Starting phenix.real_space_refine on Thu Sep 18 14:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vh4_43234/09_2025/8vh4_43234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vh4_43234/09_2025/8vh4_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vh4_43234/09_2025/8vh4_43234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vh4_43234/09_2025/8vh4_43234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vh4_43234/09_2025/8vh4_43234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vh4_43234/09_2025/8vh4_43234.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 96, 'ARG:plan': 37, 'ASN:plan1': 25, 'GLN:plan1': 38, 'ASP:plan': 43, 'PHE:plan': 10, 'TYR:plan': 7, 'HIS:plan': 16, 'TRP:plan': 1} 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: {'ASP:plan': 8, 'GLU:plan': 9, 'ARG:plan': 5, 'GLN:plan1': 2} 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: 4.30, per 1000 atoms: 0.25 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: 1.72 Conformation dependent library (CDL) restraints added in 931.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.10 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: 4.70 Time building geometry restraints manager: 2.20 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.750 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.290 ------------------------------------------------------------------------------- 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= 0.308 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 : 8.89 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A1918 TYR 0.015 0.002 TYR A1739 PHE 0.024 0.002 PHE A 199 TRP 0.038 0.003 TRP A1376 HIS 0.013 0.002 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00610 (17579) covalent geometry : angle 1.01075 (24057) hydrogen bonds : bond 0.15229 ( 675) hydrogen bonds : angle 7.28621 ( 1911) *********************** 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 : 0.607 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: 0.1132 time to fit residues: 27.0476 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 : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 800 ASN A1021 ASN A1560 ASN A1584 HIS A1758 HIS A1871 ASN A2113 GLN A2328 ASN ** A2353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2369 ASN A2468 ASN A2505 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.064587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.050620 restraints weight = 108843.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.050564 restraints weight = 80534.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.051050 restraints weight = 69997.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.051118 restraints weight = 51243.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.051430 restraints weight = 46838.477| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17579 Z= 0.225 Angle : 0.727 11.429 24057 Z= 0.371 Chirality : 0.045 0.201 3012 Planarity : 0.005 0.058 3020 Dihedral : 8.040 175.321 2562 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.06 % Allowed : 6.71 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.24 (0.16), residues: 2366 helix: -0.95 (0.16), residues: 990 sheet: -3.16 (0.25), residues: 306 loop : -3.01 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2456 TYR 0.017 0.002 TYR A2099 PHE 0.026 0.002 PHE A 671 TRP 0.072 0.003 TRP A2104 HIS 0.006 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00486 (17579) covalent geometry : angle 0.72741 (24057) hydrogen bonds : bond 0.04131 ( 675) hydrogen bonds : angle 5.18757 ( 1911) *********************** 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 107 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1162 MET cc_start: 0.8507 (ptp) cc_final: 0.8281 (ptp) REVERT: A 1338 MET cc_start: 0.8014 (mtt) cc_final: 0.7410 (mtt) REVERT: A 1354 LEU cc_start: 0.8931 (tp) cc_final: 0.8644 (tt) REVERT: A 1702 MET cc_start: 0.8742 (mmm) cc_final: 0.7995 (mmm) REVERT: A 2470 MET cc_start: 0.8131 (ttt) cc_final: 0.7443 (mtp) REVERT: B 131 ASP cc_start: 0.8841 (m-30) cc_final: 0.8116 (p0) REVERT: B 132 ASP cc_start: 0.8456 (m-30) cc_final: 0.8191 (m-30) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.0984 time to fit residues: 18.0518 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 : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 159 optimal weight: 0.0000 chunk 148 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 43 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.5924 ------------------------------------------------------------------------------- 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 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN A2236 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.065506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.051893 restraints weight = 109990.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051180 restraints weight = 77554.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.051844 restraints weight = 72734.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.051946 restraints weight = 52578.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052330 restraints weight = 48344.022| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2339 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= 0.118 Angle : 0.601 7.802 24057 Z= 0.304 Chirality : 0.043 0.213 3012 Planarity : 0.004 0.052 3020 Dihedral : 7.335 179.868 2562 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.17), residues: 2366 helix: -0.29 (0.17), residues: 999 sheet: -2.80 (0.26), residues: 309 loop : -2.71 (0.17), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2523 TYR 0.014 0.001 TYR A1645 PHE 0.017 0.001 PHE A 671 TRP 0.064 0.002 TRP A2104 HIS 0.007 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00256 (17579) covalent geometry : angle 0.60085 (24057) hydrogen bonds : bond 0.03318 ( 675) hydrogen bonds : angle 4.71083 ( 1911) *********************** 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 100 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1338 MET cc_start: 0.8058 (mtt) cc_final: 0.7600 (mtt) REVERT: A 2521 MET cc_start: 0.8489 (ptp) cc_final: 0.8267 (ptp) REVERT: B 131 ASP cc_start: 0.8820 (m-30) cc_final: 0.8588 (m-30) REVERT: B 132 ASP cc_start: 0.8283 (m-30) cc_final: 0.7227 (t70) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1027 time to fit residues: 17.9207 Evaluate side-chains 81 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 76 optimal weight: 0.0570 chunk 137 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- 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** A1019 HIS A1405 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.064465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.050645 restraints weight = 108785.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050106 restraints weight = 76414.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.050542 restraints weight = 67749.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.051010 restraints weight = 49688.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.051109 restraints weight = 44994.260| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17579 Z= 0.152 Angle : 0.608 8.029 24057 Z= 0.309 Chirality : 0.043 0.179 3012 Planarity : 0.004 0.049 3020 Dihedral : 7.126 178.281 2562 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.17), residues: 2366 helix: 0.08 (0.17), residues: 1006 sheet: -2.74 (0.26), residues: 325 loop : -2.57 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2456 TYR 0.012 0.001 TYR A1747 PHE 0.023 0.001 PHE A1545 TRP 0.054 0.002 TRP A2104 HIS 0.007 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00342 (17579) covalent geometry : angle 0.60826 (24057) hydrogen bonds : bond 0.03200 ( 675) hydrogen bonds : angle 4.54246 ( 1911) *********************** 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 100 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1068 ASN cc_start: 0.8089 (m-40) cc_final: 0.7803 (m-40) REVERT: A 1162 MET cc_start: 0.8397 (ptp) cc_final: 0.8179 (ptp) REVERT: A 1338 MET cc_start: 0.8047 (mtt) cc_final: 0.7590 (mtt) REVERT: A 2470 MET cc_start: 0.8351 (ttt) cc_final: 0.8055 (ttm) REVERT: B 59 MET cc_start: 0.8428 (mtt) cc_final: 0.8201 (mmm) REVERT: B 131 ASP cc_start: 0.8731 (m-30) cc_final: 0.8501 (m-30) REVERT: B 132 ASP cc_start: 0.8411 (m-30) cc_final: 0.7260 (t70) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1051 time to fit residues: 18.1732 Evaluate side-chains 81 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 174 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 85 optimal weight: 0.0020 chunk 82 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 A1644 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.065010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.051353 restraints weight = 108872.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050830 restraints weight = 77415.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.051251 restraints weight = 69785.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.051677 restraints weight = 51280.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051757 restraints weight = 46739.631| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 17579 Z= 0.111 Angle : 0.580 9.096 24057 Z= 0.292 Chirality : 0.042 0.170 3012 Planarity : 0.004 0.049 3020 Dihedral : 6.918 175.424 2562 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.17), residues: 2366 helix: 0.31 (0.17), residues: 1004 sheet: -2.52 (0.27), residues: 314 loop : -2.42 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2523 TYR 0.018 0.001 TYR A2099 PHE 0.014 0.001 PHE A1047 TRP 0.034 0.001 TRP A1376 HIS 0.007 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00248 (17579) covalent geometry : angle 0.58033 (24057) hydrogen bonds : bond 0.02993 ( 675) hydrogen bonds : angle 4.39698 ( 1911) *********************** 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 99 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1338 MET cc_start: 0.8010 (mtt) cc_final: 0.7548 (mtt) REVERT: A 2155 MET cc_start: 0.7233 (ppp) cc_final: 0.6724 (ppp) REVERT: A 2458 MET cc_start: 0.7310 (tmm) cc_final: 0.6807 (tmm) REVERT: B 131 ASP cc_start: 0.8697 (m-30) cc_final: 0.8453 (m-30) REVERT: B 132 ASP cc_start: 0.8544 (m-30) cc_final: 0.7405 (t70) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1007 time to fit residues: 17.4709 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 : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 127 optimal weight: 0.6980 chunk 161 optimal weight: 0.0770 chunk 117 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 0.0000 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 overall best weight: 0.4542 ------------------------------------------------------------------------------- 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** A1101 ASN A2505 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.065178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.051576 restraints weight = 108888.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.051061 restraints weight = 76853.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051676 restraints weight = 70100.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.051699 restraints weight = 51747.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.052051 restraints weight = 47756.781| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17579 Z= 0.102 Angle : 0.560 7.686 24057 Z= 0.281 Chirality : 0.042 0.172 3012 Planarity : 0.004 0.048 3020 Dihedral : 6.705 170.678 2562 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.18), residues: 2366 helix: 0.50 (0.17), residues: 1006 sheet: -2.35 (0.27), residues: 320 loop : -2.23 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 767 TYR 0.014 0.001 TYR A1992 PHE 0.013 0.001 PHE A1545 TRP 0.036 0.002 TRP A1376 HIS 0.008 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00229 (17579) covalent geometry : angle 0.56047 (24057) hydrogen bonds : bond 0.02833 ( 675) hydrogen bonds : angle 4.25002 ( 1911) *********************** 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 103 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1338 MET cc_start: 0.8008 (mtt) cc_final: 0.7513 (mtt) REVERT: A 2458 MET cc_start: 0.7408 (tmm) cc_final: 0.6946 (tmm) REVERT: B 131 ASP cc_start: 0.8771 (m-30) cc_final: 0.8526 (m-30) REVERT: B 132 ASP cc_start: 0.8628 (m-30) cc_final: 0.7429 (t70) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0925 time to fit residues: 16.6260 Evaluate side-chains 81 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 218 optimal weight: 0.0270 chunk 177 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 134 optimal weight: 0.0370 chunk 237 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 206 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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** A1872 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.064684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.051102 restraints weight = 108174.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.050458 restraints weight = 76684.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.050888 restraints weight = 70384.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.051392 restraints weight = 51304.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.051463 restraints weight = 46343.111| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17579 Z= 0.116 Angle : 0.573 7.989 24057 Z= 0.288 Chirality : 0.042 0.176 3012 Planarity : 0.004 0.048 3020 Dihedral : 6.573 166.276 2562 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.18), residues: 2366 helix: 0.68 (0.18), residues: 1000 sheet: -2.16 (0.28), residues: 314 loop : -2.14 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2456 TYR 0.011 0.001 TYR A1747 PHE 0.010 0.001 PHE A1047 TRP 0.011 0.001 TRP A1376 HIS 0.009 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00261 (17579) covalent geometry : angle 0.57277 (24057) hydrogen bonds : bond 0.02842 ( 675) hydrogen bonds : angle 4.21735 ( 1911) *********************** 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 101 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1338 MET cc_start: 0.8018 (mtt) cc_final: 0.7499 (mtt) REVERT: A 2106 MET cc_start: 0.8676 (ttm) cc_final: 0.8441 (ttm) REVERT: B 131 ASP cc_start: 0.8782 (m-30) cc_final: 0.8531 (m-30) REVERT: B 132 ASP cc_start: 0.8676 (m-30) cc_final: 0.7452 (t70) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0962 time to fit residues: 16.9994 Evaluate side-chains 79 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 10 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 225 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 22 optimal weight: 0.0770 chunk 229 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A1039 HIS A2505 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.064806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.051109 restraints weight = 107879.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.050479 restraints weight = 74792.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.050907 restraints weight = 68800.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.051366 restraints weight = 50443.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.051430 restraints weight = 46234.103| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17579 Z= 0.107 Angle : 0.555 7.823 24057 Z= 0.279 Chirality : 0.042 0.164 3012 Planarity : 0.004 0.048 3020 Dihedral : 6.402 160.487 2562 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.18), residues: 2366 helix: 0.81 (0.18), residues: 997 sheet: -2.12 (0.28), residues: 322 loop : -2.07 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2456 TYR 0.011 0.001 TYR A1992 PHE 0.010 0.001 PHE A1047 TRP 0.036 0.002 TRP A1376 HIS 0.009 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00244 (17579) covalent geometry : angle 0.55541 (24057) hydrogen bonds : bond 0.02741 ( 675) hydrogen bonds : angle 4.11871 ( 1911) *********************** 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 100 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 842 MET cc_start: 0.8554 (tpp) cc_final: 0.8192 (tpp) REVERT: A 2521 MET cc_start: 0.8535 (ptt) cc_final: 0.7183 (ppp) REVERT: B 131 ASP cc_start: 0.8790 (m-30) cc_final: 0.8557 (m-30) REVERT: B 132 ASP cc_start: 0.8788 (m-30) cc_final: 0.7592 (t70) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1002 time to fit residues: 17.4356 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 : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 147 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 171 optimal weight: 0.0050 chunk 221 optimal weight: 0.0670 chunk 43 optimal weight: 0.0170 chunk 126 optimal weight: 0.0050 chunk 107 optimal weight: 0.6980 overall best weight: 0.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1407 HIS A2505 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.065443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.051894 restraints weight = 108767.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.051234 restraints weight = 74725.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.051702 restraints weight = 69430.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.052221 restraints weight = 50407.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052309 restraints weight = 46084.626| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17579 Z= 0.093 Angle : 0.550 7.940 24057 Z= 0.273 Chirality : 0.041 0.164 3012 Planarity : 0.004 0.049 3020 Dihedral : 6.151 151.895 2562 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.18), residues: 2366 helix: 0.90 (0.18), residues: 994 sheet: -1.92 (0.28), residues: 317 loop : -2.01 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 767 TYR 0.022 0.001 TYR A1649 PHE 0.012 0.001 PHE A1284 TRP 0.033 0.001 TRP A1376 HIS 0.006 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00203 (17579) covalent geometry : angle 0.55013 (24057) hydrogen bonds : bond 0.02566 ( 675) hydrogen bonds : angle 4.01635 ( 1911) *********************** 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 103 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2458 MET cc_start: 0.6993 (tmm) cc_final: 0.6765 (tmm) REVERT: A 2521 MET cc_start: 0.8555 (ptt) cc_final: 0.7336 (ppp) REVERT: B 131 ASP cc_start: 0.8850 (m-30) cc_final: 0.8610 (m-30) REVERT: B 132 ASP cc_start: 0.8808 (m-30) cc_final: 0.7631 (t70) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0929 time to fit residues: 16.6285 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 : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 164 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 100 optimal weight: 0.0980 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 109 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1407 HIS ** 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 = 0.3598 r_free = 0.3598 target = 0.064600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051242 restraints weight = 108234.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050325 restraints weight = 79862.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.050838 restraints weight = 73601.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051229 restraints weight = 53417.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.051378 restraints weight = 49534.586| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17579 Z= 0.116 Angle : 0.572 8.588 24057 Z= 0.284 Chirality : 0.042 0.193 3012 Planarity : 0.004 0.049 3020 Dihedral : 6.088 145.141 2562 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.18), residues: 2366 helix: 0.99 (0.18), residues: 993 sheet: -1.90 (0.28), residues: 323 loop : -1.96 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1067 TYR 0.011 0.001 TYR A1747 PHE 0.011 0.001 PHE A 324 TRP 0.038 0.002 TRP A1376 HIS 0.008 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00265 (17579) covalent geometry : angle 0.57168 (24057) hydrogen bonds : bond 0.02633 ( 675) hydrogen bonds : angle 4.03983 ( 1911) ********************** 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 98 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2458 MET cc_start: 0.7580 (tmm) cc_final: 0.7026 (tmm) REVERT: A 2470 MET cc_start: 0.8249 (ttm) cc_final: 0.8023 (ttp) REVERT: A 2521 MET cc_start: 0.8529 (ptt) cc_final: 0.7206 (ppp) REVERT: B 131 ASP cc_start: 0.8844 (m-30) cc_final: 0.8613 (m-30) REVERT: B 132 ASP cc_start: 0.8838 (m-30) cc_final: 0.7588 (t70) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0989 time to fit residues: 16.8893 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 : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 0.0470 chunk 45 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 131 optimal weight: 0.0370 chunk 191 optimal weight: 6.9990 chunk 181 optimal weight: 0.0970 chunk 116 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1407 HIS A2505 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.065201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051478 restraints weight = 107917.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.051077 restraints weight = 74149.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.051564 restraints weight = 66400.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051895 restraints weight = 49555.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.052018 restraints weight = 46708.787| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17579 Z= 0.093 Angle : 0.548 8.179 24057 Z= 0.271 Chirality : 0.041 0.178 3012 Planarity : 0.004 0.050 3020 Dihedral : 5.889 135.034 2562 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.18), residues: 2366 helix: 0.96 (0.18), residues: 1006 sheet: -1.76 (0.28), residues: 329 loop : -1.87 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1067 TYR 0.013 0.001 TYR A1649 PHE 0.010 0.001 PHE A 324 TRP 0.034 0.002 TRP A1376 HIS 0.007 0.001 HIS A 442 Details of bonding type rmsd covalent geometry : bond 0.00209 (17579) covalent geometry : angle 0.54759 (24057) hydrogen bonds : bond 0.02521 ( 675) hydrogen bonds : angle 3.95436 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2274.91 seconds wall clock time: 40 minutes 14.21 seconds (2414.21 seconds total)