Starting phenix.real_space_refine on Tue Feb 20 23:43:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2024/7peb_13351_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2024/7peb_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_2024/7peb_13351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2024/7peb_13351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2024/7peb_13351_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/02_2024/7peb_13351_updated.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 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. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 14.93, per 1000 atoms: 0.51 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: 11.16 Conformation dependent library (CDL) restraints added in 5.1 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: 10.67 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: 13.68 Time building geometry restraints manager: 11.91 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: 16257 17.27 - 34.54: 1355 34.54 - 51.82: 288 51.82 - 69.09: 74 69.09 - 86.36: 18 Dihedral angle restraints: 17992 sinusoidal: 7263 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 17989 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 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: 6.380 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: 0.050 Extract box with map and model: 24.670 Check model and map are aligned: 0.490 Set scattering table: 0.250 Process input model: 77.900 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 : 13.932 86.360 11000 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 % Allowed : 6.14 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2023 HIS 0.007 0.001 HIS E1315 PHE 0.025 0.001 PHE A 610 TYR 0.012 0.001 TYR E 475 ARG 0.006 0.000 ARG A1161 *********************** 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 : 3.551 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: A 532 LYS cc_start: 0.2684 (OUTLIER) cc_final: 0.2381 (tptt) REVERT: A 780 ILE cc_start: 0.9036 (mt) cc_final: 0.8693 (pt) REVERT: A 805 LEU cc_start: 0.9192 (mt) cc_final: 0.8861 (mt) REVERT: A 808 VAL cc_start: 0.7858 (t) cc_final: 0.7538 (t) REVERT: A 1074 LEU cc_start: 0.9120 (mt) cc_final: 0.8499 (mp) REVERT: A 1362 GLU cc_start: 0.7978 (tt0) cc_final: 0.7754 (tp30) REVERT: A 1401 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 1455 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7928 (tp30) REVERT: A 1546 TYR cc_start: 0.8341 (m-80) cc_final: 0.7986 (m-80) REVERT: A 1673 LEU cc_start: 0.9278 (mt) cc_final: 0.9017 (mt) REVERT: A 1752 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8744 (tt) REVERT: A 1809 GLN cc_start: 0.8283 (mt0) cc_final: 0.7966 (tm-30) REVERT: A 1913 TYR cc_start: 0.7417 (m-80) cc_final: 0.7156 (m-80) REVERT: A 2021 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9052 (pt) REVERT: A 2051 LEU cc_start: 0.8674 (mt) cc_final: 0.8437 (pp) REVERT: A 2161 GLN cc_start: 0.8083 (tm130) cc_final: 0.7827 (tm-30) REVERT: A 2199 MET cc_start: 0.8769 (mmt) cc_final: 0.8410 (mmt) REVERT: C 155 TRP cc_start: 0.7411 (t60) cc_final: 0.7122 (t60) REVERT: C 197 TRP cc_start: 0.7049 (m100) cc_final: 0.6094 (m100) REVERT: C 315 VAL cc_start: 0.7012 (t) cc_final: 0.6658 (t) REVERT: E 89 ASP cc_start: 0.8756 (t0) cc_final: 0.8287 (t0) REVERT: E 585 TRP cc_start: 0.4133 (p90) cc_final: 0.3872 (p90) REVERT: E 831 MET cc_start: 0.6292 (tpp) cc_final: 0.5524 (tpt) REVERT: E 1131 TRP cc_start: 0.8028 (t-100) cc_final: 0.7374 (t-100) REVERT: E 1132 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7162 (mm-30) REVERT: E 1172 LEU cc_start: 0.8611 (tt) cc_final: 0.8181 (tp) REVERT: E 1181 ILE cc_start: 0.8423 (mp) cc_final: 0.8222 (mm) REVERT: E 1224 ASP cc_start: 0.7763 (m-30) cc_final: 0.7011 (p0) REVERT: E 1236 VAL cc_start: 0.6529 (t) cc_final: 0.6285 (t) REVERT: E 1309 PHE cc_start: 0.6166 (m-80) cc_final: 0.5484 (m-10) REVERT: I 373 VAL cc_start: 0.7865 (m) cc_final: 0.7202 (t) REVERT: I 405 GLU cc_start: 0.6879 (tt0) cc_final: 0.6482 (tt0) outliers start: 85 outliers final: 11 residues processed: 735 average time/residue: 0.4596 time to fit residues: 517.0788 Evaluate side-chains 347 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 333 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1652 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 1323 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 186 optimal weight: 0.0070 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: 0.9002 ------------------------------------------------------------------------------- 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 ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1741 GLN A1791 HIS A2292 ASN C 242 GLN E 151 ASN E 636 HIS E 642 HIS E1210 HIS ** 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: 0.7391 moved from start: 0.2821 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= 0.223 Angle : 0.651 12.055 40390 Z= 0.328 Chirality : 0.042 0.425 4594 Planarity : 0.005 0.059 5143 Dihedral : 5.111 54.386 4023 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.05 % Favored : 97.92 % Rotamer: Outliers : 2.47 % Allowed : 12.62 % Favored : 84.91 % 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: -0.37 (0.14), residues: 3559 helix: 0.71 (0.11), residues: 2071 sheet: -2.76 (0.24), residues: 342 loop : -1.04 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 27 HIS 0.008 0.001 HIS E1312 PHE 0.037 0.002 PHE A2421 TYR 0.021 0.002 TYR I 385 ARG 0.016 0.001 ARG C 270 *********************** 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 428 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 350 time to evaluate : 3.335 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: A 488 MET cc_start: 0.0139 (mmp) cc_final: -0.0147 (tpp) REVERT: A 548 MET cc_start: 0.4407 (mtt) cc_final: 0.3796 (mmt) REVERT: A 686 HIS cc_start: 0.8112 (m90) cc_final: 0.6697 (t-90) REVERT: A 772 MET cc_start: 0.7913 (tpt) cc_final: 0.7093 (tpt) REVERT: A 805 LEU cc_start: 0.9269 (mt) cc_final: 0.9034 (mt) REVERT: A 1477 MET cc_start: 0.8515 (tpp) cc_final: 0.8173 (tpp) REVERT: A 1546 TYR cc_start: 0.8333 (m-80) cc_final: 0.8108 (m-80) REVERT: A 1566 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8341 (ttpt) REVERT: A 1575 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8970 (tt) REVERT: A 1656 TYR cc_start: 0.8656 (t80) cc_final: 0.8428 (t80) REVERT: A 1673 LEU cc_start: 0.9260 (mt) cc_final: 0.8959 (mt) REVERT: A 1809 GLN cc_start: 0.8496 (mt0) cc_final: 0.8103 (tm-30) REVERT: A 1913 TYR cc_start: 0.7637 (m-80) cc_final: 0.7353 (m-80) REVERT: A 2057 MET cc_start: 0.9090 (tmm) cc_final: 0.8705 (tmm) REVERT: A 2161 GLN cc_start: 0.8072 (tm130) cc_final: 0.7731 (tm-30) REVERT: A 2199 MET cc_start: 0.8762 (mmt) cc_final: 0.8361 (mmt) REVERT: C 100 MET cc_start: 0.8719 (tmm) cc_final: 0.8364 (tmm) REVERT: C 273 MET cc_start: 0.7860 (ttm) cc_final: 0.7631 (ttm) REVERT: C 293 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6906 (mt) REVERT: E 28 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7721 (mm) REVERT: E 31 MET cc_start: 0.8227 (ppp) cc_final: 0.7271 (mmm) REVERT: E 89 ASP cc_start: 0.8757 (t0) cc_final: 0.8426 (t0) REVERT: E 342 LEU cc_start: 0.7815 (tp) cc_final: 0.7470 (tp) REVERT: E 378 MET cc_start: 0.8887 (mmm) cc_final: 0.8260 (mmm) REVERT: E 431 GLU cc_start: 0.7545 (pt0) cc_final: 0.7199 (tt0) REVERT: E 1010 ILE cc_start: 0.6770 (mm) cc_final: 0.6306 (tp) REVERT: E 1012 ARG cc_start: 0.5178 (mmp80) cc_final: 0.4418 (mmp80) REVERT: E 1073 MET cc_start: 0.6967 (mtp) cc_final: 0.6676 (mtm) REVERT: E 1132 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7311 (pt0) REVERT: E 1224 ASP cc_start: 0.7844 (m-30) cc_final: 0.7158 (p0) REVERT: E 1309 PHE cc_start: 0.6004 (m-80) cc_final: 0.5645 (m-10) REVERT: I 370 GLN cc_start: 0.8013 (mt0) cc_final: 0.7746 (mt0) outliers start: 78 outliers final: 46 residues processed: 405 average time/residue: 0.4391 time to fit residues: 286.8552 Evaluate side-chains 329 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 280 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1502 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 670 LEU Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1058 ASP Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain E residue 1325 ILE Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 chunk 275 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 332 optimal weight: 10.0000 chunk 358 optimal weight: 0.8980 chunk 295 optimal weight: 0.8980 chunk 329 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN ** A 807 GLN ** 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 ** 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: 0.7482 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29761 Z= 0.288 Angle : 0.662 10.619 40390 Z= 0.330 Chirality : 0.043 0.274 4594 Planarity : 0.005 0.064 5143 Dihedral : 4.924 55.824 4008 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 3.23 % Allowed : 12.65 % Favored : 84.12 % 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: 0.10 (0.14), residues: 3559 helix: 1.16 (0.11), residues: 2041 sheet: -2.39 (0.25), residues: 328 loop : -1.03 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E1131 HIS 0.006 0.001 HIS E1315 PHE 0.030 0.002 PHE A2421 TYR 0.022 0.002 TYR A 451 ARG 0.005 0.001 ARG C 25 *********************** 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 402 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 300 time to evaluate : 2.969 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: A 439 LEU cc_start: -0.2733 (OUTLIER) cc_final: -0.3504 (mt) REVERT: A 532 LYS cc_start: 0.2514 (OUTLIER) cc_final: 0.2279 (tptp) REVERT: A 548 MET cc_start: 0.4355 (mtt) cc_final: 0.3850 (mmm) REVERT: A 686 HIS cc_start: 0.8329 (m90) cc_final: 0.6895 (t-90) REVERT: A 700 LEU cc_start: 0.4553 (OUTLIER) cc_final: 0.4279 (tt) REVERT: A 772 MET cc_start: 0.8021 (tpt) cc_final: 0.7395 (tmm) REVERT: A 827 MET cc_start: 0.8689 (tmm) cc_final: 0.8129 (tmm) REVERT: A 828 LEU cc_start: 0.9133 (mt) cc_final: 0.8797 (mp) REVERT: A 1477 MET cc_start: 0.8619 (tpp) cc_final: 0.8312 (tpp) REVERT: A 1546 TYR cc_start: 0.8396 (m-80) cc_final: 0.8142 (m-80) REVERT: A 1575 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9045 (tt) REVERT: A 1673 LEU cc_start: 0.9275 (mt) cc_final: 0.8948 (mt) REVERT: A 1809 GLN cc_start: 0.8574 (mt0) cc_final: 0.8164 (tm-30) REVERT: A 2076 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8333 (ttp-110) REVERT: A 2080 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8283 (tp30) REVERT: C 100 MET cc_start: 0.8860 (tmm) cc_final: 0.8363 (tmm) REVERT: E 89 ASP cc_start: 0.8804 (t0) cc_final: 0.8321 (t0) REVERT: E 342 LEU cc_start: 0.7887 (tp) cc_final: 0.7580 (tp) REVERT: E 378 MET cc_start: 0.8966 (mmm) cc_final: 0.8484 (mmm) REVERT: E 431 GLU cc_start: 0.7572 (pt0) cc_final: 0.7302 (tt0) REVERT: E 450 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8667 (mm) REVERT: E 659 VAL cc_start: 0.7367 (t) cc_final: 0.7124 (p) REVERT: E 961 ASP cc_start: 0.8091 (t70) cc_final: 0.7797 (t0) REVERT: E 1175 ASP cc_start: 0.4366 (t0) cc_final: 0.3983 (t0) REVERT: E 1218 SER cc_start: 0.7136 (t) cc_final: 0.6924 (m) REVERT: E 1309 PHE cc_start: 0.6090 (m-80) cc_final: 0.5584 (m-10) REVERT: I 404 MET cc_start: 0.4797 (mmm) cc_final: 0.4545 (mmm) outliers start: 102 outliers final: 56 residues processed: 376 average time/residue: 0.4148 time to fit residues: 257.8941 Evaluate side-chains 329 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 267 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1266 GLN Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1058 ASP Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1156 MET Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain E residue 1325 ILE Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 407 LEU 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: 2.9990 chunk 172 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 352 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 95 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN A1266 GLN A1494 HIS ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1989 ASN A2410 HIS ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS E1062 ASN ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29761 Z= 0.224 Angle : 0.604 10.377 40390 Z= 0.299 Chirality : 0.041 0.220 4594 Planarity : 0.004 0.065 5143 Dihedral : 4.795 56.174 4006 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 3.19 % Allowed : 13.44 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3559 helix: 1.39 (0.11), residues: 2038 sheet: -2.19 (0.25), residues: 341 loop : -0.99 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1916 HIS 0.011 0.001 HIS A2410 PHE 0.026 0.001 PHE A2421 TYR 0.028 0.001 TYR A 451 ARG 0.004 0.000 ARG A1811 *********************** 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 386 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 285 time to evaluate : 3.448 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: A 439 LEU cc_start: -0.3004 (OUTLIER) cc_final: -0.3255 (mt) REVERT: A 532 LYS cc_start: 0.2527 (OUTLIER) cc_final: 0.2312 (tptp) REVERT: A 548 MET cc_start: 0.4023 (mtt) cc_final: 0.3475 (mmt) REVERT: A 686 HIS cc_start: 0.8384 (m90) cc_final: 0.7298 (m-70) REVERT: A 700 LEU cc_start: 0.4269 (OUTLIER) cc_final: 0.3927 (tt) REVERT: A 1507 GLU cc_start: 0.8773 (mp0) cc_final: 0.8563 (pm20) REVERT: A 1571 LEU cc_start: 0.9412 (tp) cc_final: 0.9185 (tt) REVERT: A 1575 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9166 (tp) REVERT: A 1673 LEU cc_start: 0.9293 (mt) cc_final: 0.8962 (mt) REVERT: A 2031 LEU cc_start: 0.8766 (mp) cc_final: 0.8341 (tt) REVERT: A 2076 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8410 (ttp-110) REVERT: A 2080 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: A 2199 MET cc_start: 0.8641 (mmt) cc_final: 0.8298 (mmt) REVERT: C 100 MET cc_start: 0.8809 (tmm) cc_final: 0.8308 (tmm) REVERT: E 28 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7860 (mm) REVERT: E 89 ASP cc_start: 0.8846 (t0) cc_final: 0.8326 (t0) REVERT: E 237 MET cc_start: 0.7593 (pmm) cc_final: 0.7334 (pmm) REVERT: E 342 LEU cc_start: 0.7926 (tp) cc_final: 0.7691 (tp) REVERT: E 378 MET cc_start: 0.8927 (mmm) cc_final: 0.8503 (mmm) REVERT: E 431 GLU cc_start: 0.7550 (pt0) cc_final: 0.7226 (tt0) REVERT: E 450 LEU cc_start: 0.8936 (mm) cc_final: 0.8639 (mm) REVERT: E 602 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7261 (tp30) REVERT: E 961 ASP cc_start: 0.8073 (t70) cc_final: 0.7739 (t70) REVERT: E 1172 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8168 (mp) REVERT: E 1309 PHE cc_start: 0.6053 (m-80) cc_final: 0.5568 (m-10) outliers start: 101 outliers final: 62 residues processed: 356 average time/residue: 0.4061 time to fit residues: 238.3052 Evaluate side-chains 327 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 258 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1385 GLU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1632 ASP Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1058 ASP Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1172 LEU Chi-restraints excluded: chain E residue 1207 TYR Chi-restraints excluded: chain E residue 1236 VAL Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 0.7980 chunk 200 optimal weight: 0.4980 chunk 5 optimal weight: 20.0000 chunk 262 optimal weight: 0.0980 chunk 145 optimal weight: 0.9980 chunk 301 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 180 optimal weight: 0.9980 chunk 316 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1049 GLN ** A1716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1797 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29761 Z= 0.176 Angle : 0.577 9.935 40390 Z= 0.282 Chirality : 0.040 0.193 4594 Planarity : 0.004 0.064 5143 Dihedral : 4.655 56.364 4006 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.56 % Allowed : 14.83 % Favored : 82.61 % 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: 0.59 (0.14), residues: 3559 helix: 1.60 (0.12), residues: 2034 sheet: -2.03 (0.25), residues: 346 loop : -0.94 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1916 HIS 0.009 0.001 HIS E1210 PHE 0.023 0.001 PHE A2421 TYR 0.025 0.001 TYR A 451 ARG 0.004 0.000 ARG E1237 *********************** 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 356 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 275 time to evaluate : 3.592 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: A 548 MET cc_start: 0.3846 (mtt) cc_final: 0.3361 (mmt) REVERT: A 686 HIS cc_start: 0.8344 (m90) cc_final: 0.7316 (m-70) REVERT: A 700 LEU cc_start: 0.4657 (OUTLIER) cc_final: 0.4448 (tt) REVERT: A 766 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7924 (ptt180) REVERT: A 1546 TYR cc_start: 0.8402 (m-80) cc_final: 0.8159 (m-80) REVERT: A 1571 LEU cc_start: 0.9386 (tp) cc_final: 0.9159 (tt) REVERT: A 1575 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9128 (tp) REVERT: A 1673 LEU cc_start: 0.9312 (mt) cc_final: 0.8970 (mt) REVERT: A 2199 MET cc_start: 0.8665 (mmt) cc_final: 0.8297 (mmt) REVERT: C 100 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8386 (ppp) REVERT: C 255 MET cc_start: 0.7858 (tpp) cc_final: 0.7565 (tpp) REVERT: E 72 PRO cc_start: 0.6435 (Cg_exo) cc_final: 0.6136 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8832 (t0) cc_final: 0.8391 (t0) REVERT: E 237 MET cc_start: 0.7639 (pmm) cc_final: 0.7303 (pmm) REVERT: E 342 LEU cc_start: 0.7836 (tp) cc_final: 0.7630 (tp) REVERT: E 378 MET cc_start: 0.8880 (mmm) cc_final: 0.8461 (mmm) REVERT: E 411 GLU cc_start: 0.2332 (OUTLIER) cc_final: 0.1705 (tt0) REVERT: E 431 GLU cc_start: 0.7548 (pt0) cc_final: 0.7202 (tt0) REVERT: E 450 LEU cc_start: 0.8926 (mm) cc_final: 0.8627 (mm) REVERT: E 602 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7217 (tp30) REVERT: E 961 ASP cc_start: 0.8007 (t70) cc_final: 0.7711 (t0) REVERT: E 1156 MET cc_start: 0.7186 (mmm) cc_final: 0.6497 (mmt) REVERT: E 1172 LEU cc_start: 0.8637 (tt) cc_final: 0.8062 (mp) REVERT: E 1276 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.5542 (t80) REVERT: E 1309 PHE cc_start: 0.6200 (m-80) cc_final: 0.5679 (m-10) REVERT: I 391 LEU cc_start: 0.8955 (mt) cc_final: 0.8326 (tp) outliers start: 81 outliers final: 49 residues processed: 335 average time/residue: 0.4103 time to fit residues: 225.1106 Evaluate side-chains 314 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 259 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 659 VAL Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1276 PHE Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 0.9990 chunk 317 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 207 optimal weight: 0.5980 chunk 87 optimal weight: 0.0050 chunk 353 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1797 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: 0.7464 moved from start: 0.4333 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= 0.171 Angle : 0.569 9.916 40390 Z= 0.277 Chirality : 0.040 0.255 4594 Planarity : 0.004 0.063 5143 Dihedral : 4.591 56.572 4006 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 2.72 % Allowed : 15.46 % Favored : 81.82 % 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 (0.14), residues: 3559 helix: 1.69 (0.12), residues: 2035 sheet: -1.98 (0.25), residues: 343 loop : -0.87 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E1131 HIS 0.005 0.001 HIS C 161 PHE 0.022 0.001 PHE A 610 TYR 0.026 0.001 TYR A 451 ARG 0.012 0.000 ARG A1811 *********************** 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 354 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 268 time to evaluate : 3.221 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: A 439 LEU cc_start: -0.2443 (OUTLIER) cc_final: -0.2745 (mt) REVERT: A 548 MET cc_start: 0.4009 (mtt) cc_final: 0.3513 (mmt) REVERT: A 686 HIS cc_start: 0.8349 (m90) cc_final: 0.7334 (m-70) REVERT: A 766 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7939 (ptt180) REVERT: A 1477 MET cc_start: 0.8639 (tpp) cc_final: 0.8249 (tpp) REVERT: A 1546 TYR cc_start: 0.8412 (m-80) cc_final: 0.8089 (m-80) REVERT: A 1571 LEU cc_start: 0.9365 (tp) cc_final: 0.9145 (tt) REVERT: A 1575 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9088 (tt) REVERT: A 1590 MET cc_start: 0.8154 (mtp) cc_final: 0.7856 (mtp) REVERT: A 1601 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7369 (mt-10) REVERT: A 1673 LEU cc_start: 0.9283 (mt) cc_final: 0.8915 (mt) REVERT: A 2080 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: A 2199 MET cc_start: 0.8661 (mmt) cc_final: 0.8294 (mmt) REVERT: A 2327 MET cc_start: 0.8239 (mmm) cc_final: 0.7975 (tpt) REVERT: C 100 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8345 (ppp) REVERT: C 255 MET cc_start: 0.7936 (tpp) cc_final: 0.7585 (tpp) REVERT: E 72 PRO cc_start: 0.6432 (Cg_exo) cc_final: 0.6136 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8792 (t0) cc_final: 0.8377 (t0) REVERT: E 378 MET cc_start: 0.8850 (mmm) cc_final: 0.8386 (mmm) REVERT: E 411 GLU cc_start: 0.2175 (OUTLIER) cc_final: 0.1773 (tp30) REVERT: E 431 GLU cc_start: 0.7526 (pt0) cc_final: 0.7288 (tt0) REVERT: E 450 LEU cc_start: 0.8934 (mm) cc_final: 0.8558 (mm) REVERT: E 602 GLU cc_start: 0.7950 (mm-30) cc_final: 0.6833 (tp30) REVERT: E 961 ASP cc_start: 0.8004 (t70) cc_final: 0.7729 (t0) REVERT: E 1018 PHE cc_start: 0.6339 (p90) cc_final: 0.5706 (p90) REVERT: E 1076 LEU cc_start: 0.8872 (mt) cc_final: 0.8653 (mt) REVERT: E 1110 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8173 (p) REVERT: E 1156 MET cc_start: 0.7007 (mmm) cc_final: 0.6438 (mmt) REVERT: E 1172 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7868 (mp) REVERT: E 1276 PHE cc_start: 0.6388 (OUTLIER) cc_final: 0.5641 (t80) REVERT: E 1309 PHE cc_start: 0.6200 (m-80) cc_final: 0.5651 (m-10) REVERT: I 391 LEU cc_start: 0.8957 (mt) cc_final: 0.8387 (tp) outliers start: 86 outliers final: 58 residues processed: 334 average time/residue: 0.4207 time to fit residues: 231.9667 Evaluate side-chains 317 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 250 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1797 ASN Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 659 VAL Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1110 THR Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1172 LEU Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1276 PHE Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 0.1980 chunk 39 optimal weight: 0.2980 chunk 201 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 297 optimal weight: 0.7980 chunk 197 optimal weight: 0.3980 chunk 351 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1045 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** E 242 GLN ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29761 Z= 0.161 Angle : 0.567 10.341 40390 Z= 0.275 Chirality : 0.040 0.245 4594 Planarity : 0.004 0.063 5143 Dihedral : 4.527 56.652 4006 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 2.25 % Allowed : 16.41 % Favored : 81.34 % 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: 0.80 (0.14), residues: 3559 helix: 1.73 (0.12), residues: 2037 sheet: -1.88 (0.26), residues: 342 loop : -0.79 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E1131 HIS 0.005 0.001 HIS C 161 PHE 0.022 0.001 PHE A 610 TYR 0.022 0.001 TYR A 451 ARG 0.008 0.000 ARG A1811 *********************** 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 332 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 261 time to evaluate : 3.305 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: A 439 LEU cc_start: -0.2475 (OUTLIER) cc_final: -0.2869 (mt) REVERT: A 548 MET cc_start: 0.3847 (mtt) cc_final: 0.3408 (mmt) REVERT: A 686 HIS cc_start: 0.8339 (m90) cc_final: 0.7336 (m-70) REVERT: A 727 MET cc_start: 0.5579 (ppp) cc_final: 0.5370 (ppp) REVERT: A 766 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7975 (ptt180) REVERT: A 772 MET cc_start: 0.8108 (tpt) cc_final: 0.7451 (tpp) REVERT: A 1546 TYR cc_start: 0.8313 (m-80) cc_final: 0.8068 (m-80) REVERT: A 1571 LEU cc_start: 0.9341 (tp) cc_final: 0.9116 (tt) REVERT: A 1574 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7786 (tt0) REVERT: A 1575 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9084 (tt) REVERT: A 1590 MET cc_start: 0.8216 (mtp) cc_final: 0.7936 (mtp) REVERT: A 1673 LEU cc_start: 0.9267 (mt) cc_final: 0.8907 (mt) REVERT: A 2080 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: A 2199 MET cc_start: 0.8630 (mmt) cc_final: 0.8248 (mmt) REVERT: C 100 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8311 (ppp) REVERT: C 255 MET cc_start: 0.7931 (tpp) cc_final: 0.7537 (tpp) REVERT: E 72 PRO cc_start: 0.6863 (Cg_exo) cc_final: 0.6591 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8754 (t0) cc_final: 0.8276 (t0) REVERT: E 378 MET cc_start: 0.8805 (mmm) cc_final: 0.8323 (mmm) REVERT: E 411 GLU cc_start: 0.2351 (OUTLIER) cc_final: 0.1680 (tt0) REVERT: E 431 GLU cc_start: 0.7512 (pt0) cc_final: 0.7272 (tt0) REVERT: E 450 LEU cc_start: 0.8919 (mm) cc_final: 0.8548 (mm) REVERT: E 602 GLU cc_start: 0.7834 (mm-30) cc_final: 0.6873 (tp30) REVERT: E 961 ASP cc_start: 0.7975 (t70) cc_final: 0.7684 (t0) REVERT: E 1012 ARG cc_start: 0.5185 (mmp80) cc_final: 0.4515 (mmp80) REVERT: E 1076 LEU cc_start: 0.8899 (mt) cc_final: 0.8557 (mt) REVERT: E 1110 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8137 (p) REVERT: E 1172 LEU cc_start: 0.8490 (tt) cc_final: 0.7840 (mp) REVERT: E 1309 PHE cc_start: 0.6187 (m-80) cc_final: 0.5592 (m-10) REVERT: I 391 LEU cc_start: 0.8935 (mt) cc_final: 0.8390 (tp) REVERT: I 401 MET cc_start: 0.8392 (ppp) cc_final: 0.8142 (ppp) outliers start: 71 outliers final: 46 residues processed: 316 average time/residue: 0.3866 time to fit residues: 204.1717 Evaluate side-chains 301 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 248 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 659 VAL Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1110 THR Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 0.5980 chunk 140 optimal weight: 0.5980 chunk 210 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 239 optimal weight: 0.1980 chunk 173 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 276 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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** A1797 ASN ** 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** E1062 ASN ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 370 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29761 Z= 0.160 Angle : 0.582 10.861 40390 Z= 0.280 Chirality : 0.040 0.236 4594 Planarity : 0.004 0.063 5143 Dihedral : 4.481 56.751 4006 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 2.21 % Allowed : 16.73 % Favored : 81.06 % 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: 0.88 (0.15), residues: 3559 helix: 1.78 (0.12), residues: 2040 sheet: -1.74 (0.25), residues: 354 loop : -0.77 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP E1131 HIS 0.009 0.001 HIS A2355 PHE 0.022 0.001 PHE A 610 TYR 0.022 0.001 TYR A2125 ARG 0.007 0.000 ARG A1811 *********************** 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 326 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 256 time to evaluate : 3.484 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: A 439 LEU cc_start: -0.2577 (OUTLIER) cc_final: -0.2951 (mt) REVERT: A 548 MET cc_start: 0.3834 (mtt) cc_final: 0.3403 (mmt) REVERT: A 686 HIS cc_start: 0.8343 (m90) cc_final: 0.7357 (m-70) REVERT: A 772 MET cc_start: 0.8206 (tpt) cc_final: 0.7537 (tpp) REVERT: A 1571 LEU cc_start: 0.9344 (tp) cc_final: 0.9115 (tt) REVERT: A 1575 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9064 (tt) REVERT: A 1590 MET cc_start: 0.8247 (mtp) cc_final: 0.7954 (mtp) REVERT: A 1673 LEU cc_start: 0.9250 (mt) cc_final: 0.8888 (mt) REVERT: A 1930 ILE cc_start: 0.8967 (tp) cc_final: 0.8685 (tt) REVERT: A 2080 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: A 2199 MET cc_start: 0.8620 (mmt) cc_final: 0.8242 (mmt) REVERT: C 100 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8244 (tmm) REVERT: C 255 MET cc_start: 0.7988 (tpp) cc_final: 0.7568 (tpp) REVERT: E 31 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.7467 (mmt) REVERT: E 72 PRO cc_start: 0.6863 (Cg_exo) cc_final: 0.6590 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8703 (t0) cc_final: 0.8215 (t0) REVERT: E 237 MET cc_start: 0.7404 (pmm) cc_final: 0.7125 (pmm) REVERT: E 411 GLU cc_start: 0.2342 (OUTLIER) cc_final: 0.1896 (tp30) REVERT: E 450 LEU cc_start: 0.8929 (mm) cc_final: 0.8572 (mm) REVERT: E 602 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7164 (tp30) REVERT: E 961 ASP cc_start: 0.7962 (t70) cc_final: 0.7686 (t0) REVERT: E 1012 ARG cc_start: 0.5165 (mmp80) cc_final: 0.4509 (mmp80) REVERT: E 1076 LEU cc_start: 0.9137 (mt) cc_final: 0.8873 (mt) REVERT: E 1110 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8173 (p) REVERT: E 1172 LEU cc_start: 0.8439 (tt) cc_final: 0.7726 (mp) REVERT: E 1276 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5515 (t80) REVERT: I 370 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: I 391 LEU cc_start: 0.8912 (mt) cc_final: 0.8390 (tp) REVERT: I 401 MET cc_start: 0.8426 (ppp) cc_final: 0.8064 (ppp) outliers start: 70 outliers final: 47 residues processed: 309 average time/residue: 0.4024 time to fit residues: 206.6099 Evaluate side-chains 300 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 244 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2418 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 659 VAL Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1110 THR Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1276 PHE Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 1.9990 chunk 337 optimal weight: 4.9990 chunk 307 optimal weight: 0.0470 chunk 327 optimal weight: 0.6980 chunk 336 optimal weight: 0.3980 chunk 197 optimal weight: 0.1980 chunk 142 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 310 optimal weight: 3.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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** ** E 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29761 Z= 0.162 Angle : 0.602 11.419 40390 Z= 0.290 Chirality : 0.040 0.317 4594 Planarity : 0.004 0.063 5143 Dihedral : 4.400 56.870 4004 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 2.12 % Allowed : 17.17 % Favored : 80.71 % 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: 0.91 (0.15), residues: 3559 helix: 1.80 (0.12), residues: 2035 sheet: -1.61 (0.26), residues: 351 loop : -0.76 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E1131 HIS 0.011 0.001 HIS C 94 PHE 0.022 0.001 PHE A 610 TYR 0.020 0.001 TYR A 451 ARG 0.004 0.000 ARG A1811 *********************** 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 315 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 248 time to evaluate : 3.211 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: A 686 HIS cc_start: 0.8344 (m90) cc_final: 0.7356 (m-70) REVERT: A 1151 TYR cc_start: 0.7582 (m-80) cc_final: 0.7122 (m-80) REVERT: A 1571 LEU cc_start: 0.9336 (tp) cc_final: 0.9130 (tt) REVERT: A 1575 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9036 (tt) REVERT: A 1930 ILE cc_start: 0.8974 (tp) cc_final: 0.8688 (tt) REVERT: A 2080 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8249 (tp30) REVERT: A 2199 MET cc_start: 0.8602 (mmt) cc_final: 0.8227 (mmt) REVERT: C 100 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8434 (ppp) REVERT: C 255 MET cc_start: 0.8007 (tpp) cc_final: 0.7581 (tpp) REVERT: E 31 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.7466 (mmp) REVERT: E 72 PRO cc_start: 0.6860 (Cg_exo) cc_final: 0.6581 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8692 (t0) cc_final: 0.8202 (t0) REVERT: E 93 MET cc_start: 0.6326 (ppp) cc_final: 0.6112 (ppp) REVERT: E 237 MET cc_start: 0.7457 (pmm) cc_final: 0.7151 (pmm) REVERT: E 378 MET cc_start: 0.8637 (mmm) cc_final: 0.8345 (mmm) REVERT: E 411 GLU cc_start: 0.2332 (OUTLIER) cc_final: 0.1882 (tp30) REVERT: E 450 LEU cc_start: 0.8937 (mm) cc_final: 0.8569 (mm) REVERT: E 602 GLU cc_start: 0.7986 (mm-30) cc_final: 0.6966 (tp30) REVERT: E 647 MET cc_start: 0.6329 (tpp) cc_final: 0.5717 (tpp) REVERT: E 961 ASP cc_start: 0.7966 (t70) cc_final: 0.7673 (t0) REVERT: E 1012 ARG cc_start: 0.5204 (mmp80) cc_final: 0.4568 (mmp80) REVERT: E 1110 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8169 (p) REVERT: E 1172 LEU cc_start: 0.8435 (tt) cc_final: 0.7709 (mp) REVERT: E 1276 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5291 (t80) REVERT: I 370 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8321 (pm20) REVERT: I 391 LEU cc_start: 0.8905 (mt) cc_final: 0.8392 (tp) REVERT: I 401 MET cc_start: 0.8460 (ppp) cc_final: 0.8085 (ppp) outliers start: 67 outliers final: 50 residues processed: 301 average time/residue: 0.4010 time to fit residues: 201.6328 Evaluate side-chains 300 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 242 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1701 MET Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2418 LEU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 659 VAL Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1110 THR Chi-restraints excluded: chain E residue 1131 TRP Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1276 PHE Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 382 HIS Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 2.9990 chunk 215 optimal weight: 0.0870 chunk 346 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 164 optimal weight: 0.0570 chunk 240 optimal weight: 0.9990 chunk 363 optimal weight: 1.9990 chunk 334 optimal weight: 6.9990 chunk 289 optimal weight: 0.0040 chunk 30 optimal weight: 0.5980 chunk 223 optimal weight: 0.4980 overall best weight: 0.2488 ------------------------------------------------------------------------------- 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** ** E 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29761 Z= 0.156 Angle : 0.601 11.904 40390 Z= 0.288 Chirality : 0.039 0.178 4594 Planarity : 0.004 0.063 5143 Dihedral : 4.359 56.592 4004 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 1.93 % Allowed : 17.52 % Favored : 80.55 % 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: 0.91 (0.15), residues: 3559 helix: 1.79 (0.12), residues: 2043 sheet: -1.48 (0.26), residues: 350 loop : -0.80 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 99 HIS 0.004 0.001 HIS C 161 PHE 0.022 0.001 PHE A 610 TYR 0.029 0.001 TYR E 605 ARG 0.004 0.000 ARG A1811 ********************** 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 319 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 258 time to evaluate : 3.022 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: A 548 MET cc_start: 0.3960 (mtt) cc_final: 0.3519 (mmt) REVERT: A 686 HIS cc_start: 0.8296 (m90) cc_final: 0.7347 (m-70) REVERT: A 772 MET cc_start: 0.7914 (tpt) cc_final: 0.7514 (tpp) REVERT: A 1481 MET cc_start: 0.7881 (mmt) cc_final: 0.7568 (mmt) REVERT: A 1546 TYR cc_start: 0.8204 (m-80) cc_final: 0.7990 (m-80) REVERT: A 1571 LEU cc_start: 0.9323 (tp) cc_final: 0.9115 (tt) REVERT: A 1575 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9003 (tt) REVERT: A 1930 ILE cc_start: 0.8947 (tp) cc_final: 0.8666 (tt) REVERT: A 2080 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: A 2199 MET cc_start: 0.8577 (mmt) cc_final: 0.8197 (mmt) REVERT: C 100 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8478 (ppp) REVERT: C 255 MET cc_start: 0.8003 (tpp) cc_final: 0.7565 (tpp) REVERT: C 273 MET cc_start: 0.7559 (ptm) cc_final: 0.7324 (ptm) REVERT: E 31 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.7455 (mmp) REVERT: E 72 PRO cc_start: 0.6874 (Cg_exo) cc_final: 0.6589 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8669 (t0) cc_final: 0.8167 (t0) REVERT: E 237 MET cc_start: 0.7387 (pmm) cc_final: 0.7056 (pmm) REVERT: E 411 GLU cc_start: 0.2147 (OUTLIER) cc_final: 0.1783 (tp30) REVERT: E 450 LEU cc_start: 0.8945 (mm) cc_final: 0.8653 (mm) REVERT: E 602 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6682 (tp30) REVERT: E 605 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6922 (t80) REVERT: E 647 MET cc_start: 0.6364 (tpp) cc_final: 0.5605 (tpt) REVERT: E 961 ASP cc_start: 0.7965 (t70) cc_final: 0.7665 (t0) REVERT: E 1012 ARG cc_start: 0.5135 (mmp80) cc_final: 0.4517 (mmp80) REVERT: E 1172 LEU cc_start: 0.8368 (tt) cc_final: 0.7677 (mp) REVERT: I 328 ARG cc_start: 0.7788 (tmm160) cc_final: 0.7562 (tmm-80) REVERT: I 370 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8508 (pm20) REVERT: I 391 LEU cc_start: 0.8878 (mt) cc_final: 0.8368 (tp) REVERT: I 401 MET cc_start: 0.8466 (ppp) cc_final: 0.8091 (ppp) outliers start: 61 outliers final: 49 residues processed: 303 average time/residue: 0.4030 time to fit residues: 201.8873 Evaluate side-chains 303 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 247 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1515 MET Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1701 MET Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2080 GLU Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2418 LEU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 605 TYR Chi-restraints excluded: chain E residue 659 VAL Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1076 LEU Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1131 TRP Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 382 HIS Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 266 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 290 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** A1525 GLN A1744 HIS ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 370 GLN ** 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 = 0.4215 r_free = 0.4215 target = 0.108225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.089780 restraints weight = 123889.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.092950 restraints weight = 69411.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.092584 restraints weight = 39614.220| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29761 Z= 0.186 Angle : 0.610 11.686 40390 Z= 0.294 Chirality : 0.040 0.173 4594 Planarity : 0.004 0.064 5143 Dihedral : 4.396 58.398 4004 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 2.09 % Allowed : 17.55 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3559 helix: 1.81 (0.12), residues: 2038 sheet: -1.41 (0.27), residues: 351 loop : -0.77 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 99 HIS 0.005 0.001 HIS C 161 PHE 0.022 0.001 PHE A 610 TYR 0.020 0.001 TYR A 451 ARG 0.006 0.000 ARG A2076 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6515.22 seconds wall clock time: 119 minutes 57.31 seconds (7197.31 seconds total)