Starting phenix.real_space_refine on Mon Nov 18 21:52:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh4_43234/11_2024/8vh4_43234.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh4_43234/11_2024/8vh4_43234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh4_43234/11_2024/8vh4_43234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh4_43234/11_2024/8vh4_43234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh4_43234/11_2024/8vh4_43234.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vh4_43234/11_2024/8vh4_43234.cif" } resolution = 4.1 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= 0.001 sd= 0.061 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 8 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 11076 2.51 5 N 2937 2.21 5 O 3145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17266 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 15964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2235, 15964 Classifications: {'peptide': 2235} Incomplete info: {'truncation_to_alanine': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 84, 'TRANS': 2148} Chain breaks: 18 Unresolved non-hydrogen bonds: 1830 Unresolved non-hydrogen angles: 2215 Unresolved non-hydrogen dihedrals: 1525 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 38, 'HIS:plan': 16, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 1, 'ASP:plan': 43, 'PHE:plan': 10, 'GLU:plan': 96, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 1123 Chain: "B" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1210 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 93 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} Time building chain proxies: 10.33, per 1000 atoms: 0.60 Number of scatterers: 17266 At special positions: 0 Unit cell: (111.188, 132.848, 245.48, 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 99 16.00 P 8 15.00 Mg 1 11.99 O 3145 8.00 N 2937 7.00 C 11076 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: 4.40 Conformation dependent library (CDL) restraints added in 2.4 seconds 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4594 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 21 sheets defined 44.8% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.634A pdb=" N LEU A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 45 removed outlier: 3.789A pdb=" N LEU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.902A pdb=" N CYS A 86 " --> pdb=" O TRP A 82 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 114 through 125 removed outlier: 3.643A pdb=" N ILE A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 158 through 170 removed outlier: 3.808A pdb=" N LEU A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.505A pdb=" N GLN A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.711A pdb=" N VAL A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 250 through 258 removed outlier: 3.778A pdb=" N VAL A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.685A pdb=" N THR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.953A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 319 removed outlier: 4.240A pdb=" N SER A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 removed outlier: 3.664A pdb=" N ASN A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 360 removed outlier: 4.640A pdb=" N GLU A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.610A 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 380 through 381 No H-bonds generated for 'chain 'A' and resid 380 through 381' Processing helix chain 'A' and resid 382 through 388 removed outlier: 3.527A pdb=" N ILE A 388 " --> pdb=" O HIS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 408 removed outlier: 3.549A pdb=" N GLU A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.619A pdb=" N PHE A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 434 removed outlier: 3.647A pdb=" N LYS A 434 " --> pdb=" O ASN A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.695A pdb=" N ASN A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 removed outlier: 3.709A pdb=" N ALA A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 490 Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 497 through 503 removed outlier: 3.688A pdb=" N GLN A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 526 through 540 removed outlier: 5.097A pdb=" N MET A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 3.899A pdb=" N LEU A 545 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 570 removed outlier: 3.882A pdb=" N GLN A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 599 through 613 removed outlier: 4.092A pdb=" N SER A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 638 removed outlier: 4.366A pdb=" N LEU A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 659 removed outlier: 3.873A pdb=" N GLN A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 671 through 685 removed outlier: 3.840A pdb=" N ILE A 675 " --> pdb=" O PHE A 671 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE A 683 " --> pdb=" O MET A 679 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 704 removed outlier: 3.692A pdb=" N MET A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.756A pdb=" N LYS A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.647A 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 743 through 751 Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.655A 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 removed outlier: 3.718A pdb=" N ILE A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 801 Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.539A pdb=" N SER A1001 " --> pdb=" O ILE A 997 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A1002 " --> pdb=" O ASP A 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 997 through 1002' Processing helix chain 'A' and resid 1006 through 1013 removed outlier: 3.918A pdb=" N HIS A1012 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A1013 " --> pdb=" O LEU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.629A pdb=" N CYS A1031 " --> pdb=" O PRO A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1057 removed outlier: 3.532A pdb=" N MET A1057 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.780A pdb=" N LEU A1193 " --> pdb=" O PRO A1189 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A1194 " --> pdb=" O GLU A1190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1189 through 1194' Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.839A pdb=" N GLY A1265 " --> pdb=" O PRO A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 removed outlier: 3.557A pdb=" N MET A1288 " --> pdb=" O PRO A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1328 removed outlier: 4.013A pdb=" N ILE A1319 " --> pdb=" O ALA A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1356 Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 3.880A pdb=" N MET A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1424 removed outlier: 3.706A pdb=" N LYS A1423 " --> pdb=" O ASP A1420 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A1424 " --> pdb=" O LEU A1421 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1420 through 1424' Processing helix chain 'A' and resid 1427 through 1430 Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1466 through 1473 Processing helix chain 'A' and resid 1494 through 1510 removed outlier: 3.750A pdb=" N ALA A1498 " --> pdb=" O SER A1494 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A1510 " --> pdb=" O ASN A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1521 removed outlier: 3.553A pdb=" N GLN A1521 " --> pdb=" O VAL A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1538 removed outlier: 3.842A pdb=" N VAL A1528 " --> pdb=" O PRO A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1560 removed outlier: 3.653A pdb=" N ASN A1560 " --> pdb=" O LEU A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1579 Processing helix chain 'A' and resid 1599 through 1610 removed outlier: 4.059A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A1610 " --> pdb=" O ILE A1606 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1655 Processing helix chain 'A' and resid 1703 through 1713 Processing helix chain 'A' and resid 1770 through 1792 Processing helix chain 'A' and resid 1828 through 1835 removed outlier: 3.605A pdb=" N LYS A1832 " --> pdb=" O ASP A1828 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1856 Processing helix chain 'A' and resid 1865 through 1869 removed outlier: 3.547A pdb=" N ILE A1868 " --> pdb=" O PRO A1865 " (cutoff:3.500A) removed outlier: 3.742A 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: 3.966A pdb=" N LEU A1885 " --> pdb=" O PRO A1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1924 removed outlier: 3.775A pdb=" N VAL A1922 " --> pdb=" O ARG A1918 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 removed outlier: 3.594A 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 2022 removed outlier: 3.544A pdb=" N GLN A2022 " --> pdb=" O GLY A2019 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2053 through 2068 Processing helix chain 'A' and resid 2070 through 2077 Processing helix chain 'A' and resid 2079 through 2085 Processing helix chain 'A' and resid 2086 through 2089 removed outlier: 3.759A pdb=" N GLN A2089 " --> pdb=" O LEU A2086 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2086 through 2089' Processing helix chain 'A' and resid 2094 through 2099 Processing helix chain 'A' and resid 2104 through 2114 removed outlier: 3.830A pdb=" N LEU A2110 " --> pdb=" O MET A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2133 removed outlier: 3.667A pdb=" N ASP A2130 " --> pdb=" O ALA A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 3.684A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2208 through 2211 removed outlier: 3.750A pdb=" N LYS A2211 " --> pdb=" O PRO A2208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2208 through 2211' Processing helix chain 'A' and resid 2346 through 2351 Processing helix chain 'A' and resid 2390 through 2396 removed outlier: 4.334A pdb=" N LEU A2393 " --> pdb=" O VAL A2390 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG A2394 " --> pdb=" O HIS A2391 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A2396 " --> pdb=" O LEU A2393 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2525 removed outlier: 3.736A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A2508 " --> pdb=" O VAL A2504 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A2509 " --> pdb=" O GLN A2505 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A2512 " --> pdb=" O GLU A2508 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG A2523 " --> pdb=" O GLU A2519 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A2524 " --> pdb=" O LYS A2520 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A2525 " --> pdb=" O MET A2521 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 104 through 109 removed outlier: 3.621A pdb=" N SER B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.524A pdb=" N TRP B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 removed outlier: 3.655A pdb=" N CYS B 159 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N THR B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 192 through 206 removed outlier: 3.833A pdb=" N ILE B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE B 197 " --> pdb=" O VAL B 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: 6.804A pdb=" N LEU A1016 " --> pdb=" O ASP A1041 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU A1040 " --> pdb=" O ASP A1064 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE A1088 " --> pdb=" O ILE A1113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1177 through 1179 removed outlier: 6.640A pdb=" N LEU A1201 " --> pdb=" O LEU A1226 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU A1250 " --> pdb=" O ASP A1274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1376 through 1379 removed outlier: 7.032A pdb=" N MET A1335 " --> pdb=" O ASN A1391 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TRP A1393 " --> pdb=" O MET A1335 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A1337 " --> pdb=" O TRP A1393 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N LEU A1414 " --> pdb=" O ARG A1334 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS A1336 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A1416 " --> pdb=" O LYS A1336 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N MET A1338 " --> pdb=" O LEU A1416 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL A1418 " --> pdb=" O MET A1338 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE A1448 " --> pdb=" O ALA A1413 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL A1447 " --> pdb=" O ARG A1483 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR A1485 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A1449 " --> pdb=" O TYR A1485 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1582 through 1583 Processing sheet with id=AA6, first strand: chain 'A' and resid 1690 through 1691 removed outlier: 3.551A pdb=" N THR A1766 " --> pdb=" O LEU A1749 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A1749 " --> pdb=" O THR A1766 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1741 through 1743 removed outlier: 6.546A pdb=" N ALA A1746 " --> pdb=" O TRP A1742 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1813 through 1814 removed outlier: 3.849A pdb=" N TYR A1814 " --> pdb=" O ILE A1825 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A1825 " --> pdb=" O TYR A1814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 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: 3.904A pdb=" N SER A1892 " --> pdb=" O ILE A1907 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1875 through 1876 removed outlier: 3.598A pdb=" N MET A1947 " --> pdb=" O ALA A1904 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AB4, first strand: chain 'A' and resid 2140 through 2144 removed outlier: 6.288A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR A2475 " --> pdb=" O VAL A2455 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A2455 " --> pdb=" O TYR A2475 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2155 through 2157 Processing sheet with id=AB6, first strand: chain 'A' and resid 2199 through 2207 removed outlier: 3.806A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A2218 " --> pdb=" O CYS A2201 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A2203 " --> pdb=" O VAL A2216 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A2212 " --> pdb=" O LEU A2207 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS A2236 " --> pdb=" O VAL A2226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2247 through 2249 removed outlier: 3.588A pdb=" N VAL A2265 " --> pdb=" O ALA A2273 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A2273 " --> pdb=" O VAL A2265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2300 through 2303 removed outlier: 6.993A pdb=" N GLY A2318 " --> pdb=" O MET A2301 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU A2303 " --> pdb=" O TRP A2316 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TRP A2316 " --> pdb=" O LEU A2303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 3.889A pdb=" N THR A2356 " --> pdb=" O ALA A2366 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A2358 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR A2364 " --> pdb=" O VAL A2358 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 3.626A pdb=" N THR A2416 " --> pdb=" O GLY A2428 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A2428 " --> pdb=" O THR A2416 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N HIS A2433 " --> pdb=" O THR A2429 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A2446 " --> pdb=" O LEU A2436 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 41 through 42 removed outlier: 6.558A pdb=" N PHE B 41 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.209A pdb=" N ILE B 118 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL B 153 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 120 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN B 155 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 122 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 181 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 152 " --> pdb=" O ARG B 181 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1911 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: 9.58 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2940 1.32 - 1.45: 4281 1.45 - 1.57: 10205 1.57 - 1.69: 12 1.69 - 1.82: 141 Bond restraints: 17579 Sorted by residual: bond pdb=" O3A ANP A2602 " pdb=" PB ANP A2602 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" CA GLY A 180 " pdb=" C GLY A 180 " ideal model delta sigma weight residual 1.515 1.465 0.050 9.30e-03 1.16e+04 2.90e+01 bond pdb=" N3B ANP A2602 " pdb=" PG ANP A2602 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" N3B GNP B 302 " pdb=" PG GNP B 302 " ideal model delta sigma weight residual 1.801 1.700 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C ASP A 204 " pdb=" N TYR A 205 " ideal model delta sigma weight residual 1.335 1.275 0.059 1.25e-02 6.40e+03 2.25e+01 ... (remaining 17574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 23833 4.15 - 8.30: 201 8.30 - 12.45: 16 12.45 - 16.60: 5 16.60 - 20.76: 2 Bond angle restraints: 24057 Sorted by residual: angle pdb=" N GLY A 180 " pdb=" CA GLY A 180 " pdb=" C GLY A 180 " ideal model delta sigma weight residual 110.96 90.20 20.76 1.49e+00 4.50e-01 1.94e+02 angle pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta sigma weight residual 110.81 129.29 -18.48 1.60e+00 3.91e-01 1.33e+02 angle pdb=" N GLY A1891 " pdb=" CA GLY A1891 " pdb=" C GLY A1891 " ideal model delta sigma weight residual 111.14 97.91 13.23 1.46e+00 4.69e-01 8.21e+01 angle pdb=" C GLU A 201 " pdb=" CA GLU A 201 " pdb=" CB GLU A 201 " ideal model delta sigma weight residual 112.00 98.32 13.68 1.61e+00 3.86e-01 7.22e+01 angle pdb=" N VAL A 176 " pdb=" CA VAL A 176 " pdb=" C VAL A 176 " ideal model delta sigma weight residual 110.72 103.14 7.58 1.01e+00 9.80e-01 5.63e+01 ... (remaining 24052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 10279 35.28 - 70.56: 186 70.56 - 105.84: 14 105.84 - 141.12: 0 141.12 - 176.40: 1 Dihedral angle restraints: 10480 sinusoidal: 3453 harmonic: 7027 Sorted by residual: dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -147.30 24.70 0 2.50e+00 1.60e-01 9.76e+01 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 -138.66 -41.34 0 5.00e+00 4.00e-02 6.84e+01 dihedral pdb=" CA LEU A1673 " pdb=" C LEU A1673 " pdb=" N SER A1674 " pdb=" CA SER A1674 " ideal model delta harmonic sigma weight residual 180.00 144.52 35.48 0 5.00e+00 4.00e-02 5.04e+01 ... (remaining 10477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 2985 0.177 - 0.354: 21 0.354 - 0.531: 4 0.531 - 0.708: 1 0.708 - 0.886: 1 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CA MET A 206 " pdb=" N MET A 206 " pdb=" C MET A 206 " pdb=" CB MET A 206 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" CA TYR A1894 " pdb=" N TYR A1894 " pdb=" C TYR A1894 " pdb=" CB TYR A1894 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 3009 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A2496 " 0.029 2.00e-02 2.50e+03 5.75e-02 3.30e+01 pdb=" C TRP A2496 " -0.099 2.00e-02 2.50e+03 pdb=" O TRP A2496 " 0.038 2.00e-02 2.50e+03 pdb=" N ASP A2497 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 206 " -0.023 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C MET A 206 " 0.081 2.00e-02 2.50e+03 pdb=" O MET A 206 " -0.030 2.00e-02 2.50e+03 pdb=" N ILE A 207 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 178 " -0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C LYS A 178 " 0.077 2.00e-02 2.50e+03 pdb=" O LYS A 178 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU A 179 " -0.027 2.00e-02 2.50e+03 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 193 2.60 - 3.18: 15063 3.18 - 3.75: 26128 3.75 - 4.33: 34308 4.33 - 4.90: 56468 Nonbonded interactions: 132160 Sorted by model distance: nonbonded pdb=" N GLY A 180 " pdb=" O GLY A 180 " model vdw 2.031 2.496 nonbonded pdb="MG MG B 301 " pdb=" O2B GNP B 302 " model vdw 2.044 2.170 nonbonded pdb="MG MG B 301 " pdb=" O1A GNP B 302 " model vdw 2.077 2.170 nonbonded pdb="MG MG B 301 " pdb=" O2G GNP B 302 " model vdw 2.112 2.170 nonbonded pdb="MG MG B 301 " pdb=" N3B GNP B 302 " model vdw 2.120 2.250 ... (remaining 132155 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 43.670 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 0.144 17579 Z= 0.401 Angle : 1.011 20.756 24057 Z= 0.573 Chirality : 0.059 0.886 3012 Planarity : 0.007 0.071 3020 Dihedral : 14.893 176.396 5886 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.65 (0.14), residues: 2366 helix: -2.65 (0.13), residues: 981 sheet: -3.29 (0.25), residues: 309 loop : -3.39 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A1376 HIS 0.013 0.002 HIS A 185 PHE 0.024 0.002 PHE A 199 TYR 0.015 0.002 TYR A1739 ARG 0.003 0.000 ARG A1918 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1338 MET cc_start: 0.7907 (mtt) cc_final: 0.7641 (mtp) REVERT: A 1354 LEU cc_start: 0.8269 (tp) cc_final: 0.7968 (tt) REVERT: A 1947 MET cc_start: 0.8726 (ptp) cc_final: 0.8421 (ptm) REVERT: A 2521 MET cc_start: 0.8561 (ptp) cc_final: 0.8171 (ptp) REVERT: B 132 ASP cc_start: 0.6834 (m-30) cc_final: 0.6370 (t0) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2770 time to fit residues: 68.4568 Evaluate side-chains 89 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 0.2980 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 0.0980 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 0.0570 chunk 217 optimal weight: 4.9990 overall best weight: 0.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 227 HIS ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS A 398 HIS ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 800 ASN A1021 ASN A1269 ASN A1560 ASN A1758 HIS A2113 GLN A2328 ASN A2369 ASN A2468 ASN A2505 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17579 Z= 0.185 Angle : 0.646 8.616 24057 Z= 0.330 Chirality : 0.043 0.209 3012 Planarity : 0.005 0.054 3020 Dihedral : 8.025 177.368 2562 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.12 % Allowed : 5.08 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % 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: -3.27 (0.16), residues: 2366 helix: -1.10 (0.16), residues: 993 sheet: -3.02 (0.25), residues: 293 loop : -2.95 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A2104 HIS 0.008 0.001 HIS A 227 PHE 0.031 0.001 PHE A 671 TYR 0.018 0.001 TYR A2099 ARG 0.003 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1702 MET cc_start: 0.8777 (mmm) cc_final: 0.8196 (mmm) REVERT: A 1947 MET cc_start: 0.8796 (ptp) cc_final: 0.8450 (ptm) REVERT: A 1989 MET cc_start: 0.8189 (mmp) cc_final: 0.7956 (tpp) REVERT: A 2155 MET cc_start: 0.6724 (ppp) cc_final: 0.6425 (ppp) REVERT: A 2470 MET cc_start: 0.7942 (ttt) cc_final: 0.7436 (mtp) REVERT: B 131 ASP cc_start: 0.7739 (m-30) cc_final: 0.7436 (p0) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.2632 time to fit residues: 52.3530 Evaluate side-chains 82 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 175 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2236 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17579 Z= 0.188 Angle : 0.596 7.987 24057 Z= 0.302 Chirality : 0.042 0.219 3012 Planarity : 0.004 0.050 3020 Dihedral : 7.187 177.268 2562 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % 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: -2.49 (0.17), residues: 2366 helix: -0.27 (0.17), residues: 1001 sheet: -2.77 (0.26), residues: 315 loop : -2.68 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A2214 HIS 0.006 0.001 HIS A2236 PHE 0.017 0.001 PHE A 671 TYR 0.012 0.001 TYR A1747 ARG 0.003 0.000 ARG A2523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1947 MET cc_start: 0.8838 (ptp) cc_final: 0.8592 (ptp) REVERT: A 2155 MET cc_start: 0.6270 (ppp) cc_final: 0.5876 (ppp) REVERT: A 2458 MET cc_start: 0.7643 (ttp) cc_final: 0.7287 (ttp) REVERT: A 2459 MET cc_start: 0.7995 (ptt) cc_final: 0.7639 (ptt) REVERT: A 2521 MET cc_start: 0.8596 (ptp) cc_final: 0.8346 (ptp) REVERT: B 128 GLU cc_start: 0.7524 (pm20) cc_final: 0.7156 (pm20) REVERT: B 132 ASP cc_start: 0.7212 (m-30) cc_final: 0.5837 (t70) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2450 time to fit residues: 44.2526 Evaluate side-chains 84 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 3.9990 chunk 164 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN A1405 HIS ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17579 Z= 0.237 Angle : 0.616 8.256 24057 Z= 0.311 Chirality : 0.043 0.210 3012 Planarity : 0.004 0.050 3020 Dihedral : 7.042 176.891 2562 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % 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: -2.09 (0.17), residues: 2366 helix: 0.15 (0.17), residues: 1000 sheet: -2.58 (0.26), residues: 319 loop : -2.55 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A2104 HIS 0.007 0.001 HIS A 543 PHE 0.019 0.001 PHE A1047 TYR 0.013 0.001 TYR A1992 ARG 0.003 0.000 ARG A2456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1068 ASN cc_start: 0.7883 (m-40) cc_final: 0.7592 (m-40) REVERT: A 1947 MET cc_start: 0.8844 (ptp) cc_final: 0.8622 (ptp) REVERT: A 2470 MET cc_start: 0.7977 (ttt) cc_final: 0.7719 (ttm) REVERT: B 128 GLU cc_start: 0.7560 (pm20) cc_final: 0.7208 (pm20) REVERT: B 132 ASP cc_start: 0.7165 (m-30) cc_final: 0.5889 (t70) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2413 time to fit residues: 44.4693 Evaluate side-chains 82 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 HIS A1101 ASN A1584 HIS ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 17579 Z= 0.252 Angle : 0.626 11.122 24057 Z= 0.316 Chirality : 0.043 0.191 3012 Planarity : 0.004 0.050 3020 Dihedral : 6.980 174.813 2562 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % 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: -1.84 (0.17), residues: 2366 helix: 0.38 (0.17), residues: 1000 sheet: -2.50 (0.27), residues: 314 loop : -2.43 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A1376 HIS 0.008 0.001 HIS A 442 PHE 0.021 0.001 PHE A1545 TYR 0.029 0.002 TYR A2099 ARG 0.003 0.000 ARG A2522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1338 MET cc_start: 0.8136 (mtt) cc_final: 0.7760 (mtt) REVERT: A 1947 MET cc_start: 0.8859 (ptp) cc_final: 0.8603 (ptp) REVERT: A 2458 MET cc_start: 0.7294 (tmm) cc_final: 0.6891 (tmm) REVERT: B 128 GLU cc_start: 0.7547 (pm20) cc_final: 0.7188 (pm20) REVERT: B 132 ASP cc_start: 0.7130 (m-30) cc_final: 0.5787 (t70) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2437 time to fit residues: 40.8003 Evaluate side-chains 82 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 0.0370 chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 0.2980 chunk 121 optimal weight: 0.9980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS A1407 HIS ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17579 Z= 0.167 Angle : 0.572 7.893 24057 Z= 0.287 Chirality : 0.042 0.170 3012 Planarity : 0.004 0.049 3020 Dihedral : 6.776 170.702 2562 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % 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: -1.60 (0.18), residues: 2366 helix: 0.56 (0.18), residues: 1003 sheet: -2.34 (0.27), residues: 322 loop : -2.27 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1376 HIS 0.007 0.001 HIS A 442 PHE 0.012 0.001 PHE A1047 TYR 0.013 0.001 TYR A1992 ARG 0.002 0.000 ARG A2456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1338 MET cc_start: 0.8182 (mtt) cc_final: 0.7782 (mtt) REVERT: A 1947 MET cc_start: 0.8831 (ptp) cc_final: 0.8587 (ptp) REVERT: A 2106 MET cc_start: 0.8552 (ptm) cc_final: 0.8262 (tmm) REVERT: A 2458 MET cc_start: 0.7111 (tmm) cc_final: 0.6789 (tmm) REVERT: A 2470 MET cc_start: 0.8045 (ttt) cc_final: 0.7792 (ttm) REVERT: B 128 GLU cc_start: 0.7517 (pm20) cc_final: 0.7123 (pm20) REVERT: B 132 ASP cc_start: 0.7147 (m-30) cc_final: 0.5896 (t70) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2509 time to fit residues: 42.6699 Evaluate side-chains 78 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17579 Z= 0.274 Angle : 0.640 9.212 24057 Z= 0.321 Chirality : 0.044 0.187 3012 Planarity : 0.004 0.049 3020 Dihedral : 6.826 167.107 2562 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % 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: -1.55 (0.18), residues: 2366 helix: 0.58 (0.17), residues: 1003 sheet: -2.21 (0.27), residues: 308 loop : -2.29 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1376 HIS 0.008 0.001 HIS A 442 PHE 0.019 0.002 PHE A1047 TYR 0.018 0.001 TYR A 250 ARG 0.004 0.000 ARG A2456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1947 MET cc_start: 0.8890 (ptp) cc_final: 0.8465 (ptp) REVERT: A 2106 MET cc_start: 0.8768 (ptm) cc_final: 0.8443 (tmm) REVERT: A 2458 MET cc_start: 0.7399 (tmm) cc_final: 0.6924 (tmm) REVERT: A 2470 MET cc_start: 0.8276 (ttt) cc_final: 0.7851 (ttm) REVERT: B 131 ASP cc_start: 0.7787 (m-30) cc_final: 0.7543 (p0) REVERT: B 132 ASP cc_start: 0.7259 (m-30) cc_final: 0.5869 (t70) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2541 time to fit residues: 42.0269 Evaluate side-chains 78 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 0.0270 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 157 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 HIS A1872 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17579 Z= 0.154 Angle : 0.571 8.195 24057 Z= 0.285 Chirality : 0.042 0.162 3012 Planarity : 0.004 0.049 3020 Dihedral : 6.563 162.250 2562 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % 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: -1.31 (0.18), residues: 2366 helix: 0.79 (0.18), residues: 993 sheet: -2.18 (0.28), residues: 318 loop : -2.10 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1376 HIS 0.007 0.001 HIS A 442 PHE 0.011 0.001 PHE A1047 TYR 0.018 0.001 TYR A1649 ARG 0.002 0.000 ARG A 767 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1947 MET cc_start: 0.8841 (ptp) cc_final: 0.8606 (ptp) REVERT: A 2458 MET cc_start: 0.7189 (tmm) cc_final: 0.6785 (tmm) REVERT: A 2470 MET cc_start: 0.8214 (ttt) cc_final: 0.7850 (ttm) REVERT: B 128 GLU cc_start: 0.7235 (pm20) cc_final: 0.6966 (pm20) REVERT: B 132 ASP cc_start: 0.7201 (m-30) cc_final: 0.5877 (t70) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2636 time to fit residues: 44.5768 Evaluate side-chains 78 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 0.0870 chunk 202 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 129 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17579 Z= 0.260 Angle : 0.626 9.466 24057 Z= 0.315 Chirality : 0.043 0.177 3012 Planarity : 0.004 0.048 3020 Dihedral : 6.579 156.739 2562 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % 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: -1.32 (0.18), residues: 2366 helix: 0.80 (0.18), residues: 992 sheet: -2.06 (0.27), residues: 312 loop : -2.17 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A1376 HIS 0.008 0.001 HIS A 442 PHE 0.024 0.001 PHE A1047 TYR 0.020 0.002 TYR A1092 ARG 0.002 0.000 ARG A2456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: A 1947 MET cc_start: 0.8894 (ptp) cc_final: 0.8477 (ptp) REVERT: A 2458 MET cc_start: 0.7369 (tmm) cc_final: 0.6928 (tmm) REVERT: A 2470 MET cc_start: 0.8212 (ttt) cc_final: 0.7760 (ttm) REVERT: B 128 GLU cc_start: 0.6924 (pm20) cc_final: 0.6711 (pm20) REVERT: B 132 ASP cc_start: 0.7312 (m-30) cc_final: 0.5914 (t70) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2444 time to fit residues: 41.4427 Evaluate side-chains 77 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 220 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 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 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17579 Z= 0.212 Angle : 0.593 8.483 24057 Z= 0.296 Chirality : 0.043 0.168 3012 Planarity : 0.004 0.049 3020 Dihedral : 6.445 151.272 2562 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % 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: -1.20 (0.18), residues: 2366 helix: 0.87 (0.18), residues: 995 sheet: -2.09 (0.27), residues: 327 loop : -2.04 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A1376 HIS 0.005 0.001 HIS A 442 PHE 0.019 0.001 PHE A1047 TYR 0.014 0.001 TYR A1649 ARG 0.003 0.000 ARG A2456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.7622 (mmm) cc_final: 0.7096 (mtp) REVERT: A 1338 MET cc_start: 0.8388 (mtp) cc_final: 0.8146 (mtp) REVERT: A 2458 MET cc_start: 0.7374 (tmm) cc_final: 0.6894 (tmm) REVERT: A 2470 MET cc_start: 0.8180 (ttt) cc_final: 0.7771 (ttm) REVERT: B 132 ASP cc_start: 0.7242 (m-30) cc_final: 0.5774 (t70) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2378 time to fit residues: 41.0520 Evaluate side-chains 76 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 175 optimal weight: 0.0770 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 195 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.064165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050269 restraints weight = 107270.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049757 restraints weight = 73102.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050285 restraints weight = 65528.426| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17579 Z= 0.147 Angle : 0.566 8.047 24057 Z= 0.279 Chirality : 0.042 0.165 3012 Planarity : 0.004 0.050 3020 Dihedral : 6.161 141.956 2562 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % 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: -1.03 (0.18), residues: 2366 helix: 1.04 (0.18), residues: 989 sheet: -1.85 (0.28), residues: 313 loop : -2.01 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A1376 HIS 0.006 0.001 HIS A 442 PHE 0.024 0.001 PHE A 324 TYR 0.015 0.001 TYR A1649 ARG 0.002 0.000 ARG A 767 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.70 seconds wall clock time: 51 minutes 48.77 seconds (3108.77 seconds total)