Starting phenix.real_space_refine on Sun Jun 29 10:17:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vh5_43235/06_2025/8vh5_43235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vh5_43235/06_2025/8vh5_43235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vh5_43235/06_2025/8vh5_43235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vh5_43235/06_2025/8vh5_43235.map" model { file = "/net/cci-nas-00/data/ceres_data/8vh5_43235/06_2025/8vh5_43235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vh5_43235/06_2025/8vh5_43235.cif" } resolution = 4.0 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= 0.003 sd= 0.066 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 21724 2.51 5 N 5738 2.21 5 O 6082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33744 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 15573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2221, 15573 Classifications: {'peptide': 2221} Incomplete info: {'truncation_to_alanine': 580} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 2135} Chain breaks: 21 Unresolved non-hydrogen bonds: 2116 Unresolved non-hydrogen angles: 2560 Unresolved non-hydrogen dihedrals: 1751 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 42, 'HIS:plan': 17, 'TYR:plan': 6, 'ASN:plan1': 37, 'TRP:plan': 1, 'ASP:plan': 45, 'PHE:plan': 10, 'GLU:plan': 105, 'ARG:plan': 45} Unresolved non-hydrogen planarities: 1255 Chain: "B" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1200 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 15587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2221, 15587 Classifications: {'peptide': 2221} Incomplete info: {'truncation_to_alanine': 575} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 2135} Chain breaks: 21 Unresolved non-hydrogen bonds: 2103 Unresolved non-hydrogen angles: 2547 Unresolved non-hydrogen dihedrals: 1740 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 42, 'HIS:plan': 17, 'TYR:plan': 6, 'ASN:plan1': 36, 'TRP:plan': 1, 'ASP:plan': 45, 'PHE:plan': 11, 'GLU:plan': 104, 'ARG:plan': 45} Unresolved non-hydrogen planarities: 1254 Chain: "D" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1200 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.32, per 1000 atoms: 0.60 Number of scatterers: 33744 At special positions: 0 Unit cell: (145.844, 181.944, 203.604, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 182 16.00 P 16 15.00 Mg 2 11.99 O 6082 8.00 N 5738 7.00 C 21724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.51 Conformation dependent library (CDL) restraints added in 7.9 seconds 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9136 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 42 sheets defined 46.4% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.05 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.527A pdb=" N PHE A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 removed outlier: 4.266A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 92 Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.441A pdb=" N MET A 96 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.862A pdb=" N LEU A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.626A pdb=" N VAL A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 235 through 243 removed outlier: 3.803A pdb=" N GLU A 240 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.621A pdb=" N THR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 4.110A pdb=" N ILE A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.190A pdb=" N HIS A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.511A pdb=" N TYR A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 324 removed outlier: 4.191A pdb=" N SER A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 4.292A pdb=" N TRP A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.714A pdb=" N LEU A 384 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 408 removed outlier: 3.513A pdb=" N GLU A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.543A pdb=" N PHE A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 439 removed outlier: 3.900A pdb=" N ILE A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.601A pdb=" N ASN A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 470 removed outlier: 3.614A pdb=" N ALA A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 494 removed outlier: 3.823A pdb=" N MET A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.526A pdb=" N GLN A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 526 through 540 Processing helix chain 'A' and resid 541 through 553 removed outlier: 3.567A pdb=" N LEU A 545 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 4.598A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 585 through 596 removed outlier: 3.521A pdb=" N VAL A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 removed outlier: 3.612A pdb=" N SER A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 641 through 659 removed outlier: 3.778A pdb=" N GLN A 645 " --> pdb=" O VAL A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 671 through 685 removed outlier: 3.658A pdb=" N ILE A 683 " --> pdb=" O MET A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 704 removed outlier: 3.728A pdb=" N MET A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.577A pdb=" N LYS A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 719 " --> pdb=" O ARG A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 732 Processing helix chain 'A' and resid 744 through 751 Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.619A pdb=" N SER A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 783 through 795 Processing helix chain 'A' and resid 798 through 801 removed outlier: 3.610A pdb=" N ASN A 801 " --> pdb=" O VAL A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 801' Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 996 through 1001 removed outlier: 4.328A pdb=" N ALA A 999 " --> pdb=" O ASP A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1011 Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.613A pdb=" N CYS A1031 " --> pdb=" O PRO A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1057 removed outlier: 3.707A pdb=" N MET A1057 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1195 removed outlier: 3.716A pdb=" N ASN A1194 " --> pdb=" O ALA A1191 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A1195 " --> pdb=" O ILE A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1245 Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.955A pdb=" N GLY A1265 " --> pdb=" O PRO A1262 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A1266 " --> pdb=" O GLU A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 removed outlier: 3.532A pdb=" N LYS A1290 " --> pdb=" O GLU A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1328 Processing helix chain 'A' and resid 1348 through 1355 Processing helix chain 'A' and resid 1398 through 1402 Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 3.865A pdb=" N MET A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1466 through 1474 removed outlier: 3.936A pdb=" N THR A1470 " --> pdb=" O MET A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1510 removed outlier: 3.576A pdb=" N ASN A1510 " --> pdb=" O ASN A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1524 through 1541 removed outlier: 3.930A pdb=" N VAL A1528 " --> pdb=" O PRO A1524 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS A1539 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1559 Processing helix chain 'A' and resid 1568 through 1579 Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 4.074A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1656 Processing helix chain 'A' and resid 1703 through 1711 Processing helix chain 'A' and resid 1770 through 1792 Processing helix chain 'A' and resid 1829 through 1835 Processing helix chain 'A' and resid 1852 through 1856 Processing helix chain 'A' and resid 1865 through 1869 removed outlier: 3.577A pdb=" N ILE A1868 " --> pdb=" O PRO A1865 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A1869 " --> pdb=" O ARG A1866 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1865 through 1869' Processing helix chain 'A' and resid 1881 through 1886 removed outlier: 3.731A pdb=" N LEU A1885 " --> pdb=" O PRO A1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1926 removed outlier: 3.759A pdb=" N VAL A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A1926 " --> pdb=" O VAL A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 removed outlier: 3.634A pdb=" N LEU A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1988 Processing helix chain 'A' and resid 2017 through 2021 removed outlier: 3.654A pdb=" N ILE A2020 " --> pdb=" O ASP A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2052 through 2069 removed outlier: 3.928A pdb=" N VAL A2056 " --> pdb=" O GLN A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2079 removed outlier: 3.785A pdb=" N LYS A2078 " --> pdb=" O VAL A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2084 Processing helix chain 'A' and resid 2085 through 2089 removed outlier: 4.002A pdb=" N GLN A2089 " --> pdb=" O LEU A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 3.711A pdb=" N LEU A2110 " --> pdb=" O MET A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2132 Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 3.673A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2208 through 2211 Processing helix chain 'A' and resid 2347 through 2351 Processing helix chain 'A' and resid 2389 through 2394 removed outlier: 3.657A pdb=" N ARG A2394 " --> pdb=" O VAL A2390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2524 removed outlier: 3.968A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A2508 " --> pdb=" O VAL A2504 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A2523 " --> pdb=" O GLU A2519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A2524 " --> pdb=" O LYS A2520 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 removed outlier: 3.636A pdb=" N GLU B 60 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.652A pdb=" N ALA B 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 156 through 163 removed outlier: 3.902A pdb=" N CYS B 159 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.653A pdb=" N GLY B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 208 removed outlier: 3.594A pdb=" N PHE B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.527A pdb=" N PHE C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 removed outlier: 4.266A pdb=" N LEU C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 92 Processing helix chain 'C' and resid 92 through 100 removed outlier: 4.441A pdb=" N MET C 96 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.862A pdb=" N LEU C 119 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'C' and resid 158 through 170 Processing helix chain 'C' and resid 173 through 188 removed outlier: 4.354A pdb=" N LEU C 184 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 202 through 213 Processing helix chain 'C' and resid 218 through 233 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.802A pdb=" N GLU C 240 " --> pdb=" O CYS C 236 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.622A pdb=" N THR C 278 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 removed outlier: 4.110A pdb=" N ILE C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.191A pdb=" N HIS C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 302 removed outlier: 3.511A pdb=" N TYR C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 324 removed outlier: 4.190A pdb=" N SER C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 360 removed outlier: 4.292A pdb=" N TRP C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS C 360 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 379 Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.714A pdb=" N LEU C 384 " --> pdb=" O GLN C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 408 removed outlier: 3.511A pdb=" N GLU C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 427 removed outlier: 3.543A pdb=" N PHE C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 439 removed outlier: 3.900A pdb=" N ILE C 435 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 436 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 removed outlier: 3.601A pdb=" N ASN C 444 " --> pdb=" O GLY C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 470 removed outlier: 3.615A pdb=" N ALA C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 494 removed outlier: 3.823A pdb=" N MET C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) Proline residue: C 485 - end of helix Processing helix chain 'C' and resid 497 through 509 removed outlier: 3.526A pdb=" N GLN C 501 " --> pdb=" O SER C 497 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 526 through 540 Processing helix chain 'C' and resid 541 through 553 removed outlier: 3.567A pdb=" N LEU C 545 " --> pdb=" O ASP C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 4.598A pdb=" N LEU C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 580 Processing helix chain 'C' and resid 585 through 596 removed outlier: 3.521A pdb=" N VAL C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 613 removed outlier: 3.612A pdb=" N SER C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 641 through 659 removed outlier: 3.777A pdb=" N GLN C 645 " --> pdb=" O VAL C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 669 Processing helix chain 'C' and resid 671 through 685 removed outlier: 3.657A pdb=" N ILE C 683 " --> pdb=" O MET C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 704 removed outlier: 3.727A pdb=" N MET C 704 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 719 removed outlier: 3.576A pdb=" N LYS C 709 " --> pdb=" O ASP C 705 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 719 " --> pdb=" O ARG C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 732 Processing helix chain 'C' and resid 744 through 751 Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.618A pdb=" N SER C 764 " --> pdb=" O LEU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 781 Processing helix chain 'C' and resid 783 through 795 Processing helix chain 'C' and resid 798 through 801 removed outlier: 3.610A pdb=" N ASN C 801 " --> pdb=" O VAL C 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 798 through 801' Processing helix chain 'C' and resid 834 through 851 Processing helix chain 'C' and resid 996 through 1001 removed outlier: 4.329A pdb=" N ALA C 999 " --> pdb=" O ASP C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1011 Processing helix chain 'C' and resid 1027 through 1034 removed outlier: 3.612A pdb=" N CYS C1031 " --> pdb=" O PRO C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1053 through 1057 removed outlier: 3.707A pdb=" N MET C1057 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1189 through 1195 removed outlier: 3.716A pdb=" N ASN C1194 " --> pdb=" O ALA C1191 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C1195 " --> pdb=" O ILE C1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 1240 through 1245 Processing helix chain 'C' and resid 1261 through 1267 removed outlier: 3.956A pdb=" N GLY C1265 " --> pdb=" O PRO C1262 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS C1266 " --> pdb=" O GLU C1263 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1291 removed outlier: 3.531A pdb=" N LYS C1290 " --> pdb=" O GLU C1287 " (cutoff:3.500A) Processing helix chain 'C' and resid 1316 through 1328 Processing helix chain 'C' and resid 1348 through 1355 Processing helix chain 'C' and resid 1398 through 1402 Processing helix chain 'C' and resid 1404 through 1409 removed outlier: 3.865A pdb=" N MET C1409 " --> pdb=" O PRO C1406 " (cutoff:3.500A) Processing helix chain 'C' and resid 1426 through 1431 Processing helix chain 'C' and resid 1431 through 1442 Processing helix chain 'C' and resid 1466 through 1474 removed outlier: 3.935A pdb=" N THR C1470 " --> pdb=" O MET C1466 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1510 removed outlier: 3.577A pdb=" N ASN C1510 " --> pdb=" O ASN C1506 " (cutoff:3.500A) Processing helix chain 'C' and resid 1517 through 1520 Processing helix chain 'C' and resid 1524 through 1541 removed outlier: 3.929A pdb=" N VAL C1528 " --> pdb=" O PRO C1524 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS C1539 " --> pdb=" O LEU C1535 " (cutoff:3.500A) Processing helix chain 'C' and resid 1549 through 1559 Processing helix chain 'C' and resid 1568 through 1579 Processing helix chain 'C' and resid 1599 through 1608 removed outlier: 4.074A pdb=" N LEU C1603 " --> pdb=" O GLU C1599 " (cutoff:3.500A) Processing helix chain 'C' and resid 1645 through 1656 Processing helix chain 'C' and resid 1703 through 1711 Processing helix chain 'C' and resid 1770 through 1792 Processing helix chain 'C' and resid 1829 through 1835 Processing helix chain 'C' and resid 1852 through 1856 Processing helix chain 'C' and resid 1865 through 1869 removed outlier: 3.576A pdb=" N ILE C1868 " --> pdb=" O PRO C1865 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C1869 " --> pdb=" O ARG C1866 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1865 through 1869' Processing helix chain 'C' and resid 1881 through 1886 removed outlier: 3.730A pdb=" N LEU C1885 " --> pdb=" O PRO C1881 " (cutoff:3.500A) Processing helix chain 'C' and resid 1913 through 1926 removed outlier: 3.758A pdb=" N VAL C1923 " --> pdb=" O GLN C1919 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS C1926 " --> pdb=" O VAL C1922 " (cutoff:3.500A) Processing helix chain 'C' and resid 1954 through 1962 removed outlier: 3.635A pdb=" N LEU C1958 " --> pdb=" O SER C1954 " (cutoff:3.500A) Processing helix chain 'C' and resid 1969 through 1988 Processing helix chain 'C' and resid 2017 through 2021 removed outlier: 3.654A pdb=" N ILE C2020 " --> pdb=" O ASP C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2040 through 2045 Processing helix chain 'C' and resid 2052 through 2069 removed outlier: 3.928A pdb=" N VAL C2056 " --> pdb=" O GLN C2052 " (cutoff:3.500A) Processing helix chain 'C' and resid 2070 through 2079 removed outlier: 3.785A pdb=" N LYS C2078 " --> pdb=" O VAL C2074 " (cutoff:3.500A) Processing helix chain 'C' and resid 2079 through 2084 Processing helix chain 'C' and resid 2085 through 2089 removed outlier: 4.002A pdb=" N GLN C2089 " --> pdb=" O LEU C2086 " (cutoff:3.500A) Processing helix chain 'C' and resid 2094 through 2099 Processing helix chain 'C' and resid 2104 through 2115 removed outlier: 3.710A pdb=" N LEU C2110 " --> pdb=" O MET C2106 " (cutoff:3.500A) Processing helix chain 'C' and resid 2124 through 2132 Processing helix chain 'C' and resid 2134 through 2139 removed outlier: 3.674A pdb=" N VAL C2138 " --> pdb=" O SER C2134 " (cutoff:3.500A) Processing helix chain 'C' and resid 2208 through 2211 Processing helix chain 'C' and resid 2347 through 2351 Processing helix chain 'C' and resid 2389 through 2394 removed outlier: 3.657A pdb=" N ARG C2394 " --> pdb=" O VAL C2390 " (cutoff:3.500A) Processing helix chain 'C' and resid 2499 through 2524 removed outlier: 3.969A pdb=" N GLN C2505 " --> pdb=" O PRO C2501 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C2508 " --> pdb=" O VAL C2504 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C2523 " --> pdb=" O GLU C2519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C2524 " --> pdb=" O LYS C2520 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.636A pdb=" N GLU D 60 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 removed outlier: 3.652A pdb=" N ALA D 110 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG D 113 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 156 through 163 removed outlier: 3.901A pdb=" N CYS D 159 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.654A pdb=" N GLY D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 208 removed outlier: 3.594A pdb=" N PHE D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 796 through 797 Processing sheet with id=AA2, first strand: chain 'A' and resid 1016 through 1017 removed outlier: 6.829A pdb=" N LEU A1016 " --> pdb=" O ASP A1041 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A1040 " --> pdb=" O ASP A1064 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A1113 " --> pdb=" O PHE A1088 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1177 through 1179 removed outlier: 7.162A pdb=" N LEU A1178 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU A1225 " --> pdb=" O HIS A1251 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A1250 " --> pdb=" O ASP A1274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1330 through 1331 Processing sheet with id=AA5, first strand: chain 'A' and resid 1373 through 1380 removed outlier: 3.782A pdb=" N MET A1335 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N LEU A1414 " --> pdb=" O ARG A1334 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS A1336 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU A1416 " --> pdb=" O LYS A1336 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET A1338 " --> pdb=" O LEU A1416 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL A1418 " --> pdb=" O MET A1338 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL A1340 " --> pdb=" O VAL A1418 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ILE A1448 " --> pdb=" O ALA A1413 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A1447 " --> pdb=" O ILE A1482 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A1484 " --> pdb=" O VAL A1447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1547 through 1548 Processing sheet with id=AA7, first strand: chain 'A' and resid 1690 through 1693 Processing sheet with id=AA8, first strand: chain 'A' and resid 1695 through 1696 removed outlier: 3.654A pdb=" N TYR A1814 " --> pdb=" O ILE A1825 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AB1, first strand: chain 'A' and resid 1875 through 1876 removed outlier: 3.769A pdb=" N MET A1947 " --> pdb=" O ALA A1904 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A1939 " --> pdb=" O MET A1944 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AB3, first strand: chain 'A' and resid 2140 through 2144 removed outlier: 6.530A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A2142 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET A2459 " --> pdb=" O LEU A2471 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A2457 " --> pdb=" O LEU A2473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2155 through 2157 removed outlier: 6.522A pdb=" N GLY A2177 " --> pdb=" O VAL A2194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2201 through 2207 removed outlier: 4.222A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A2218 " --> pdb=" O CYS A2201 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2245 through 2249 Processing sheet with id=AB7, first strand: chain 'A' and resid 2272 through 2273 removed outlier: 3.536A pdb=" N LEU A2291 " --> pdb=" O LEU A2272 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2300 through 2302 removed outlier: 6.670A pdb=" N GLY A2318 " --> pdb=" O MET A2301 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.872A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A2385 " --> pdb=" O VAL A2375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2416 through 2419 removed outlier: 3.574A pdb=" N LEU A2436 " --> pdb=" O ARG A2446 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG A2446 " --> pdb=" O LEU A2436 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.272A pdb=" N ILE B 46 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL B 121 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE B 48 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AC5, first strand: chain 'C' and resid 1016 through 1017 removed outlier: 6.829A pdb=" N LEU C1016 " --> pdb=" O ASP C1041 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU C1040 " --> pdb=" O ASP C1064 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU C1063 " --> pdb=" O ASN C1089 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C1113 " --> pdb=" O PHE C1088 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1177 through 1179 removed outlier: 7.162A pdb=" N LEU C1178 " --> pdb=" O ASP C1202 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU C1225 " --> pdb=" O HIS C1251 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU C1250 " --> pdb=" O ASP C1274 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1330 through 1331 Processing sheet with id=AC8, first strand: chain 'C' and resid 1373 through 1380 removed outlier: 3.782A pdb=" N MET C1335 " --> pdb=" O VAL C1389 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N LEU C1414 " --> pdb=" O ARG C1334 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS C1336 " --> pdb=" O LEU C1414 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU C1416 " --> pdb=" O LYS C1336 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N MET C1338 " --> pdb=" O LEU C1416 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL C1418 " --> pdb=" O MET C1338 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL C1340 " --> pdb=" O VAL C1418 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ILE C1448 " --> pdb=" O ALA C1413 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR C1415 " --> pdb=" O ILE C1448 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL C1450 " --> pdb=" O TYR C1415 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA C1417 " --> pdb=" O VAL C1450 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C1447 " --> pdb=" O ILE C1482 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP C1484 " --> pdb=" O VAL C1447 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1547 through 1548 Processing sheet with id=AD1, first strand: chain 'C' and resid 1690 through 1693 Processing sheet with id=AD2, first strand: chain 'C' and resid 1695 through 1696 removed outlier: 3.655A pdb=" N TYR C1814 " --> pdb=" O ILE C1825 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1840 through 1841 Processing sheet with id=AD4, first strand: chain 'C' and resid 1875 through 1876 removed outlier: 3.769A pdb=" N MET C1947 " --> pdb=" O ALA C1904 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C1939 " --> pdb=" O MET C1944 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU C1948 " --> pdb=" O LEU C1935 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU C1935 " --> pdb=" O GLU C1948 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 2000 through 2002 Processing sheet with id=AD6, first strand: chain 'C' and resid 2140 through 2144 removed outlier: 6.531A pdb=" N LEU C2140 " --> pdb=" O ASP C2497 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP C2497 " --> pdb=" O LEU C2140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG C2142 " --> pdb=" O VAL C2495 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N MET C2459 " --> pdb=" O LEU C2471 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C2457 " --> pdb=" O LEU C2473 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 2155 through 2157 removed outlier: 6.522A pdb=" N GLY C2177 " --> pdb=" O VAL C2194 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 2201 through 2207 removed outlier: 4.222A pdb=" N CYS C2201 " --> pdb=" O GLY C2218 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY C2218 " --> pdb=" O CYS C2201 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 2245 through 2249 Processing sheet with id=AE1, first strand: chain 'C' and resid 2272 through 2273 removed outlier: 3.536A pdb=" N LEU C2291 " --> pdb=" O LEU C2272 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 2300 through 2302 removed outlier: 6.670A pdb=" N GLY C2318 " --> pdb=" O MET C2301 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 2354 through 2359 removed outlier: 6.872A pdb=" N ALA C2366 " --> pdb=" O ILE C2355 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL C2357 " --> pdb=" O TYR C2364 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR C2364 " --> pdb=" O VAL C2357 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS C2367 " --> pdb=" O VAL C2372 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL C2372 " --> pdb=" O LYS C2367 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY C2385 " --> pdb=" O VAL C2375 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 2416 through 2419 removed outlier: 3.574A pdb=" N LEU C2436 " --> pdb=" O ARG C2446 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG C2446 " --> pdb=" O LEU C2436 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP C2438 " --> pdb=" O LEU C2444 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C2444 " --> pdb=" O ASP C2438 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AE6, first strand: chain 'D' and resid 96 through 97 removed outlier: 6.271A pdb=" N ILE D 46 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL D 121 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 48 " --> pdb=" O VAL D 121 " (cutoff:3.500A) 1510 hydrogen bonds defined for protein. 4236 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: 30.51 Time building geometry restraints manager: 9.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5512 1.31 - 1.44: 8535 1.44 - 1.56: 20022 1.56 - 1.69: 26 1.69 - 1.82: 266 Bond restraints: 34361 Sorted by residual: bond pdb=" O3A ANP A2602 " pdb=" PB ANP A2602 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O3A ANP C2602 " pdb=" PB ANP C2602 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C THR A 213 " pdb=" O THR A 213 " ideal model delta sigma weight residual 1.236 1.304 -0.068 1.28e-02 6.10e+03 2.85e+01 bond pdb=" N3B GNP B 302 " pdb=" PG GNP B 302 " ideal model delta sigma weight residual 1.801 1.697 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" N3B GNP D 302 " pdb=" PG GNP D 302 " ideal model delta sigma weight residual 1.801 1.697 0.104 2.00e-02 2.50e+03 2.71e+01 ... (remaining 34356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 46643 3.30 - 6.61: 397 6.61 - 9.91: 55 9.91 - 13.22: 8 13.22 - 16.52: 4 Bond angle restraints: 47107 Sorted by residual: angle pdb=" C THR A 213 " pdb=" N ASN A 214 " pdb=" CA ASN A 214 " ideal model delta sigma weight residual 120.72 105.17 15.55 1.67e+00 3.59e-01 8.67e+01 angle pdb=" C SER C 210 " pdb=" N ALA C 211 " pdb=" CA ALA C 211 " ideal model delta sigma weight residual 122.60 108.22 14.38 1.88e+00 2.83e-01 5.85e+01 angle pdb=" N LEU C 179 " pdb=" CA LEU C 179 " pdb=" C LEU C 179 " ideal model delta sigma weight residual 113.18 104.34 8.84 1.21e+00 6.83e-01 5.33e+01 angle pdb=" N ASP A 204 " pdb=" CA ASP A 204 " pdb=" C ASP A 204 " ideal model delta sigma weight residual 111.75 102.71 9.04 1.28e+00 6.10e-01 4.99e+01 angle pdb=" N ILE A 148 " pdb=" CA ILE A 148 " pdb=" C ILE A 148 " ideal model delta sigma weight residual 113.16 103.16 10.00 1.49e+00 4.50e-01 4.50e+01 ... (remaining 47102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 20031 34.55 - 69.09: 313 69.09 - 103.64: 26 103.64 - 138.19: 2 138.19 - 172.74: 2 Dihedral angle restraints: 20374 sinusoidal: 6404 harmonic: 13970 Sorted by residual: dihedral pdb=" CA SER A 986 " pdb=" C SER A 986 " pdb=" N LEU A 987 " pdb=" CA LEU A 987 " ideal model delta harmonic sigma weight residual 180.00 -148.48 -31.52 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" CA SER C 986 " pdb=" C SER C 986 " pdb=" N LEU C 987 " pdb=" CA LEU C 987 " ideal model delta harmonic sigma weight residual -180.00 -148.48 -31.52 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" O2B GDP C2601 " pdb=" O3A GDP C2601 " pdb=" PB GDP C2601 " pdb=" PA GDP C2601 " ideal model delta sinusoidal sigma weight residual -180.00 -73.54 -106.46 1 2.00e+01 2.50e-03 3.08e+01 ... (remaining 20371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5423 0.086 - 0.172: 481 0.172 - 0.259: 21 0.259 - 0.345: 9 0.345 - 0.431: 2 Chirality restraints: 5936 Sorted by residual: chirality pdb=" CG LEU C1178 " pdb=" CB LEU C1178 " pdb=" CD1 LEU C1178 " pdb=" CD2 LEU C1178 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CG LEU A1178 " pdb=" CB LEU A1178 " pdb=" CD1 LEU A1178 " pdb=" CD2 LEU A1178 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CB VAL C1074 " pdb=" CA VAL C1074 " pdb=" CG1 VAL C1074 " pdb=" CG2 VAL C1074 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 5933 not shown) Planarity restraints: 5925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 172 " -0.031 2.00e-02 2.50e+03 6.22e-02 3.87e+01 pdb=" C ALA C 172 " 0.108 2.00e-02 2.50e+03 pdb=" O ALA C 172 " -0.041 2.00e-02 2.50e+03 pdb=" N ASN C 173 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 209 " 0.030 2.00e-02 2.50e+03 6.11e-02 3.73e+01 pdb=" C LEU A 209 " -0.106 2.00e-02 2.50e+03 pdb=" O LEU A 209 " 0.040 2.00e-02 2.50e+03 pdb=" N SER A 210 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C2496 " -0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C TRP C2496 " 0.094 2.00e-02 2.50e+03 pdb=" O TRP C2496 " -0.036 2.00e-02 2.50e+03 pdb=" N ASP C2497 " -0.031 2.00e-02 2.50e+03 ... (remaining 5922 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 262 2.52 - 3.11: 25882 3.11 - 3.71: 54194 3.71 - 4.30: 71821 4.30 - 4.90: 116602 Nonbonded interactions: 268761 Sorted by model distance: nonbonded pdb=" ND2 ASN C 173 " pdb=" CG2 VAL C 176 " model vdw 1.920 3.540 nonbonded pdb="MG MG D 301 " pdb=" O2B GNP D 302 " model vdw 1.988 2.170 nonbonded pdb="MG MG B 301 " pdb=" O2B GNP B 302 " model vdw 1.989 2.170 nonbonded pdb="MG MG B 301 " pdb=" O1A GNP B 302 " model vdw 2.057 2.170 nonbonded pdb="MG MG D 301 " pdb=" O1A GNP D 302 " model vdw 2.058 2.170 ... (remaining 268756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 211 or (resid 212 through 213 and (name N or na \ me CA or name C or name O or name CB )) or resid 214 through 2329 or (resid 2330 \ and (name N or name CA or name C or name O or name CB )) or resid 2331 through \ 2527 or resid 2601 or resid 2602)) selection = (chain 'C' and (resid 12 through 177 or (resid 178 and (name N or name CA or nam \ e C or name O or name CB )) or resid 179 through 181 or (resid 182 through 183 a \ nd (name N or name CA or name C or name O or name CB )) or resid 184 through 201 \ or (resid 202 through 203 and (name N or name CA or name C or name O or name CB \ )) or resid 204 through 207 or (resid 208 through 209 and (name N or name CA or \ name C or name O or name CB )) or resid 210 through 2304 or (resid 2305 through \ 2309 and (name N or name CA or name C or name O or name CB )) or resid 2310 thr \ ough 2333 or (resid 2334 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2335 through 2527 or resid 2601 or resid 2602)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.320 Check model and map are aligned: 0.250 Set scattering table: 0.340 Process input model: 101.400 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.170 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 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 : 0.006 0.146 34361 Z= 0.314 Angle : 0.865 16.525 47107 Z= 0.479 Chirality : 0.051 0.431 5936 Planarity : 0.006 0.070 5925 Dihedral : 13.906 172.737 11238 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.03 % Allowed : 8.86 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.99 (0.10), residues: 4692 helix: -2.16 (0.09), residues: 1948 sheet: -3.41 (0.17), residues: 644 loop : -2.77 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A2104 HIS 0.012 0.001 HIS A 543 PHE 0.018 0.002 PHE C 553 TYR 0.024 0.002 TYR A1739 ARG 0.005 0.000 ARG C 276 Details of bonding type rmsd hydrogen bonds : bond 0.19249 ( 1510) hydrogen bonds : angle 8.11653 ( 4236) covalent geometry : bond 0.00626 (34361) covalent geometry : angle 0.86485 (47107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1288 MET cc_start: 0.8882 (ptp) cc_final: 0.8648 (ttp) REVERT: A 2426 TRP cc_start: 0.6996 (m100) cc_final: 0.6795 (m-10) REVERT: C 2106 MET cc_start: 0.7264 (mtp) cc_final: 0.6962 (ttm) outliers start: 1 outliers final: 1 residues processed: 234 average time/residue: 0.4605 time to fit residues: 184.3987 Evaluate side-chains 161 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1349 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 403 optimal weight: 6.9990 chunk 362 optimal weight: 0.6980 chunk 201 optimal weight: 7.9990 chunk 123 optimal weight: 0.5980 chunk 244 optimal weight: 4.9990 chunk 193 optimal weight: 0.0050 chunk 374 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 434 optimal weight: 8.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1194 ASN A1216 HIS A1278 ASN A1305 ASN A1333 ASN A1489 ASN A1684 HIS A1758 HIS A1872 ASN A1971 GLN A1986 HIS A2353 ASN A2369 ASN C 173 ASN C 185 HIS ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 GLN C1021 ASN C1194 ASN C1216 HIS C1278 ASN C1305 ASN C1333 ASN C1486 HIS C1489 ASN C1758 HIS C1872 ASN C1971 GLN C1986 HIS C2353 ASN C2369 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.092119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.060013 restraints weight = 224282.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.056104 restraints weight = 204484.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.056147 restraints weight = 200715.741| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34361 Z= 0.125 Angle : 0.598 9.083 47107 Z= 0.309 Chirality : 0.042 0.237 5936 Planarity : 0.004 0.053 5925 Dihedral : 7.700 171.374 5077 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.85 % Allowed : 12.42 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -2.59 (0.12), residues: 4692 helix: -0.58 (0.11), residues: 2024 sheet: -2.96 (0.18), residues: 594 loop : -2.47 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1705 HIS 0.010 0.001 HIS A 408 PHE 0.028 0.001 PHE B 41 TYR 0.015 0.001 TYR A1739 ARG 0.006 0.000 ARG C1968 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 1510) hydrogen bonds : angle 5.35296 ( 4236) covalent geometry : bond 0.00262 (34361) covalent geometry : angle 0.59815 (47107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 3.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1168 MET cc_start: 0.8605 (mmm) cc_final: 0.8148 (tpt) REVERT: A 1288 MET cc_start: 0.8552 (ptp) cc_final: 0.8312 (ttp) REVERT: A 1788 MET cc_start: 0.8379 (mtt) cc_final: 0.7884 (mtm) REVERT: A 1949 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7609 (mt) REVERT: A 2315 MET cc_start: 0.7277 (mmt) cc_final: 0.7028 (mmm) REVERT: A 2458 MET cc_start: 0.8879 (ttp) cc_final: 0.7815 (ptt) REVERT: C 405 MET cc_start: 0.7223 (tmm) cc_final: 0.5951 (ttp) REVERT: C 465 MET cc_start: 0.8877 (mmm) cc_final: 0.8502 (mmm) REVERT: C 1702 MET cc_start: 0.8295 (mmm) cc_final: 0.8053 (mmm) REVERT: C 1788 MET cc_start: 0.7651 (mtm) cc_final: 0.7450 (mtm) REVERT: D 131 ASP cc_start: 0.5517 (p0) cc_final: 0.5279 (p0) outliers start: 26 outliers final: 5 residues processed: 193 average time/residue: 0.5146 time to fit residues: 181.1385 Evaluate side-chains 161 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 5.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain D residue 166 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 434 optimal weight: 4.9990 chunk 462 optimal weight: 20.0000 chunk 414 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 210 optimal weight: 20.0000 chunk 219 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 HIS ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN A1584 HIS A1854 GLN ** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1971 GLN A2173 HIS A2505 GLN C 177 GLN C 385 HIS C1971 GLN ** C1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2173 HIS C2505 GLN D 44 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.079847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.060546 restraints weight = 269275.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.059343 restraints weight = 178525.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.059507 restraints weight = 168770.777| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34361 Z= 0.227 Angle : 0.686 10.688 47107 Z= 0.345 Chirality : 0.043 0.173 5936 Planarity : 0.004 0.046 5925 Dihedral : 7.026 155.791 5076 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.70 % Allowed : 14.91 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -2.07 (0.12), residues: 4692 helix: -0.05 (0.11), residues: 2002 sheet: -2.86 (0.18), residues: 622 loop : -2.20 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C1376 HIS 0.007 0.001 HIS C1574 PHE 0.027 0.002 PHE A1026 TYR 0.017 0.002 TYR A2018 ARG 0.006 0.001 ARG A2514 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 1510) hydrogen bonds : angle 5.06276 ( 4236) covalent geometry : bond 0.00498 (34361) covalent geometry : angle 0.68581 (47107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 4.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 HIS cc_start: 0.2875 (OUTLIER) cc_final: 0.2574 (m-70) REVERT: A 988 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8153 (p0) REVERT: A 1788 MET cc_start: 0.7971 (mtt) cc_final: 0.7584 (mtm) REVERT: A 1949 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 2315 MET cc_start: 0.7526 (mmt) cc_final: 0.7203 (mmm) REVERT: A 2458 MET cc_start: 0.8880 (ttp) cc_final: 0.7821 (ptt) REVERT: C 988 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8115 (p0) REVERT: C 1989 MET cc_start: 0.7919 (tmm) cc_final: 0.7706 (tmm) REVERT: C 2106 MET cc_start: 0.7415 (ttt) cc_final: 0.6952 (ttm) outliers start: 52 outliers final: 18 residues processed: 197 average time/residue: 0.6158 time to fit residues: 219.0514 Evaluate side-chains 172 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 6.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 988 ASP Chi-restraints excluded: chain C residue 1808 LEU Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 178 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 142 optimal weight: 5.9990 chunk 464 optimal weight: 0.7980 chunk 37 optimal weight: 50.0000 chunk 240 optimal weight: 0.0970 chunk 199 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 420 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 315 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 HIS ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2173 HIS C 385 HIS C 645 GLN C1101 ASN C2173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.090365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.058654 restraints weight = 223197.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.054381 restraints weight = 210663.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.054684 restraints weight = 246811.946| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34361 Z= 0.112 Angle : 0.544 9.189 47107 Z= 0.278 Chirality : 0.040 0.194 5936 Planarity : 0.004 0.049 5925 Dihedral : 6.576 148.330 5076 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.63 % Allowed : 16.08 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4692 helix: 0.42 (0.12), residues: 2014 sheet: -2.60 (0.18), residues: 668 loop : -2.01 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1705 HIS 0.029 0.001 HIS A 385 PHE 0.014 0.001 PHE A1026 TYR 0.018 0.001 TYR C1739 ARG 0.004 0.000 ARG D 181 Details of bonding type rmsd hydrogen bonds : bond 0.02803 ( 1510) hydrogen bonds : angle 4.65772 ( 4236) covalent geometry : bond 0.00245 (34361) covalent geometry : angle 0.54396 (47107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 3.741 Fit side-chains revert: symmetry clash REVERT: A 842 MET cc_start: 0.8980 (mmm) cc_final: 0.8735 (ptm) REVERT: A 1949 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7735 (mt) REVERT: A 2315 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7458 (mmm) REVERT: A 2458 MET cc_start: 0.8843 (ttp) cc_final: 0.8019 (ptt) REVERT: B 139 MET cc_start: -0.0505 (OUTLIER) cc_final: -0.0764 (ptm) REVERT: C 465 MET cc_start: 0.8611 (mmm) cc_final: 0.8355 (mmp) REVERT: C 988 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8043 (p0) REVERT: C 1590 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7118 (tp) REVERT: C 1989 MET cc_start: 0.8330 (tmm) cc_final: 0.8059 (tmm) REVERT: C 2458 MET cc_start: 0.9160 (ttp) cc_final: 0.8572 (ptt) outliers start: 50 outliers final: 17 residues processed: 199 average time/residue: 0.4154 time to fit residues: 151.7129 Evaluate side-chains 177 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 4.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain C residue 988 ASP Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1590 LEU Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 178 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 475 optimal weight: 7.9990 chunk 437 optimal weight: 10.0000 chunk 351 optimal weight: 0.9990 chunk 443 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 273 optimal weight: 0.0870 chunk 456 optimal weight: 9.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN A 645 GLN A2173 HIS C 177 GLN C 444 ASN C 847 GLN C1019 HIS C1854 GLN C2149 ASN C2173 HIS C2453 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.089838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.057984 restraints weight = 222147.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.054081 restraints weight = 215681.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.053681 restraints weight = 235948.849| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34361 Z= 0.156 Angle : 0.583 10.222 47107 Z= 0.293 Chirality : 0.041 0.172 5936 Planarity : 0.004 0.046 5925 Dihedral : 6.198 134.741 5076 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.26 % Allowed : 16.25 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 4692 helix: 0.57 (0.12), residues: 2016 sheet: -2.49 (0.19), residues: 658 loop : -1.88 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1376 HIS 0.008 0.001 HIS A 408 PHE 0.029 0.001 PHE A1026 TYR 0.014 0.001 TYR C1739 ARG 0.004 0.000 ARG D 181 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 1510) hydrogen bonds : angle 4.53679 ( 4236) covalent geometry : bond 0.00347 (34361) covalent geometry : angle 0.58265 (47107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 153 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.7614 (tmm) cc_final: 0.7322 (ptm) REVERT: A 842 MET cc_start: 0.9100 (mmm) cc_final: 0.8855 (ptm) REVERT: A 1057 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7747 (mmp) REVERT: A 1830 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8138 (tt) REVERT: A 1831 MET cc_start: 0.9200 (pmm) cc_final: 0.8913 (pmm) REVERT: A 1949 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7926 (mt) REVERT: A 2315 MET cc_start: 0.7730 (mmt) cc_final: 0.7510 (mmm) REVERT: A 2458 MET cc_start: 0.8847 (ttp) cc_final: 0.8036 (ptt) REVERT: B 139 MET cc_start: -0.0418 (OUTLIER) cc_final: -0.0808 (ptm) REVERT: C 405 MET cc_start: 0.6903 (ppp) cc_final: 0.5974 (ttp) REVERT: C 465 MET cc_start: 0.8429 (mmm) cc_final: 0.8193 (mmm) REVERT: C 538 PHE cc_start: 0.3543 (OUTLIER) cc_final: 0.3253 (m-80) REVERT: C 842 MET cc_start: 0.9070 (mmm) cc_final: 0.8654 (ptm) REVERT: C 988 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8100 (p0) REVERT: C 1830 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8052 (tt) REVERT: C 1989 MET cc_start: 0.8341 (tmm) cc_final: 0.8085 (tmm) REVERT: C 2458 MET cc_start: 0.9199 (ttp) cc_final: 0.8677 (ptt) outliers start: 69 outliers final: 30 residues processed: 207 average time/residue: 0.3906 time to fit residues: 147.6689 Evaluate side-chains 188 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain A residue 2470 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 988 ASP Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1266 CYS Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1692 ILE Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 178 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 11 optimal weight: 30.0000 chunk 272 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 477 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 242 optimal weight: 50.0000 chunk 271 optimal weight: 30.0000 chunk 78 optimal weight: 0.3980 chunk 206 optimal weight: 20.0000 chunk 357 optimal weight: 0.6980 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS A 468 HIS ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 HIS A1182 GLN A2333 GLN ** A2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 HIS C 594 GLN C1182 GLN C1584 HIS C2333 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.077997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059936 restraints weight = 269864.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.057483 restraints weight = 207469.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.057917 restraints weight = 217020.628| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 34361 Z= 0.344 Angle : 0.816 10.542 47107 Z= 0.406 Chirality : 0.047 0.178 5936 Planarity : 0.005 0.053 5925 Dihedral : 6.624 113.571 5076 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 2.58 % Allowed : 17.16 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.12), residues: 4692 helix: 0.15 (0.12), residues: 1996 sheet: -2.46 (0.19), residues: 662 loop : -1.99 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP C1376 HIS 0.016 0.002 HIS A 408 PHE 0.035 0.002 PHE C1883 TYR 0.033 0.003 TYR C1277 ARG 0.016 0.001 ARG A2514 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 1510) hydrogen bonds : angle 5.13646 ( 4236) covalent geometry : bond 0.00761 (34361) covalent geometry : angle 0.81620 (47107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 154 time to evaluate : 4.152 Fit side-chains revert: symmetry clash REVERT: A 1788 MET cc_start: 0.7628 (mtp) cc_final: 0.7386 (mtp) REVERT: A 1830 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8043 (tt) REVERT: A 1949 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8006 (mt) REVERT: A 2458 MET cc_start: 0.8899 (ttp) cc_final: 0.8133 (ptt) REVERT: C 405 MET cc_start: 0.6914 (ppp) cc_final: 0.6054 (ttp) REVERT: C 465 MET cc_start: 0.7940 (mmm) cc_final: 0.7604 (mmm) REVERT: C 538 PHE cc_start: 0.1441 (OUTLIER) cc_final: 0.0759 (m-80) REVERT: C 644 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8651 (mm) REVERT: C 842 MET cc_start: 0.8633 (mmm) cc_final: 0.8266 (mmm) REVERT: C 1271 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8737 (p) REVERT: C 1788 MET cc_start: 0.8287 (mtm) cc_final: 0.8062 (mtm) REVERT: C 1830 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8097 (tt) REVERT: C 1831 MET cc_start: 0.9039 (pmm) cc_final: 0.8748 (pmm) REVERT: C 2315 MET cc_start: 0.7957 (mmt) cc_final: 0.7646 (mmm) outliers start: 79 outliers final: 40 residues processed: 217 average time/residue: 0.5186 time to fit residues: 208.1273 Evaluate side-chains 196 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2106 MET Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1266 CYS Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1692 ILE Chi-restraints excluded: chain C residue 1808 LEU Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 2205 VAL Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2470 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 166 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 7 optimal weight: 9.9990 chunk 378 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 477 optimal weight: 6.9990 chunk 466 optimal weight: 50.0000 chunk 305 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 441 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 114 optimal weight: 0.0970 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2149 ASN A2453 ASN C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.089269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.057967 restraints weight = 222846.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.054284 restraints weight = 220044.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.054068 restraints weight = 229038.226| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34361 Z= 0.136 Angle : 0.596 11.420 47107 Z= 0.298 Chirality : 0.042 0.276 5936 Planarity : 0.004 0.043 5925 Dihedral : 6.099 110.774 5076 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.57 % Allowed : 18.40 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 4692 helix: 0.49 (0.12), residues: 2018 sheet: -2.37 (0.19), residues: 676 loop : -1.85 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 372 HIS 0.009 0.001 HIS A 408 PHE 0.015 0.001 PHE A1026 TYR 0.017 0.001 TYR C1739 ARG 0.003 0.000 ARG A2514 Details of bonding type rmsd hydrogen bonds : bond 0.02822 ( 1510) hydrogen bonds : angle 4.64425 ( 4236) covalent geometry : bond 0.00306 (34361) covalent geometry : angle 0.59612 (47107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 11.540 Fit side-chains revert: symmetry clash REVERT: A 1830 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7832 (tt) REVERT: A 1949 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7694 (mt) REVERT: A 2458 MET cc_start: 0.8897 (ttp) cc_final: 0.8460 (ptt) REVERT: C 405 MET cc_start: 0.7517 (ppp) cc_final: 0.6754 (ttp) REVERT: C 465 MET cc_start: 0.8424 (mmm) cc_final: 0.7958 (mmm) REVERT: C 538 PHE cc_start: 0.3178 (OUTLIER) cc_final: 0.2807 (m-80) REVERT: C 842 MET cc_start: 0.9274 (mmm) cc_final: 0.8842 (ptp) REVERT: C 2315 MET cc_start: 0.7909 (mmt) cc_final: 0.7663 (mmm) REVERT: C 2458 MET cc_start: 0.9072 (ttp) cc_final: 0.8312 (ptt) outliers start: 48 outliers final: 32 residues processed: 193 average time/residue: 0.7081 time to fit residues: 255.6205 Evaluate side-chains 184 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 4.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1232 ILE Chi-restraints excluded: chain C residue 1266 CYS Chi-restraints excluded: chain C residue 1338 MET Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1590 LEU Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 30.0000 chunk 154 optimal weight: 0.0570 chunk 434 optimal weight: 0.0000 chunk 446 optimal weight: 7.9990 chunk 200 optimal weight: 40.0000 chunk 416 optimal weight: 3.9990 chunk 401 optimal weight: 0.0970 chunk 161 optimal weight: 7.9990 chunk 445 optimal weight: 4.9990 chunk 459 optimal weight: 9.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2008 ASN C2008 ASN 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 = 0.089569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.058326 restraints weight = 222114.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.054029 restraints weight = 217616.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.053784 restraints weight = 250505.263| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34361 Z= 0.107 Angle : 0.565 16.891 47107 Z= 0.280 Chirality : 0.041 0.511 5936 Planarity : 0.004 0.045 5925 Dihedral : 5.767 103.792 5076 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.44 % Allowed : 18.86 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 4692 helix: 0.72 (0.12), residues: 2028 sheet: -2.23 (0.19), residues: 686 loop : -1.77 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 349 HIS 0.005 0.001 HIS C2510 PHE 0.014 0.001 PHE A1026 TYR 0.014 0.001 TYR A1645 ARG 0.003 0.000 ARG A2514 Details of bonding type rmsd hydrogen bonds : bond 0.02509 ( 1510) hydrogen bonds : angle 4.36103 ( 4236) covalent geometry : bond 0.00240 (34361) covalent geometry : angle 0.56519 (47107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 3.780 Fit side-chains revert: symmetry clash REVERT: A 465 MET cc_start: 0.7585 (tmm) cc_final: 0.7225 (ptm) REVERT: A 1949 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7588 (mt) REVERT: A 2458 MET cc_start: 0.8882 (ttp) cc_final: 0.8429 (ptt) REVERT: C 405 MET cc_start: 0.7514 (ppp) cc_final: 0.6806 (ttp) REVERT: C 465 MET cc_start: 0.8498 (mmm) cc_final: 0.8290 (mmm) REVERT: C 538 PHE cc_start: 0.4093 (OUTLIER) cc_final: 0.3774 (m-80) REVERT: C 712 MET cc_start: 0.9520 (ttp) cc_final: 0.8934 (ppp) REVERT: C 842 MET cc_start: 0.9314 (mmm) cc_final: 0.8807 (ptm) REVERT: C 1057 MET cc_start: 0.8156 (mmp) cc_final: 0.7899 (mmp) REVERT: C 1831 MET cc_start: 0.9135 (pmm) cc_final: 0.8902 (pmm) REVERT: C 2315 MET cc_start: 0.7805 (mmt) cc_final: 0.7540 (mmm) REVERT: C 2458 MET cc_start: 0.9166 (ttp) cc_final: 0.8422 (ptt) REVERT: C 2521 MET cc_start: 0.7509 (ppp) cc_final: 0.7140 (ppp) outliers start: 44 outliers final: 34 residues processed: 190 average time/residue: 0.3940 time to fit residues: 134.9456 Evaluate side-chains 185 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 3.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1338 MET Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1232 ILE Chi-restraints excluded: chain C residue 1266 CYS Chi-restraints excluded: chain C residue 1338 MET Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1590 LEU Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 406 optimal weight: 3.9990 chunk 157 optimal weight: 0.3980 chunk 251 optimal weight: 6.9990 chunk 291 optimal weight: 30.0000 chunk 198 optimal weight: 9.9990 chunk 234 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 chunk 445 optimal weight: 6.9990 chunk 371 optimal weight: 3.9990 chunk 397 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2008 ASN C2008 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.089124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.057996 restraints weight = 222223.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.054168 restraints weight = 224024.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.053805 restraints weight = 229098.795| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.004 0.052 34361 Z= 0.165 Angle : 0.608 14.303 47107 Z= 0.300 Chirality : 0.042 0.216 5936 Planarity : 0.004 0.048 5925 Dihedral : 5.773 97.421 5076 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.47 % Allowed : 18.83 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 4692 helix: 0.76 (0.12), residues: 2004 sheet: -2.26 (0.20), residues: 676 loop : -1.70 (0.15), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1376 HIS 0.004 0.001 HIS A1453 PHE 0.014 0.001 PHE A1026 TYR 0.013 0.001 TYR A1645 ARG 0.005 0.000 ARG A2514 Details of bonding type rmsd hydrogen bonds : bond 0.02675 ( 1510) hydrogen bonds : angle 4.43484 ( 4236) covalent geometry : bond 0.00368 (34361) covalent geometry : angle 0.60779 (47107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1830 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8171 (tt) REVERT: A 1949 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7662 (mt) REVERT: A 2155 MET cc_start: 0.7387 (pmm) cc_final: 0.7159 (pmm) REVERT: A 2425 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8241 (mt) REVERT: A 2458 MET cc_start: 0.8837 (ttp) cc_final: 0.8387 (ptt) REVERT: C 405 MET cc_start: 0.7602 (ppp) cc_final: 0.7014 (ttp) REVERT: C 465 MET cc_start: 0.8264 (mmm) cc_final: 0.7669 (mmm) REVERT: C 538 PHE cc_start: 0.3283 (OUTLIER) cc_final: 0.2918 (m-80) REVERT: C 712 MET cc_start: 0.9466 (ttp) cc_final: 0.8867 (ppp) REVERT: C 842 MET cc_start: 0.9302 (mmm) cc_final: 0.8853 (ptm) REVERT: C 1057 MET cc_start: 0.8262 (mmp) cc_final: 0.7994 (mmp) REVERT: C 1949 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7834 (mt) REVERT: C 2315 MET cc_start: 0.7800 (mmt) cc_final: 0.7517 (mmm) REVERT: C 2458 MET cc_start: 0.9082 (ttp) cc_final: 0.8420 (ptt) outliers start: 45 outliers final: 34 residues processed: 191 average time/residue: 0.3789 time to fit residues: 131.3965 Evaluate side-chains 189 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 3.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1232 ILE Chi-restraints excluded: chain C residue 1266 CYS Chi-restraints excluded: chain C residue 1338 MET Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1590 LEU Chi-restraints excluded: chain C residue 1692 ILE Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1949 LEU Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 26 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 431 optimal weight: 30.0000 chunk 219 optimal weight: 0.3980 chunk 271 optimal weight: 6.9990 chunk 314 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 379 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 301 GLN A2008 ASN B 94 GLN C2008 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.089452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.057991 restraints weight = 221740.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.053856 restraints weight = 215804.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.053547 restraints weight = 240493.092| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34361 Z= 0.113 Angle : 0.566 14.870 47107 Z= 0.279 Chirality : 0.041 0.199 5936 Planarity : 0.004 0.047 5925 Dihedral : 5.566 91.821 5076 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.41 % Allowed : 18.99 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.99 (0.13), residues: 4692 helix: 0.86 (0.12), residues: 2024 sheet: -2.19 (0.20), residues: 684 loop : -1.66 (0.15), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1705 HIS 0.004 0.001 HIS C2510 PHE 0.013 0.001 PHE A1026 TYR 0.014 0.001 TYR A1645 ARG 0.002 0.000 ARG A2514 Details of bonding type rmsd hydrogen bonds : bond 0.02466 ( 1510) hydrogen bonds : angle 4.27313 ( 4236) covalent geometry : bond 0.00255 (34361) covalent geometry : angle 0.56581 (47107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1830 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8191 (tt) REVERT: A 1949 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7634 (mt) REVERT: A 2155 MET cc_start: 0.7298 (pmm) cc_final: 0.7093 (pmm) REVERT: A 2425 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8337 (mt) REVERT: A 2458 MET cc_start: 0.8802 (ttp) cc_final: 0.8405 (ptt) REVERT: C 405 MET cc_start: 0.7909 (ppp) cc_final: 0.7240 (ttp) REVERT: C 465 MET cc_start: 0.8554 (mmm) cc_final: 0.7955 (mmm) REVERT: C 538 PHE cc_start: 0.4253 (OUTLIER) cc_final: 0.3975 (m-80) REVERT: C 712 MET cc_start: 0.9511 (ttp) cc_final: 0.8954 (ppp) REVERT: C 842 MET cc_start: 0.9350 (mmm) cc_final: 0.8846 (ptm) REVERT: C 1057 MET cc_start: 0.8315 (mmp) cc_final: 0.8069 (mmp) REVERT: C 1949 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7930 (mt) REVERT: C 2315 MET cc_start: 0.7822 (mmt) cc_final: 0.7574 (mmm) REVERT: C 2458 MET cc_start: 0.9121 (ttp) cc_final: 0.8439 (ptt) outliers start: 43 outliers final: 31 residues processed: 189 average time/residue: 0.3758 time to fit residues: 128.9326 Evaluate side-chains 185 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1232 ILE Chi-restraints excluded: chain C residue 1266 CYS Chi-restraints excluded: chain C residue 1338 MET Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1419 TYR Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1949 LEU Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 188 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 3 optimal weight: 0.0570 chunk 280 optimal weight: 5.9990 chunk 157 optimal weight: 0.0980 chunk 183 optimal weight: 0.5980 overall best weight: 2.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2008 ASN C2008 ASN D 44 GLN D 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.089040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.057495 restraints weight = 222038.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053188 restraints weight = 215510.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.052865 restraints weight = 251689.957| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34361 Z= 0.173 Angle : 0.611 14.116 47107 Z= 0.301 Chirality : 0.042 0.219 5936 Planarity : 0.004 0.048 5925 Dihedral : 5.546 85.790 5076 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.44 % Allowed : 18.83 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 4692 helix: 0.82 (0.12), residues: 2012 sheet: -2.26 (0.20), residues: 698 loop : -1.65 (0.15), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 372 HIS 0.004 0.001 HIS A1453 PHE 0.013 0.001 PHE C1436 TYR 0.013 0.001 TYR A1645 ARG 0.005 0.000 ARG A2514 Details of bonding type rmsd hydrogen bonds : bond 0.02680 ( 1510) hydrogen bonds : angle 4.38605 ( 4236) covalent geometry : bond 0.00386 (34361) covalent geometry : angle 0.61071 (47107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12272.29 seconds wall clock time: 223 minutes 15.73 seconds (13395.73 seconds total)