --> pdb=" O PHE E1048 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 1111 through 1113 removed outlier: 4.039A pdb=" N ALA E1092 " --> pdb=" O THR E1088 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E1087 " --> pdb=" O ALA E1072 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA E1072 " --> pdb=" O ALA E1087 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 1169 through 1173 removed outlier: 6.649A pdb=" N GLY E1184 " --> pdb=" O THR E1170 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU E1172 " --> pdb=" O VAL E1182 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL E1182 " --> pdb=" O LEU E1172 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR E1207 " --> pdb=" O ILE E1190 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET E1205 " --> pdb=" O VAL E1192 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 1227 through 1230 removed outlier: 3.919A pdb=" N SER E1229 " --> pdb=" O ARG E1237 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN E1248 " --> pdb=" O ILE E1238 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 1146 through 1151 removed outlier: 4.164A pdb=" N GLN E1159 " --> pdb=" O ILE E1149 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP E1151 " --> pdb=" O LYS E1157 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS E1157 " --> pdb=" O ASP E1151 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 1276 through 1280 removed outlier: 3.868A pdb=" N ASN E1288 " --> pdb=" O ILE E1279 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 329 through 333 Processing sheet with id= X, first strand: chain 'I' and resid 342 through 344 1404 hydrogen bonds defined for protein. 3819 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: 13.55 Time building geometry restraints manager: 12.85 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: 9584 1.34 - 1.46: 6072 1.46 - 1.58: 13789 1.58 - 1.69: 6 1.69 - 1.81: 310 Bond restraints: 29761 Sorted by residual: bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.598 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.602 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C5 IHP A2601 " pdb=" O15 IHP A2601 " ideal model delta sigma weight residual 1.389 1.444 -0.055 2.00e-02 2.50e+03 7.44e+00 bond pdb=" O15 IHP A2601 " pdb=" P5 IHP A2601 " ideal model delta sigma weight residual 1.675 1.623 0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" C1 IHP A2601 " pdb=" O11 IHP A2601 " ideal model delta sigma weight residual 1.392 1.443 -0.051 2.00e-02 2.50e+03 6.62e+00 ... (remaining 29756 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.93: 944 106.93 - 113.71: 16695 113.71 - 120.49: 11099 120.49 - 127.27: 11253 127.27 - 134.05: 399 Bond angle restraints: 40390 Sorted by residual: angle pdb=" C LEU A 757 " pdb=" N GLY A 758 " pdb=" CA GLY A 758 " ideal model delta sigma weight residual 119.99 123.82 -3.83 1.13e+00 7.83e-01 1.15e+01 angle pdb=" C GLY I 323 " pdb=" N ALA I 324 " pdb=" CA ALA I 324 " ideal model delta sigma weight residual 121.80 128.61 -6.81 2.44e+00 1.68e-01 7.79e+00 angle pdb=" CA LYS A1024 " pdb=" CB LYS A1024 " pdb=" CG LYS A1024 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.61e+00 angle pdb=" C PRO E 80 " pdb=" N CYS E 81 " pdb=" CA CYS E 81 " ideal model delta sigma weight residual 121.76 127.64 -5.88 2.19e+00 2.09e-01 7.20e+00 angle pdb=" CA PHE A 610 " pdb=" CB PHE A 610 " pdb=" CG PHE A 610 " ideal model delta sigma weight residual 113.80 116.47 -2.67 1.00e+00 1.00e+00 7.10e+00 ... (remaining 40385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 16223 17.27 - 34.54: 1353 34.54 - 51.82: 288 51.82 - 69.09: 74 69.09 - 86.36: 18 Dihedral angle restraints: 17956 sinusoidal: 7227 harmonic: 10729 Sorted by residual: dihedral pdb=" CA UNK A 17 " pdb=" C UNK A 17 " pdb=" N UNK A 18 " pdb=" CA UNK A 18 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+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 180.00 153.46 26.54 0 5.00e+00 4.00e-02 2.82e+01 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 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 17953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3999 0.058 - 0.117: 532 0.117 - 0.175: 59 0.175 - 0.233: 1 0.233 - 0.292: 3 Chirality restraints: 4594 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 2.61 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU A 395 " pdb=" CB LEU A 395 " pdb=" CD1 LEU A 395 " pdb=" CD2 LEU A 395 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.95e+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 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 4591 not shown) Planarity restraints: 5143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A1157 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO A1158 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.032 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 5.67e-02 5.14e+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 ASN E1105 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO E1106 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E1106 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E1106 " -0.031 5.00e-02 4.00e+02 ... (remaining 5140 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5178 2.78 - 3.31: 28882 3.31 - 3.84: 47518 3.84 - 4.37: 56227 4.37 - 4.90: 95030 Nonbonded interactions: 232835 Sorted by model distance: nonbonded pdb=" O GLY A2337 " pdb=" NH1 ARG A2339 " model vdw 2.245 2.520 nonbonded pdb=" O ALA A1268 " pdb=" NE1 TRP A1283 " model vdw 2.251 2.520 nonbonded pdb=" O THR E1163 " pdb=" OH TYR E1193 " model vdw 2.255 2.440 nonbonded pdb=" O THR A 484 " pdb=" OG SER A 487 " model vdw 2.259 2.440 nonbonded pdb=" O LEU I 319 " pdb=" OH TYR I 326 " model vdw 2.281 2.440 ... (remaining 232830 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 193 5.16 5 C 18556 2.51 5 N 5084 2.21 5 O 5301 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 25.530 Check model and map are aligned: 0.420 Process input model: 78.560 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.280 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 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 0.077 29761 Z= 0.151 Angle : 0.521 7.784 40390 Z= 0.280 Chirality : 0.040 0.292 4594 Planarity : 0.005 0.057 5143 Dihedral : 13.944 86.360 10964 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.09 % Favored : 94.86 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.12), residues: 3559 helix: -1.44 (0.10), residues: 2088 sheet: -3.26 (0.23), residues: 348 loop : -1.44 (0.18), residues: 1123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 674 time to evaluate : 3.583 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: 85 outliers final: 11 residues processed: 735 average time/residue: 0.4819 time to fit residues: 547.2106 Evaluate side-chains 332 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 321 time to evaluate : 3.749 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2762 time to fit residues: 10.4793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 1.9990 chunk 276 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 186 optimal weight: 0.1980 chunk 147 optimal weight: 0.9980 chunk 286 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 ASN ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 GLN A1266 GLN A1366 HIS ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1741 GLN A1791 HIS ** A1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN C 242 GLN E 151 ASN E 636 HIS E 642 HIS ** E1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 376 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 29761 Z= 0.226 Angle : 0.658 11.533 40390 Z= 0.331 Chirality : 0.042 0.400 4594 Planarity : 0.005 0.065 5143 Dihedral : 4.522 52.649 3962 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.86 % Rotamer Outliers : 2.34 % 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: -0.40 (0.14), residues: 3559 helix: 0.68 (0.11), residues: 2073 sheet: -2.73 (0.24), residues: 338 loop : -1.05 (0.18), residues: 1148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 339 time to evaluate : 3.663 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 outliers start: 74 outliers final: 43 residues processed: 389 average time/residue: 0.4333 time to fit residues: 274.4213 Evaluate side-chains 317 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 274 time to evaluate : 3.745 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2844 time to fit residues: 28.0014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 275 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 358 optimal weight: 0.9990 chunk 295 optimal weight: 0.6980 chunk 329 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 GLN ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1758 GLN ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS E1210 HIS ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 29761 Z= 0.276 Angle : 0.655 10.505 40390 Z= 0.326 Chirality : 0.043 0.275 4594 Planarity : 0.005 0.064 5143 Dihedral : 4.525 57.366 3962 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer Outliers : 1.93 % 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: 0.13 (0.14), residues: 3559 helix: 1.18 (0.11), residues: 2043 sheet: -2.32 (0.25), residues: 331 loop : -1.03 (0.18), residues: 1185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 296 time to evaluate : 3.849 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 outliers start: 61 outliers final: 16 residues processed: 340 average time/residue: 0.4506 time to fit residues: 253.3437 Evaluate side-chains 275 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 259 time to evaluate : 3.790 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3600 time to fit residues: 15.5941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 328 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 158 optimal weight: 0.3980 chunk 222 optimal weight: 4.9990 chunk 333 optimal weight: 5.9990 chunk 352 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 315 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2410 HIS ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS E1062 ASN ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 29761 Z= 0.181 Angle : 0.591 10.869 40390 Z= 0.290 Chirality : 0.040 0.232 4594 Planarity : 0.004 0.064 5143 Dihedral : 4.365 57.207 3962 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer Outliers : 1.39 % 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: 0.44 (0.14), residues: 3559 helix: 1.49 (0.11), residues: 2035 sheet: -2.10 (0.25), residues: 330 loop : -1.02 (0.18), residues: 1194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 282 time to evaluate : 3.366 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 outliers start: 44 outliers final: 15 residues processed: 311 average time/residue: 0.4237 time to fit residues: 220.1759 Evaluate side-chains 266 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 3.449 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3058 time to fit residues: 13.1740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 0.9980 chunk 200 optimal weight: 0.2980 chunk 5 optimal weight: 9.9990 chunk 262 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 180 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1049 GLN ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 29761 Z= 0.209 Angle : 0.607 11.942 40390 Z= 0.295 Chirality : 0.041 0.221 4594 Planarity : 0.004 0.064 5143 Dihedral : 4.314 58.938 3962 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3559 helix: 1.58 (0.12), residues: 2042 sheet: -2.15 (0.25), residues: 336 loop : -0.91 (0.18), residues: 1181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 270 time to evaluate : 4.359 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 outliers start: 45 outliers final: 15 residues processed: 301 average time/residue: 0.4312 time to fit residues: 216.7921 Evaluate side-chains 263 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 248 time to evaluate : 3.818 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3018 time to fit residues: 13.9684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 0.7980 chunk 317 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 353 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1366 HIS A1494 HIS A1541 HIS ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1797 ASN ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 370 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 29761 Z= 0.187 Angle : 0.590 12.927 40390 Z= 0.286 Chirality : 0.040 0.256 4594 Planarity : 0.004 0.064 5143 Dihedral : 4.288 59.883 3962 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer Outliers : 1.52 % 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: 0.72 (0.14), residues: 3559 helix: 1.70 (0.12), residues: 2040 sheet: -2.09 (0.24), residues: 351 loop : -0.81 (0.18), residues: 1168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 256 time to evaluate : 3.647 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 outliers start: 48 outliers final: 16 residues processed: 294 average time/residue: 0.4293 time to fit residues: 209.9361 Evaluate side-chains 260 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 244 time to evaluate : 3.776 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3115 time to fit residues: 14.8002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 1.9990 chunk 39 optimal weight: 0.0270 chunk 201 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 297 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 351 optimal weight: 20.0000 chunk 220 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1045 ASN ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 HIS A1797 ASN ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 29761 Z= 0.226 Angle : 0.621 13.243 40390 Z= 0.303 Chirality : 0.041 0.223 4594 Planarity : 0.004 0.064 5143 Dihedral : 4.327 56.957 3962 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.66 % Rotamer Outliers : 1.14 % 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: 0.65 (0.14), residues: 3559 helix: 1.59 (0.12), residues: 2050 sheet: -2.00 (0.25), residues: 347 loop : -0.83 (0.19), residues: 1162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 251 time to evaluate : 3.519 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 outliers start: 36 outliers final: 15 residues processed: 272 average time/residue: 0.4113 time to fit residues: 186.8133 Evaluate side-chains 249 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 234 time to evaluate : 3.712 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2877 time to fit residues: 13.2301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 223 optimal weight: 2.9990 chunk 239 optimal weight: 0.2980 chunk 173 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 276 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 29761 Z= 0.177 Angle : 0.626 14.413 40390 Z= 0.299 Chirality : 0.040 0.215 4594 Planarity : 0.004 0.063 5143 Dihedral : 4.293 55.636 3962 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.80 % Rotamer Outliers : 0.73 % 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: 0.71 (0.15), residues: 3559 helix: 1.64 (0.12), residues: 2047 sheet: -1.91 (0.24), residues: 356 loop : -0.79 (0.19), residues: 1156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 255 time to evaluate : 3.556 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 outliers start: 23 outliers final: 14 residues processed: 270 average time/residue: 0.4217 time to fit residues: 190.8515 Evaluate side-chains 253 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 239 time to evaluate : 3.733 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3577 time to fit residues: 14.6731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 0.9990 chunk 337 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 327 optimal weight: 0.6980 chunk 336 optimal weight: 2.9990 chunk 197 optimal weight: 0.0040 chunk 142 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 ASN ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 29761 Z= 0.202 Angle : 0.633 14.116 40390 Z= 0.304 Chirality : 0.041 0.268 4594 Planarity : 0.004 0.063 5143 Dihedral : 4.299 53.219 3962 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.38 % Rotamer Outliers : 0.51 % 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: 0.75 (0.15), residues: 3559 helix: 1.65 (0.12), residues: 2041 sheet: -1.81 (0.25), residues: 350 loop : -0.75 (0.19), residues: 1168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 245 time to evaluate : 3.494 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 outliers start: 16 outliers final: 9 residues processed: 256 average time/residue: 0.4173 time to fit residues: 178.6642 Evaluate side-chains 242 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 233 time to evaluate : 4.050 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3085 time to fit residues: 10.3769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 346 optimal weight: 0.8980 chunk 211 optimal weight: 0.5980 chunk 164 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 363 optimal weight: 0.4980 chunk 334 optimal weight: 5.9990 chunk 289 optimal weight: 0.0470 chunk 30 optimal weight: 0.0870 chunk 223 optimal weight: 0.0980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 29761 Z= 0.162 Angle : 0.633 11.723 40390 Z= 0.300 Chirality : 0.040 0.208 4594 Planarity : 0.004 0.063 5143 Dihedral : 4.182 52.210 3962 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer Outliers : 0.16 % 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: 0.85 (0.15), residues: 3559 helix: 1.73 (0.12), residues: 2043 sheet: -1.70 (0.25), residues: 347 loop : -0.74 (0.19), residues: 1169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 255 time to evaluate : 3.852 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 outliers start: 5 outliers final: 1 residues processed: 255 average time/residue: 0.4956 time to fit residues: 211.9587 Evaluate side-chains 240 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 3.775 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3399 time to fit residues: 5.7594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 308 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 266 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 290 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.107746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.088403 restraints weight = 123523.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.090340 restraints weight = 62743.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.091558 restraints weight = 39423.702| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 29761 Z= 0.177 Angle : 0.631 15.495 40390 Z= 0.301 Chirality : 0.040 0.232 4594 Planarity : 0.004 0.063 5143 Dihedral : 4.167 50.161 3962 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer Outliers : 0.44 % 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: 0.88 (0.15), residues: 3559 helix: 1.72 (0.12), residues: 2051 sheet: -1.64 (0.25), residues: 356 loop : -0.69 (0.19), residues: 1152 =============================================================================== Job complete usr+sys time: 6247.34 seconds wall clock time: 115 minutes 20.98 seconds (6920.98 seconds total)