Starting phenix.real_space_refine on Tue Aug 26 06:44:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vh5_43235/08_2025/8vh5_43235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vh5_43235/08_2025/8vh5_43235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vh5_43235/08_2025/8vh5_43235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vh5_43235/08_2025/8vh5_43235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vh5_43235/08_2025/8vh5_43235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vh5_43235/08_2025/8vh5_43235.map" } resolution = 4.0 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= 0.003 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 21724 2.51 5 N 5738 2.21 5 O 6082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33744 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 15573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2221, 15573 Classifications: {'peptide': 2221} Incomplete info: {'truncation_to_alanine': 580} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 2135} Chain breaks: 21 Unresolved non-hydrogen bonds: 2116 Unresolved non-hydrogen angles: 2560 Unresolved non-hydrogen dihedrals: 1751 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLU:plan': 105, 'ARG:plan': 45, 'ASN:plan1': 37, 'GLN:plan1': 42, 'ASP:plan': 45, 'PHE:plan': 10, 'TYR:plan': 6, 'HIS:plan': 17, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 1255 Chain: "B" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1200 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 9, 'ARG:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 15587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2221, 15587 Classifications: {'peptide': 2221} Incomplete info: {'truncation_to_alanine': 575} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 2135} Chain breaks: 21 Unresolved non-hydrogen bonds: 2103 Unresolved non-hydrogen angles: 2547 Unresolved non-hydrogen dihedrals: 1740 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLU:plan': 104, 'ARG:plan': 45, 'ASN:plan1': 36, 'GLN:plan1': 42, 'ASP:plan': 45, 'PHE:plan': 11, 'TYR:plan': 6, 'HIS:plan': 17, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 1254 Chain: "D" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1200 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 9, 'ARG:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.85, per 1000 atoms: 0.20 Number of scatterers: 33744 At special positions: 0 Unit cell: (145.844, 181.944, 203.604, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 182 16.00 P 16 15.00 Mg 2 11.99 O 6082 8.00 N 5738 7.00 C 21724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9136 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 42 sheets defined 46.4% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.527A pdb=" N PHE A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 67 removed outlier: 4.266A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 92 Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.441A pdb=" N MET A 96 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.862A pdb=" N LEU A 119 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.626A pdb=" N VAL A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 235 through 243 removed outlier: 3.803A pdb=" N GLU A 240 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.621A pdb=" N THR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 4.110A pdb=" N ILE A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.190A pdb=" N HIS A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.511A pdb=" N TYR A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 324 removed outlier: 4.191A pdb=" N SER A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 4.292A pdb=" N TRP A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.714A pdb=" N LEU A 384 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 408 removed outlier: 3.513A pdb=" N GLU A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.543A pdb=" N PHE A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 439 removed outlier: 3.900A pdb=" N ILE A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.601A pdb=" N ASN A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 470 removed outlier: 3.614A pdb=" N ALA A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 494 removed outlier: 3.823A pdb=" N MET A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.526A pdb=" N GLN A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 526 through 540 Processing helix chain 'A' and resid 541 through 553 removed outlier: 3.567A pdb=" N LEU A 545 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 4.598A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 585 through 596 removed outlier: 3.521A pdb=" N VAL A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 removed outlier: 3.612A pdb=" N SER A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 641 through 659 removed outlier: 3.778A pdb=" N GLN A 645 " --> pdb=" O VAL A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 671 through 685 removed outlier: 3.658A pdb=" N ILE A 683 " --> pdb=" O MET A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 704 removed outlier: 3.728A pdb=" N MET A 704 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.577A pdb=" N LYS A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 719 " --> pdb=" O ARG A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 732 Processing helix chain 'A' and resid 744 through 751 Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.619A pdb=" N SER A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 783 through 795 Processing helix chain 'A' and resid 798 through 801 removed outlier: 3.610A pdb=" N ASN A 801 " --> pdb=" O VAL A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 801' Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 996 through 1001 removed outlier: 4.328A pdb=" N ALA A 999 " --> pdb=" O ASP A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1011 Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.613A pdb=" N CYS A1031 " --> pdb=" O PRO A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1057 removed outlier: 3.707A pdb=" N MET A1057 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1195 removed outlier: 3.716A pdb=" N ASN A1194 " --> pdb=" O ALA A1191 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A1195 " --> pdb=" O ILE A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1245 Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.955A pdb=" N GLY A1265 " --> pdb=" O PRO A1262 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A1266 " --> pdb=" O GLU A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 removed outlier: 3.532A pdb=" N LYS A1290 " --> pdb=" O GLU A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1328 Processing helix chain 'A' and resid 1348 through 1355 Processing helix chain 'A' and resid 1398 through 1402 Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 3.865A pdb=" N MET A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1466 through 1474 removed outlier: 3.936A pdb=" N THR A1470 " --> pdb=" O MET A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1510 removed outlier: 3.576A pdb=" N ASN A1510 " --> pdb=" O ASN A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1524 through 1541 removed outlier: 3.930A pdb=" N VAL A1528 " --> pdb=" O PRO A1524 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS A1539 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1559 Processing helix chain 'A' and resid 1568 through 1579 Processing helix chain 'A' and resid 1599 through 1608 removed outlier: 4.074A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1656 Processing helix chain 'A' and resid 1703 through 1711 Processing helix chain 'A' and resid 1770 through 1792 Processing helix chain 'A' and resid 1829 through 1835 Processing helix chain 'A' and resid 1852 through 1856 Processing helix chain 'A' and resid 1865 through 1869 removed outlier: 3.577A pdb=" N ILE A1868 " --> pdb=" O PRO A1865 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A1869 " --> pdb=" O ARG A1866 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1865 through 1869' Processing helix chain 'A' and resid 1881 through 1886 removed outlier: 3.731A pdb=" N LEU A1885 " --> pdb=" O PRO A1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1926 removed outlier: 3.759A pdb=" N VAL A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A1926 " --> pdb=" O VAL A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 removed outlier: 3.634A pdb=" N LEU A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1988 Processing helix chain 'A' and resid 2017 through 2021 removed outlier: 3.654A pdb=" N ILE A2020 " --> pdb=" O ASP A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2052 through 2069 removed outlier: 3.928A pdb=" N VAL A2056 " --> pdb=" O GLN A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2079 removed outlier: 3.785A pdb=" N LYS A2078 " --> pdb=" O VAL A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2084 Processing helix chain 'A' and resid 2085 through 2089 removed outlier: 4.002A pdb=" N GLN A2089 " --> pdb=" O LEU A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2099 Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 3.711A pdb=" N LEU A2110 " --> pdb=" O MET A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2132 Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 3.673A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2208 through 2211 Processing helix chain 'A' and resid 2347 through 2351 Processing helix chain 'A' and resid 2389 through 2394 removed outlier: 3.657A pdb=" N ARG A2394 " --> pdb=" O VAL A2390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2524 removed outlier: 3.968A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A2508 " --> pdb=" O VAL A2504 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A2523 " --> pdb=" O GLU A2519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A2524 " --> pdb=" O LYS A2520 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 removed outlier: 3.636A pdb=" N GLU B 60 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.652A pdb=" N ALA B 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 156 through 163 removed outlier: 3.902A pdb=" N CYS B 159 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.653A pdb=" N GLY B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 208 removed outlier: 3.594A pdb=" N PHE B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.527A pdb=" N PHE C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 removed outlier: 4.266A pdb=" N LEU C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 92 Processing helix chain 'C' and resid 92 through 100 removed outlier: 4.441A pdb=" N MET C 96 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.862A pdb=" N LEU C 119 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'C' and resid 158 through 170 Processing helix chain 'C' and resid 173 through 188 removed outlier: 4.354A pdb=" N LEU C 184 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 202 through 213 Processing helix chain 'C' and resid 218 through 233 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.802A pdb=" N GLU C 240 " --> pdb=" O CYS C 236 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.622A pdb=" N THR C 278 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 removed outlier: 4.110A pdb=" N ILE C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.191A pdb=" N HIS C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 302 removed outlier: 3.511A pdb=" N TYR C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 324 removed outlier: 4.190A pdb=" N SER C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 360 removed outlier: 4.292A pdb=" N TRP C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS C 360 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 379 Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.714A pdb=" N LEU C 384 " --> pdb=" O GLN C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 408 removed outlier: 3.511A pdb=" N GLU C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 427 removed outlier: 3.543A pdb=" N PHE C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 439 removed outlier: 3.900A pdb=" N ILE C 435 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 436 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 removed outlier: 3.601A pdb=" N ASN C 444 " --> pdb=" O GLY C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 470 removed outlier: 3.615A pdb=" N ALA C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 494 removed outlier: 3.823A pdb=" N MET C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) Proline residue: C 485 - end of helix Processing helix chain 'C' and resid 497 through 509 removed outlier: 3.526A pdb=" N GLN C 501 " --> pdb=" O SER C 497 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 526 through 540 Processing helix chain 'C' and resid 541 through 553 removed outlier: 3.567A pdb=" N LEU C 545 " --> pdb=" O ASP C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 4.598A pdb=" N LEU C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 580 Processing helix chain 'C' and resid 585 through 596 removed outlier: 3.521A pdb=" N VAL C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 613 removed outlier: 3.612A pdb=" N SER C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 641 through 659 removed outlier: 3.777A pdb=" N GLN C 645 " --> pdb=" O VAL C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 669 Processing helix chain 'C' and resid 671 through 685 removed outlier: 3.657A pdb=" N ILE C 683 " --> pdb=" O MET C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 704 removed outlier: 3.727A pdb=" N MET C 704 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 719 removed outlier: 3.576A pdb=" N LYS C 709 " --> pdb=" O ASP C 705 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 719 " --> pdb=" O ARG C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 732 Processing helix chain 'C' and resid 744 through 751 Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.618A pdb=" N SER C 764 " --> pdb=" O LEU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 781 Processing helix chain 'C' and resid 783 through 795 Processing helix chain 'C' and resid 798 through 801 removed outlier: 3.610A pdb=" N ASN C 801 " --> pdb=" O VAL C 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 798 through 801' Processing helix chain 'C' and resid 834 through 851 Processing helix chain 'C' and resid 996 through 1001 removed outlier: 4.329A pdb=" N ALA C 999 " --> pdb=" O ASP C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1011 Processing helix chain 'C' and resid 1027 through 1034 removed outlier: 3.612A pdb=" N CYS C1031 " --> pdb=" O PRO C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1053 through 1057 removed outlier: 3.707A pdb=" N MET C1057 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1189 through 1195 removed outlier: 3.716A pdb=" N ASN C1194 " --> pdb=" O ALA C1191 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C1195 " --> pdb=" O ILE C1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 1240 through 1245 Processing helix chain 'C' and resid 1261 through 1267 removed outlier: 3.956A pdb=" N GLY C1265 " --> pdb=" O PRO C1262 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS C1266 " --> pdb=" O GLU C1263 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1291 removed outlier: 3.531A pdb=" N LYS C1290 " --> pdb=" O GLU C1287 " (cutoff:3.500A) Processing helix chain 'C' and resid 1316 through 1328 Processing helix chain 'C' and resid 1348 through 1355 Processing helix chain 'C' and resid 1398 through 1402 Processing helix chain 'C' and resid 1404 through 1409 removed outlier: 3.865A pdb=" N MET C1409 " --> pdb=" O PRO C1406 " (cutoff:3.500A) Processing helix chain 'C' and resid 1426 through 1431 Processing helix chain 'C' and resid 1431 through 1442 Processing helix chain 'C' and resid 1466 through 1474 removed outlier: 3.935A pdb=" N THR C1470 " --> pdb=" O MET C1466 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1510 removed outlier: 3.577A pdb=" N ASN C1510 " --> pdb=" O ASN C1506 " (cutoff:3.500A) Processing helix chain 'C' and resid 1517 through 1520 Processing helix chain 'C' and resid 1524 through 1541 removed outlier: 3.929A pdb=" N VAL C1528 " --> pdb=" O PRO C1524 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS C1539 " --> pdb=" O LEU C1535 " (cutoff:3.500A) Processing helix chain 'C' and resid 1549 through 1559 Processing helix chain 'C' and resid 1568 through 1579 Processing helix chain 'C' and resid 1599 through 1608 removed outlier: 4.074A pdb=" N LEU C1603 " --> pdb=" O GLU C1599 " (cutoff:3.500A) Processing helix chain 'C' and resid 1645 through 1656 Processing helix chain 'C' and resid 1703 through 1711 Processing helix chain 'C' and resid 1770 through 1792 Processing helix chain 'C' and resid 1829 through 1835 Processing helix chain 'C' and resid 1852 through 1856 Processing helix chain 'C' and resid 1865 through 1869 removed outlier: 3.576A pdb=" N ILE C1868 " --> pdb=" O PRO C1865 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C1869 " --> pdb=" O ARG C1866 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1865 through 1869' Processing helix chain 'C' and resid 1881 through 1886 removed outlier: 3.730A pdb=" N LEU C1885 " --> pdb=" O PRO C1881 " (cutoff:3.500A) Processing helix chain 'C' and resid 1913 through 1926 removed outlier: 3.758A pdb=" N VAL C1923 " --> pdb=" O GLN C1919 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS C1926 " --> pdb=" O VAL C1922 " (cutoff:3.500A) Processing helix chain 'C' and resid 1954 through 1962 removed outlier: 3.635A pdb=" N LEU C1958 " --> pdb=" O SER C1954 " (cutoff:3.500A) Processing helix chain 'C' and resid 1969 through 1988 Processing helix chain 'C' and resid 2017 through 2021 removed outlier: 3.654A pdb=" N ILE C2020 " --> pdb=" O ASP C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2040 through 2045 Processing helix chain 'C' and resid 2052 through 2069 removed outlier: 3.928A pdb=" N VAL C2056 " --> pdb=" O GLN C2052 " (cutoff:3.500A) Processing helix chain 'C' and resid 2070 through 2079 removed outlier: 3.785A pdb=" N LYS C2078 " --> pdb=" O VAL C2074 " (cutoff:3.500A) Processing helix chain 'C' and resid 2079 through 2084 Processing helix chain 'C' and resid 2085 through 2089 removed outlier: 4.002A pdb=" N GLN C2089 " --> pdb=" O LEU C2086 " (cutoff:3.500A) Processing helix chain 'C' and resid 2094 through 2099 Processing helix chain 'C' and resid 2104 through 2115 removed outlier: 3.710A pdb=" N LEU C2110 " --> pdb=" O MET C2106 " (cutoff:3.500A) Processing helix chain 'C' and resid 2124 through 2132 Processing helix chain 'C' and resid 2134 through 2139 removed outlier: 3.674A pdb=" N VAL C2138 " --> pdb=" O SER C2134 " (cutoff:3.500A) Processing helix chain 'C' and resid 2208 through 2211 Processing helix chain 'C' and resid 2347 through 2351 Processing helix chain 'C' and resid 2389 through 2394 removed outlier: 3.657A pdb=" N ARG C2394 " --> pdb=" O VAL C2390 " (cutoff:3.500A) Processing helix chain 'C' and resid 2499 through 2524 removed outlier: 3.969A pdb=" N GLN C2505 " --> pdb=" O PRO C2501 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C2508 " --> pdb=" O VAL C2504 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C2523 " --> pdb=" O GLU C2519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C2524 " --> pdb=" O LYS C2520 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.636A pdb=" N GLU D 60 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 removed outlier: 3.652A pdb=" N ALA D 110 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG D 113 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 131 Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 156 through 163 removed outlier: 3.901A pdb=" N CYS D 159 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.654A pdb=" N GLY D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 208 removed outlier: 3.594A pdb=" N PHE D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 796 through 797 Processing sheet with id=AA2, first strand: chain 'A' and resid 1016 through 1017 removed outlier: 6.829A pdb=" N LEU A1016 " --> pdb=" O ASP A1041 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A1040 " --> pdb=" O ASP A1064 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A1113 " --> pdb=" O PHE A1088 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1177 through 1179 removed outlier: 7.162A pdb=" N LEU A1178 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU A1225 " --> pdb=" O HIS A1251 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A1250 " --> pdb=" O ASP A1274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1330 through 1331 Processing sheet with id=AA5, first strand: chain 'A' and resid 1373 through 1380 removed outlier: 3.782A pdb=" N MET A1335 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N LEU A1414 " --> pdb=" O ARG A1334 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS A1336 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU A1416 " --> pdb=" O LYS A1336 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET A1338 " --> pdb=" O LEU A1416 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL A1418 " --> pdb=" O MET A1338 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL A1340 " --> pdb=" O VAL A1418 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ILE A1448 " --> pdb=" O ALA A1413 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A1447 " --> pdb=" O ILE A1482 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A1484 " --> pdb=" O VAL A1447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1547 through 1548 Processing sheet with id=AA7, first strand: chain 'A' and resid 1690 through 1693 Processing sheet with id=AA8, first strand: chain 'A' and resid 1695 through 1696 removed outlier: 3.654A pdb=" N TYR A1814 " --> pdb=" O ILE A1825 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AB1, first strand: chain 'A' and resid 1875 through 1876 removed outlier: 3.769A pdb=" N MET A1947 " --> pdb=" O ALA A1904 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A1939 " --> pdb=" O MET A1944 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AB3, first strand: chain 'A' and resid 2140 through 2144 removed outlier: 6.530A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A2142 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET A2459 " --> pdb=" O LEU A2471 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A2457 " --> pdb=" O LEU A2473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2155 through 2157 removed outlier: 6.522A pdb=" N GLY A2177 " --> pdb=" O VAL A2194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2201 through 2207 removed outlier: 4.222A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A2218 " --> pdb=" O CYS A2201 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2245 through 2249 Processing sheet with id=AB7, first strand: chain 'A' and resid 2272 through 2273 removed outlier: 3.536A pdb=" N LEU A2291 " --> pdb=" O LEU A2272 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2300 through 2302 removed outlier: 6.670A pdb=" N GLY A2318 " --> pdb=" O MET A2301 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.872A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A2385 " --> pdb=" O VAL A2375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2416 through 2419 removed outlier: 3.574A pdb=" N LEU A2436 " --> pdb=" O ARG A2446 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG A2446 " --> pdb=" O LEU A2436 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.272A pdb=" N ILE B 46 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL B 121 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE B 48 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AC5, first strand: chain 'C' and resid 1016 through 1017 removed outlier: 6.829A pdb=" N LEU C1016 " --> pdb=" O ASP C1041 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU C1040 " --> pdb=" O ASP C1064 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU C1063 " --> pdb=" O ASN C1089 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C1113 " --> pdb=" O PHE C1088 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1177 through 1179 removed outlier: 7.162A pdb=" N LEU C1178 " --> pdb=" O ASP C1202 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU C1225 " --> pdb=" O HIS C1251 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU C1250 " --> pdb=" O ASP C1274 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1330 through 1331 Processing sheet with id=AC8, first strand: chain 'C' and resid 1373 through 1380 removed outlier: 3.782A pdb=" N MET C1335 " --> pdb=" O VAL C1389 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N LEU C1414 " --> pdb=" O ARG C1334 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS C1336 " --> pdb=" O LEU C1414 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LEU C1416 " --> pdb=" O LYS C1336 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N MET C1338 " --> pdb=" O LEU C1416 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL C1418 " --> pdb=" O MET C1338 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL C1340 " --> pdb=" O VAL C1418 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ILE C1448 " --> pdb=" O ALA C1413 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR C1415 " --> pdb=" O ILE C1448 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL C1450 " --> pdb=" O TYR C1415 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA C1417 " --> pdb=" O VAL C1450 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C1447 " --> pdb=" O ILE C1482 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP C1484 " --> pdb=" O VAL C1447 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1547 through 1548 Processing sheet with id=AD1, first strand: chain 'C' and resid 1690 through 1693 Processing sheet with id=AD2, first strand: chain 'C' and resid 1695 through 1696 removed outlier: 3.655A pdb=" N TYR C1814 " --> pdb=" O ILE C1825 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1840 through 1841 Processing sheet with id=AD4, first strand: chain 'C' and resid 1875 through 1876 removed outlier: 3.769A pdb=" N MET C1947 " --> pdb=" O ALA C1904 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C1939 " --> pdb=" O MET C1944 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU C1948 " --> pdb=" O LEU C1935 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU C1935 " --> pdb=" O GLU C1948 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 2000 through 2002 Processing sheet with id=AD6, first strand: chain 'C' and resid 2140 through 2144 removed outlier: 6.531A pdb=" N LEU C2140 " --> pdb=" O ASP C2497 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP C2497 " --> pdb=" O LEU C2140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG C2142 " --> pdb=" O VAL C2495 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N MET C2459 " --> pdb=" O LEU C2471 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C2457 " --> pdb=" O LEU C2473 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 2155 through 2157 removed outlier: 6.522A pdb=" N GLY C2177 " --> pdb=" O VAL C2194 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 2201 through 2207 removed outlier: 4.222A pdb=" N CYS C2201 " --> pdb=" O GLY C2218 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY C2218 " --> pdb=" O CYS C2201 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 2245 through 2249 Processing sheet with id=AE1, first strand: chain 'C' and resid 2272 through 2273 removed outlier: 3.536A pdb=" N LEU C2291 " --> pdb=" O LEU C2272 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 2300 through 2302 removed outlier: 6.670A pdb=" N GLY C2318 " --> pdb=" O MET C2301 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 2354 through 2359 removed outlier: 6.872A pdb=" N ALA C2366 " --> pdb=" O ILE C2355 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL C2357 " --> pdb=" O TYR C2364 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR C2364 " --> pdb=" O VAL C2357 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS C2367 " --> pdb=" O VAL C2372 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL C2372 " --> pdb=" O LYS C2367 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY C2385 " --> pdb=" O VAL C2375 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 2416 through 2419 removed outlier: 3.574A pdb=" N LEU C2436 " --> pdb=" O ARG C2446 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG C2446 " --> pdb=" O LEU C2436 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP C2438 " --> pdb=" O LEU C2444 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C2444 " --> pdb=" O ASP C2438 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AE6, first strand: chain 'D' and resid 96 through 97 removed outlier: 6.271A pdb=" N ILE D 46 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL D 121 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 48 " --> pdb=" O VAL D 121 " (cutoff:3.500A) 1510 hydrogen bonds defined for protein. 4236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.57 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5512 1.31 - 1.44: 8535 1.44 - 1.56: 20022 1.56 - 1.69: 26 1.69 - 1.82: 266 Bond restraints: 34361 Sorted by residual: bond pdb=" O3A ANP A2602 " pdb=" PB ANP A2602 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O3A ANP C2602 " pdb=" PB ANP C2602 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C THR A 213 " pdb=" O THR A 213 " ideal model delta sigma weight residual 1.236 1.304 -0.068 1.28e-02 6.10e+03 2.85e+01 bond pdb=" N3B GNP B 302 " pdb=" PG GNP B 302 " ideal model delta sigma weight residual 1.801 1.697 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" N3B GNP D 302 " pdb=" PG GNP D 302 " ideal model delta sigma weight residual 1.801 1.697 0.104 2.00e-02 2.50e+03 2.71e+01 ... (remaining 34356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 46643 3.30 - 6.61: 397 6.61 - 9.91: 55 9.91 - 13.22: 8 13.22 - 16.52: 4 Bond angle restraints: 47107 Sorted by residual: angle pdb=" C THR A 213 " pdb=" N ASN A 214 " pdb=" CA ASN A 214 " ideal model delta sigma weight residual 120.72 105.17 15.55 1.67e+00 3.59e-01 8.67e+01 angle pdb=" C SER C 210 " pdb=" N ALA C 211 " pdb=" CA ALA C 211 " ideal model delta sigma weight residual 122.60 108.22 14.38 1.88e+00 2.83e-01 5.85e+01 angle pdb=" N LEU C 179 " pdb=" CA LEU C 179 " pdb=" C LEU C 179 " ideal model delta sigma weight residual 113.18 104.34 8.84 1.21e+00 6.83e-01 5.33e+01 angle pdb=" N ASP A 204 " pdb=" CA ASP A 204 " pdb=" C ASP A 204 " ideal model delta sigma weight residual 111.75 102.71 9.04 1.28e+00 6.10e-01 4.99e+01 angle pdb=" N ILE A 148 " pdb=" CA ILE A 148 " pdb=" C ILE A 148 " ideal model delta sigma weight residual 113.16 103.16 10.00 1.49e+00 4.50e-01 4.50e+01 ... (remaining 47102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 20031 34.55 - 69.09: 313 69.09 - 103.64: 26 103.64 - 138.19: 2 138.19 - 172.74: 2 Dihedral angle restraints: 20374 sinusoidal: 6404 harmonic: 13970 Sorted by residual: dihedral pdb=" CA SER A 986 " pdb=" C SER A 986 " pdb=" N LEU A 987 " pdb=" CA LEU A 987 " ideal model delta harmonic sigma weight residual 180.00 -148.48 -31.52 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" CA SER C 986 " pdb=" C SER C 986 " pdb=" N LEU C 987 " pdb=" CA LEU C 987 " ideal model delta harmonic sigma weight residual -180.00 -148.48 -31.52 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" O2B GDP C2601 " pdb=" O3A GDP C2601 " pdb=" PB GDP C2601 " pdb=" PA GDP C2601 " ideal model delta sinusoidal sigma weight residual -180.00 -73.54 -106.46 1 2.00e+01 2.50e-03 3.08e+01 ... (remaining 20371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5423 0.086 - 0.172: 481 0.172 - 0.259: 21 0.259 - 0.345: 9 0.345 - 0.431: 2 Chirality restraints: 5936 Sorted by residual: chirality pdb=" CG LEU C1178 " pdb=" CB LEU C1178 " pdb=" CD1 LEU C1178 " pdb=" CD2 LEU C1178 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CG LEU A1178 " pdb=" CB LEU A1178 " pdb=" CD1 LEU A1178 " pdb=" CD2 LEU A1178 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CB VAL C1074 " pdb=" CA VAL C1074 " pdb=" CG1 VAL C1074 " pdb=" CG2 VAL C1074 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 5933 not shown) Planarity restraints: 5925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 172 " -0.031 2.00e-02 2.50e+03 6.22e-02 3.87e+01 pdb=" C ALA C 172 " 0.108 2.00e-02 2.50e+03 pdb=" O ALA C 172 " -0.041 2.00e-02 2.50e+03 pdb=" N ASN C 173 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 209 " 0.030 2.00e-02 2.50e+03 6.11e-02 3.73e+01 pdb=" C LEU A 209 " -0.106 2.00e-02 2.50e+03 pdb=" O LEU A 209 " 0.040 2.00e-02 2.50e+03 pdb=" N SER A 210 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C2496 " -0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C TRP C2496 " 0.094 2.00e-02 2.50e+03 pdb=" O TRP C2496 " -0.036 2.00e-02 2.50e+03 pdb=" N ASP C2497 " -0.031 2.00e-02 2.50e+03 ... (remaining 5922 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 262 2.52 - 3.11: 25882 3.11 - 3.71: 54194 3.71 - 4.30: 71821 4.30 - 4.90: 116602 Nonbonded interactions: 268761 Sorted by model distance: nonbonded pdb=" ND2 ASN C 173 " pdb=" CG2 VAL C 176 " model vdw 1.920 3.540 nonbonded pdb="MG MG D 301 " pdb=" O2B GNP D 302 " model vdw 1.988 2.170 nonbonded pdb="MG MG B 301 " pdb=" O2B GNP B 302 " model vdw 1.989 2.170 nonbonded pdb="MG MG B 301 " pdb=" O1A GNP B 302 " model vdw 2.057 2.170 nonbonded pdb="MG MG D 301 " pdb=" O1A GNP D 302 " model vdw 2.058 2.170 ... (remaining 268756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 211 or (resid 212 through 213 and (name N or na \ me CA or name C or name O or name CB )) or resid 214 through 2329 or (resid 2330 \ and (name N or name CA or name C or name O or name CB )) or resid 2331 through \ 2602)) selection = (chain 'C' and (resid 12 through 177 or (resid 178 and (name N or name CA or nam \ e C or name O or name CB )) or resid 179 through 181 or (resid 182 through 183 a \ nd (name N or name CA or name C or name O or name CB )) or resid 184 through 201 \ or (resid 202 through 203 and (name N or name CA or name C or name O or name CB \ )) or resid 204 through 207 or (resid 208 through 209 and (name N or name CA or \ name C or name O or name CB )) or resid 210 through 2304 or (resid 2305 through \ 2309 and (name N or name CA or name C or name O or name CB )) or resid 2310 thr \ ough 2333 or (resid 2334 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2335 through 2602)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.320 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.146 34361 Z= 0.314 Angle : 0.865 16.525 47107 Z= 0.479 Chirality : 0.051 0.431 5936 Planarity : 0.006 0.070 5925 Dihedral : 13.906 172.737 11238 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.03 % Allowed : 8.86 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z 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: -3.99 (0.10), residues: 4692 helix: -2.16 (0.09), residues: 1948 sheet: -3.41 (0.17), residues: 644 loop : -2.77 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 276 TYR 0.024 0.002 TYR A1739 PHE 0.018 0.002 PHE C 553 TRP 0.026 0.002 TRP A2104 HIS 0.012 0.001 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00626 (34361) covalent geometry : angle 0.86485 (47107) hydrogen bonds : bond 0.19249 ( 1510) hydrogen bonds : angle 8.11653 ( 4236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1288 MET cc_start: 0.8882 (ptp) cc_final: 0.8648 (ttp) REVERT: A 2426 TRP cc_start: 0.6996 (m100) cc_final: 0.6795 (m-10) REVERT: C 2106 MET cc_start: 0.7264 (mtp) cc_final: 0.6962 (ttm) outliers start: 1 outliers final: 1 residues processed: 234 average time/residue: 0.1629 time to fit residues: 65.0324 Evaluate side-chains 161 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1349 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 432 optimal weight: 0.0870 chunk 197 optimal weight: 40.0000 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0270 chunk 470 optimal weight: 30.0000 overall best weight: 2.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1194 ASN A1216 HIS A1278 ASN A1305 ASN A1333 ASN A1489 ASN A1584 HIS A1684 HIS A1758 HIS A1871 ASN A1872 ASN A1986 HIS A2353 ASN A2369 ASN C 173 ASN C 185 HIS C 385 HIS ** C 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 GLN C1021 ASN C1194 ASN C1278 ASN C1305 ASN C1333 ASN C1486 HIS C1489 ASN C1758 HIS C1871 ASN C1872 ASN C1986 HIS C2353 ASN C2369 ASN C2505 GLN D 44 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.080735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.061611 restraints weight = 269238.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.060377 restraints weight = 176827.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.060753 restraints weight = 165814.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.060832 restraints weight = 154584.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.060706 restraints weight = 132988.946| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34361 Z= 0.219 Angle : 0.681 8.924 47107 Z= 0.349 Chirality : 0.043 0.247 5936 Planarity : 0.005 0.051 5925 Dihedral : 7.859 169.004 5077 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.01 % Allowed : 13.34 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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: -2.65 (0.12), residues: 4692 helix: -0.65 (0.11), residues: 2022 sheet: -3.17 (0.17), residues: 624 loop : -2.38 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1957 TYR 0.017 0.002 TYR A1739 PHE 0.026 0.002 PHE A1026 TRP 0.018 0.002 TRP C1376 HIS 0.015 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00477 (34361) covalent geometry : angle 0.68122 (47107) hydrogen bonds : bond 0.03870 ( 1510) hydrogen bonds : angle 5.51830 ( 4236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 1288 MET cc_start: 0.8870 (ptp) cc_final: 0.8597 (ttp) REVERT: A 1788 MET cc_start: 0.7887 (mtt) cc_final: 0.7511 (mtm) REVERT: A 1949 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7849 (mt) REVERT: A 2315 MET cc_start: 0.7367 (mmt) cc_final: 0.7061 (mmm) REVERT: A 2458 MET cc_start: 0.8908 (ttp) cc_final: 0.7756 (ptt) REVERT: B 59 MET cc_start: 0.2082 (ttt) cc_final: 0.1543 (mtp) REVERT: C 405 MET cc_start: 0.7460 (tmm) cc_final: 0.6163 (ttp) REVERT: C 465 MET cc_start: 0.8333 (mmm) cc_final: 0.8088 (mmm) REVERT: C 1788 MET cc_start: 0.8113 (mtm) cc_final: 0.7743 (mtm) REVERT: C 2458 MET cc_start: 0.9024 (ttp) cc_final: 0.8521 (ttp) REVERT: D 131 ASP cc_start: 0.5964 (p0) cc_final: 0.5378 (p0) outliers start: 31 outliers final: 10 residues processed: 186 average time/residue: 0.1550 time to fit residues: 50.8237 Evaluate side-chains 163 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1989 MET Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 166 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 382 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 2 optimal weight: 30.0000 chunk 211 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 359 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 HIS ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN A1854 GLN A2173 HIS A2505 GLN C 177 GLN C 385 HIS C 645 GLN C1019 HIS C1584 HIS C1854 GLN C2173 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.089726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.057707 restraints weight = 222142.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.054348 restraints weight = 216342.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.053702 restraints weight = 237813.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.053741 restraints weight = 188269.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.053943 restraints weight = 165099.990| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34361 Z= 0.215 Angle : 0.650 8.980 47107 Z= 0.331 Chirality : 0.043 0.185 5936 Planarity : 0.004 0.050 5925 Dihedral : 7.031 152.720 5076 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.55 % Allowed : 15.17 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.00 (0.12), residues: 4692 helix: -0.01 (0.12), residues: 2002 sheet: -2.89 (0.18), residues: 656 loop : -2.08 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2514 TYR 0.017 0.002 TYR A1739 PHE 0.027 0.002 PHE A1026 TRP 0.032 0.002 TRP A2426 HIS 0.007 0.001 HIS A1977 Details of bonding type rmsd covalent geometry : bond 0.00474 (34361) covalent geometry : angle 0.65035 (47107) hydrogen bonds : bond 0.03489 ( 1510) hydrogen bonds : angle 5.07529 ( 4236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 152 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 ILE cc_start: 0.5950 (OUTLIER) cc_final: 0.5743 (mt) REVERT: A 842 MET cc_start: 0.9566 (ptp) cc_final: 0.9238 (mmm) REVERT: A 1431 MET cc_start: 0.8422 (tpp) cc_final: 0.8214 (tpp) REVERT: A 1788 MET cc_start: 0.8447 (mtt) cc_final: 0.8059 (mtm) REVERT: A 1830 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 1949 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7820 (mt) REVERT: A 2106 MET cc_start: 0.7097 (ttm) cc_final: 0.6788 (ttm) REVERT: A 2315 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7236 (mmm) REVERT: A 2425 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8355 (mt) REVERT: A 2458 MET cc_start: 0.9022 (ttp) cc_final: 0.8081 (ptt) REVERT: A 2473 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5857 (tt) REVERT: C 842 MET cc_start: 0.9014 (mmm) cc_final: 0.8659 (ptm) REVERT: C 988 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.7965 (p0) REVERT: C 1590 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7129 (tp) REVERT: C 1788 MET cc_start: 0.8289 (mtm) cc_final: 0.8041 (mtm) REVERT: C 1947 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8455 (ptm) REVERT: C 2106 MET cc_start: 0.7290 (ttm) cc_final: 0.7087 (ttm) REVERT: C 2458 MET cc_start: 0.9054 (ttp) cc_final: 0.8185 (ptp) REVERT: D 181 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5803 (ptt90) outliers start: 78 outliers final: 27 residues processed: 218 average time/residue: 0.1429 time to fit residues: 55.7494 Evaluate side-chains 187 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1989 MET Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2315 MET Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2473 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 712 MET Chi-restraints excluded: chain C residue 988 ASP Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1590 LEU Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 1947 MET Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 181 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 317 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 323 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 303 optimal weight: 7.9990 chunk 469 optimal weight: 30.0000 chunk 287 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 363 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 HIS A2333 GLN C 444 ASN C 847 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.078322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.060412 restraints weight = 268673.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.057860 restraints weight = 205419.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.058303 restraints weight = 213953.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.058318 restraints weight = 195764.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.058350 restraints weight = 161023.929| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 34361 Z= 0.297 Angle : 0.755 9.876 47107 Z= 0.377 Chirality : 0.045 0.248 5936 Planarity : 0.005 0.058 5925 Dihedral : 6.988 128.901 5076 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 2.97 % Allowed : 17.29 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.00 (0.12), residues: 4692 helix: -0.01 (0.11), residues: 2022 sheet: -2.80 (0.19), residues: 662 loop : -2.13 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2514 TYR 0.027 0.002 TYR C1277 PHE 0.019 0.002 PHE A1026 TRP 0.025 0.003 TRP A1376 HIS 0.010 0.002 HIS C1977 Details of bonding type rmsd covalent geometry : bond 0.00657 (34361) covalent geometry : angle 0.75480 (47107) hydrogen bonds : bond 0.03482 ( 1510) hydrogen bonds : angle 5.15307 ( 4236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 152 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7294 (ptp) cc_final: 0.7073 (ppp) REVERT: A 538 PHE cc_start: 0.1124 (OUTLIER) cc_final: 0.0812 (m-80) REVERT: A 842 MET cc_start: 0.9061 (ptp) cc_final: 0.8825 (ptp) REVERT: A 1788 MET cc_start: 0.7948 (mtt) cc_final: 0.7458 (mtm) REVERT: A 1830 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8103 (tt) REVERT: A 1831 MET cc_start: 0.9038 (pmm) cc_final: 0.8646 (pmm) REVERT: A 1869 MET cc_start: 0.7665 (pmm) cc_final: 0.6810 (pmm) REVERT: A 1949 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7876 (mt) REVERT: A 1989 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7746 (tmm) REVERT: A 2062 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8811 (tp) REVERT: A 2106 MET cc_start: 0.7324 (ttm) cc_final: 0.6975 (ttm) REVERT: A 2315 MET cc_start: 0.7721 (mmt) cc_final: 0.7401 (mmm) REVERT: A 2458 MET cc_start: 0.9016 (ttp) cc_final: 0.8068 (ptt) REVERT: C 405 MET cc_start: 0.7779 (tmm) cc_final: 0.7460 (ppp) REVERT: C 465 MET cc_start: 0.7883 (mmm) cc_final: 0.7651 (mmp) REVERT: C 491 MET cc_start: 0.6223 (tpp) cc_final: 0.5874 (tpt) REVERT: C 538 PHE cc_start: 0.1114 (OUTLIER) cc_final: 0.0583 (m-80) REVERT: C 842 MET cc_start: 0.8885 (mmm) cc_final: 0.8483 (mmm) REVERT: C 1203 MET cc_start: 0.8307 (mmm) cc_final: 0.8005 (mmm) REVERT: C 1707 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.9108 (tpp80) REVERT: C 1788 MET cc_start: 0.8337 (mtm) cc_final: 0.8045 (mtm) REVERT: C 1830 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8082 (tt) REVERT: C 1883 PHE cc_start: 0.7888 (m-80) cc_final: 0.7559 (m-80) REVERT: C 1947 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8632 (ptm) REVERT: C 2458 MET cc_start: 0.9122 (ttp) cc_final: 0.8649 (ttp) REVERT: D 181 ARG cc_start: 0.3972 (OUTLIER) cc_final: 0.3298 (ptt90) outliers start: 91 outliers final: 34 residues processed: 229 average time/residue: 0.1493 time to fit residues: 61.1967 Evaluate side-chains 195 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1488 VAL Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1989 MET Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2062 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain A residue 2470 MET Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1692 ILE Chi-restraints excluded: chain C residue 1707 ARG Chi-restraints excluded: chain C residue 1808 LEU Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1947 MET Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 181 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 436 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 307 optimal weight: 0.7980 chunk 439 optimal weight: 30.0000 chunk 130 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 467 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C1216 HIS C2333 GLN C2453 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.089110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.057913 restraints weight = 222539.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.054491 restraints weight = 229727.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.054164 restraints weight = 233037.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.054069 restraints weight = 183371.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.054333 restraints weight = 164679.714| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34361 Z= 0.154 Angle : 0.590 9.196 47107 Z= 0.300 Chirality : 0.042 0.173 5936 Planarity : 0.004 0.048 5925 Dihedral : 6.473 119.712 5076 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.09 % Allowed : 18.40 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.59 (0.13), residues: 4692 helix: 0.36 (0.12), residues: 2018 sheet: -2.55 (0.19), residues: 644 loop : -1.97 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1968 TYR 0.017 0.001 TYR C1739 PHE 0.014 0.001 PHE A1026 TRP 0.014 0.001 TRP C1705 HIS 0.011 0.001 HIS A2510 Details of bonding type rmsd covalent geometry : bond 0.00343 (34361) covalent geometry : angle 0.59034 (47107) hydrogen bonds : bond 0.02898 ( 1510) hydrogen bonds : angle 4.74780 ( 4236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 153 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.7957 (ptm) cc_final: 0.7709 (tmm) REVERT: A 538 PHE cc_start: 0.2840 (OUTLIER) cc_final: 0.2633 (m-80) REVERT: A 1788 MET cc_start: 0.8074 (mtt) cc_final: 0.7780 (mtm) REVERT: A 1831 MET cc_start: 0.9073 (pmm) cc_final: 0.8823 (pmm) REVERT: A 1869 MET cc_start: 0.7758 (pmm) cc_final: 0.7484 (pmm) REVERT: A 1949 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7618 (mt) REVERT: A 1989 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8102 (tmm) REVERT: A 2458 MET cc_start: 0.8929 (ttp) cc_final: 0.8229 (ptt) REVERT: C 405 MET cc_start: 0.7790 (tmm) cc_final: 0.7571 (ppp) REVERT: C 538 PHE cc_start: 0.3123 (OUTLIER) cc_final: 0.2773 (m-80) REVERT: C 842 MET cc_start: 0.9228 (mmm) cc_final: 0.8851 (mmm) REVERT: C 1690 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8839 (pt) REVERT: C 2106 MET cc_start: 0.7359 (ttm) cc_final: 0.7065 (ttm) REVERT: C 2458 MET cc_start: 0.8965 (ttp) cc_final: 0.8695 (ttp) REVERT: C 2521 MET cc_start: 0.7766 (ppp) cc_final: 0.7547 (ppp) REVERT: D 181 ARG cc_start: 0.5347 (OUTLIER) cc_final: 0.5054 (ptt90) outliers start: 64 outliers final: 30 residues processed: 205 average time/residue: 0.1524 time to fit residues: 55.6783 Evaluate side-chains 188 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1989 MET Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1232 ILE Chi-restraints excluded: chain C residue 1338 MET Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1590 LEU Chi-restraints excluded: chain C residue 1690 ILE Chi-restraints excluded: chain C residue 1692 ILE Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2205 VAL Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 181 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 37 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 439 optimal weight: 40.0000 chunk 212 optimal weight: 7.9990 chunk 288 optimal weight: 8.9990 chunk 427 optimal weight: 0.4980 chunk 366 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS A2149 ASN C2149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.089174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.057247 restraints weight = 221296.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.053879 restraints weight = 213676.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.053277 restraints weight = 250875.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.053674 restraints weight = 185652.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.053573 restraints weight = 164983.882| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34361 Z= 0.139 Angle : 0.585 11.306 47107 Z= 0.293 Chirality : 0.041 0.200 5936 Planarity : 0.004 0.046 5925 Dihedral : 6.165 112.132 5076 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.42 % Allowed : 18.86 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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: -1.38 (0.13), residues: 4692 helix: 0.53 (0.12), residues: 2020 sheet: -2.41 (0.20), residues: 650 loop : -1.87 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2514 TYR 0.014 0.001 TYR C1739 PHE 0.012 0.001 PHE A1026 TRP 0.031 0.002 TRP C 349 HIS 0.011 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00312 (34361) covalent geometry : angle 0.58452 (47107) hydrogen bonds : bond 0.02720 ( 1510) hydrogen bonds : angle 4.56203 ( 4236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 155 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.8187 (ptm) cc_final: 0.7861 (tmm) REVERT: A 842 MET cc_start: 0.9031 (mmm) cc_final: 0.8750 (ptm) REVERT: A 1788 MET cc_start: 0.7894 (mtt) cc_final: 0.7638 (mtm) REVERT: A 1830 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8188 (tt) REVERT: A 1831 MET cc_start: 0.9149 (pmm) cc_final: 0.8883 (pmm) REVERT: A 1949 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7655 (mt) REVERT: A 1989 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.8006 (tmm) REVERT: A 2374 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: A 2458 MET cc_start: 0.8975 (ttp) cc_final: 0.8192 (ptt) REVERT: B 59 MET cc_start: 0.2048 (ttt) cc_final: 0.1686 (mtp) REVERT: C 538 PHE cc_start: 0.3994 (OUTLIER) cc_final: 0.3634 (m-80) REVERT: C 842 MET cc_start: 0.9314 (mmm) cc_final: 0.8999 (mmm) REVERT: C 1788 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7880 (mtm) REVERT: C 1831 MET cc_start: 0.9147 (pmm) cc_final: 0.8930 (pmm) REVERT: C 2419 LEU cc_start: 0.8736 (tt) cc_final: 0.8512 (tp) REVERT: C 2458 MET cc_start: 0.9042 (ttp) cc_final: 0.8833 (ttp) REVERT: C 2521 MET cc_start: 0.7864 (ppp) cc_final: 0.7591 (ppp) REVERT: D 181 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.5371 (ptt90) outliers start: 74 outliers final: 49 residues processed: 219 average time/residue: 0.1497 time to fit residues: 58.4390 Evaluate side-chains 207 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1015 LYS Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1097 PHE Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1692 ILE Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 1989 MET Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2374 GLU Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain A residue 2470 MET Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1232 ILE Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 1338 MET Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1590 LEU Chi-restraints excluded: chain C residue 1692 ILE Chi-restraints excluded: chain C residue 1788 MET Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1884 LEU Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2205 VAL Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 181 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 394 optimal weight: 3.9990 chunk 452 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 327 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 412 optimal weight: 0.7980 chunk 251 optimal weight: 0.7980 chunk 243 optimal weight: 10.0000 chunk 192 optimal weight: 30.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C1977 HIS ** 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 = 0.4209 r_free = 0.4209 target = 0.089419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.057938 restraints weight = 221937.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.055110 restraints weight = 215888.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.054541 restraints weight = 228037.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.054684 restraints weight = 176231.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.054869 restraints weight = 157210.678| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34361 Z= 0.116 Angle : 0.561 11.865 47107 Z= 0.281 Chirality : 0.041 0.189 5936 Planarity : 0.004 0.046 5925 Dihedral : 5.882 106.972 5076 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.12 % Allowed : 19.29 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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: -1.23 (0.13), residues: 4692 helix: 0.66 (0.12), residues: 2030 sheet: -2.37 (0.20), residues: 662 loop : -1.78 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1968 TYR 0.014 0.001 TYR A1645 PHE 0.012 0.001 PHE A1026 TRP 0.015 0.001 TRP C1705 HIS 0.008 0.001 HIS C2510 Details of bonding type rmsd covalent geometry : bond 0.00261 (34361) covalent geometry : angle 0.56108 (47107) hydrogen bonds : bond 0.02557 ( 1510) hydrogen bonds : angle 4.38827 ( 4236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 151 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.7873 (ptm) cc_final: 0.7617 (tmm) REVERT: A 505 LEU cc_start: 0.8362 (mm) cc_final: 0.8139 (mp) REVERT: A 1788 MET cc_start: 0.7941 (mtt) cc_final: 0.7668 (mtm) REVERT: A 1831 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8861 (pmm) REVERT: A 1949 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7629 (mt) REVERT: A 2155 MET cc_start: 0.8150 (ppp) cc_final: 0.6671 (ppp) REVERT: A 2458 MET cc_start: 0.8923 (ttp) cc_final: 0.8124 (ptt) REVERT: A 2521 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7360 (tmm) REVERT: B 59 MET cc_start: 0.1853 (ttt) cc_final: 0.1524 (mtp) REVERT: C 405 MET cc_start: 0.6950 (ppp) cc_final: 0.6188 (ttp) REVERT: C 538 PHE cc_start: 0.2790 (OUTLIER) cc_final: 0.2501 (m-80) REVERT: C 842 MET cc_start: 0.9279 (mmm) cc_final: 0.8866 (ptm) REVERT: C 1690 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8862 (pt) REVERT: C 1831 MET cc_start: 0.9142 (pmm) cc_final: 0.8613 (pmm) REVERT: C 1949 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7854 (mt) REVERT: C 2315 MET cc_start: 0.7851 (mmt) cc_final: 0.7562 (mmm) REVERT: C 2458 MET cc_start: 0.8931 (ttp) cc_final: 0.8191 (ptp) REVERT: C 2521 MET cc_start: 0.7792 (ppp) cc_final: 0.7501 (ppp) REVERT: D 181 ARG cc_start: 0.5156 (OUTLIER) cc_final: 0.4799 (ptt90) outliers start: 65 outliers final: 43 residues processed: 206 average time/residue: 0.1443 time to fit residues: 52.3049 Evaluate side-chains 200 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1015 LYS Chi-restraints excluded: chain A residue 1097 PHE Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2470 MET Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1232 ILE Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 1338 MET Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1690 ILE Chi-restraints excluded: chain C residue 1692 ILE Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1884 LEU Chi-restraints excluded: chain C residue 1949 LEU Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2205 VAL Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 181 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 465 optimal weight: 50.0000 chunk 32 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 378 optimal weight: 4.9990 chunk 331 optimal weight: 0.2980 chunk 46 optimal weight: 7.9990 chunk 415 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 chunk 438 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 overall best weight: 1.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2453 ASN ** C1977 HIS ** 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 = 0.4206 r_free = 0.4206 target = 0.089334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.057548 restraints weight = 221084.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.053991 restraints weight = 215800.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.053624 restraints weight = 263887.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.053654 restraints weight = 199103.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.053995 restraints weight = 163638.107| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34361 Z= 0.126 Angle : 0.566 12.941 47107 Z= 0.282 Chirality : 0.041 0.213 5936 Planarity : 0.004 0.046 5925 Dihedral : 5.767 101.391 5076 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.42 % Allowed : 19.16 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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: -1.17 (0.13), residues: 4692 helix: 0.71 (0.12), residues: 2030 sheet: -2.31 (0.19), residues: 670 loop : -1.76 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2514 TYR 0.013 0.001 TYR A1645 PHE 0.011 0.001 PHE A1026 TRP 0.016 0.001 TRP A 349 HIS 0.007 0.001 HIS C2510 Details of bonding type rmsd covalent geometry : bond 0.00282 (34361) covalent geometry : angle 0.56629 (47107) hydrogen bonds : bond 0.02546 ( 1510) hydrogen bonds : angle 4.34615 ( 4236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 150 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6330 (mt) REVERT: A 465 MET cc_start: 0.8070 (ptm) cc_final: 0.7786 (tmm) REVERT: A 1788 MET cc_start: 0.7942 (mtt) cc_final: 0.7657 (mtm) REVERT: A 1830 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8162 (tt) REVERT: A 1831 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8936 (pmm) REVERT: A 1949 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7508 (mt) REVERT: A 2155 MET cc_start: 0.8102 (ppp) cc_final: 0.6817 (ppp) REVERT: A 2458 MET cc_start: 0.8936 (ttp) cc_final: 0.8063 (ptt) REVERT: A 2521 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7253 (tmm) REVERT: B 59 MET cc_start: 0.2027 (ttt) cc_final: 0.1646 (mtp) REVERT: B 139 MET cc_start: 0.2061 (ttt) cc_final: 0.1625 (ptm) REVERT: C 405 MET cc_start: 0.7111 (ppp) cc_final: 0.6223 (ttp) REVERT: C 538 PHE cc_start: 0.3810 (OUTLIER) cc_final: 0.3494 (m-80) REVERT: C 842 MET cc_start: 0.9357 (mmm) cc_final: 0.9051 (mmm) REVERT: C 1057 MET cc_start: 0.8207 (mmp) cc_final: 0.7927 (mmp) REVERT: C 1097 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8026 (t80) REVERT: C 1175 MET cc_start: 0.8388 (tpp) cc_final: 0.7874 (mmm) REVERT: C 1590 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7340 (tp) REVERT: C 1831 MET cc_start: 0.9153 (pmm) cc_final: 0.8713 (pmm) REVERT: C 1949 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7917 (mt) REVERT: C 2315 MET cc_start: 0.7857 (mmt) cc_final: 0.7594 (mmm) REVERT: C 2458 MET cc_start: 0.8940 (ttp) cc_final: 0.8089 (ptp) outliers start: 74 outliers final: 47 residues processed: 214 average time/residue: 0.1493 time to fit residues: 56.8177 Evaluate side-chains 203 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 147 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1015 LYS Chi-restraints excluded: chain A residue 1097 PHE Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1419 TYR Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1947 MET Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2459 MET Chi-restraints excluded: chain A residue 2470 MET Chi-restraints excluded: chain A residue 2521 MET Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1097 PHE Chi-restraints excluded: chain C residue 1232 ILE Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 1338 MET Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1590 LEU Chi-restraints excluded: chain C residue 1692 ILE Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1884 LEU Chi-restraints excluded: chain C residue 1949 LEU Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2205 VAL Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 158 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 429 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 299 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 328 optimal weight: 8.9990 chunk 461 optimal weight: 0.8980 chunk 276 optimal weight: 5.9990 chunk 446 optimal weight: 0.9980 chunk 358 optimal weight: 0.9990 chunk 430 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2008 ASN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1977 HIS ** 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 = 0.4215 r_free = 0.4215 target = 0.089645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.058642 restraints weight = 221141.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.054777 restraints weight = 224909.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.054586 restraints weight = 245774.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.054674 restraints weight = 182308.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.054865 restraints weight = 169114.732| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34361 Z= 0.102 Angle : 0.559 13.614 47107 Z= 0.275 Chirality : 0.041 0.198 5936 Planarity : 0.004 0.046 5925 Dihedral : 5.599 96.532 5076 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.77 % Allowed : 19.88 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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: -1.03 (0.13), residues: 4692 helix: 0.82 (0.12), residues: 2036 sheet: -2.21 (0.20), residues: 664 loop : -1.69 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1968 TYR 0.014 0.001 TYR A1645 PHE 0.011 0.001 PHE A1026 TRP 0.025 0.001 TRP C2104 HIS 0.007 0.001 HIS A1929 Details of bonding type rmsd covalent geometry : bond 0.00227 (34361) covalent geometry : angle 0.55893 (47107) hydrogen bonds : bond 0.02408 ( 1510) hydrogen bonds : angle 4.21161 ( 4236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.6373 (mt) REVERT: A 465 MET cc_start: 0.7941 (ptm) cc_final: 0.7646 (tmm) REVERT: A 1830 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 1831 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8940 (pmm) REVERT: A 1949 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7662 (mt) REVERT: A 2155 MET cc_start: 0.8025 (ppp) cc_final: 0.6558 (ppp) REVERT: A 2374 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: A 2458 MET cc_start: 0.8918 (ttp) cc_final: 0.8170 (ptt) REVERT: A 2521 MET cc_start: 0.7972 (tmm) cc_final: 0.7443 (tmm) REVERT: B 59 MET cc_start: 0.1883 (ttt) cc_final: 0.1408 (mtp) REVERT: B 139 MET cc_start: 0.1984 (ttt) cc_final: 0.1474 (ptm) REVERT: C 405 MET cc_start: 0.7607 (ppp) cc_final: 0.6965 (ttp) REVERT: C 538 PHE cc_start: 0.3273 (OUTLIER) cc_final: 0.2986 (m-80) REVERT: C 712 MET cc_start: 0.9459 (ttp) cc_final: 0.9154 (ppp) REVERT: C 842 MET cc_start: 0.9322 (mmm) cc_final: 0.8901 (ptm) REVERT: C 1057 MET cc_start: 0.8178 (mmp) cc_final: 0.7888 (mmp) REVERT: C 1097 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7855 (t80) REVERT: C 1175 MET cc_start: 0.8530 (tpp) cc_final: 0.8098 (mmm) REVERT: C 1831 MET cc_start: 0.9182 (pmm) cc_final: 0.8844 (pmm) REVERT: C 1949 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7811 (mt) REVERT: C 2315 MET cc_start: 0.7910 (mmt) cc_final: 0.7634 (mmm) REVERT: C 2458 MET cc_start: 0.8894 (ttp) cc_final: 0.8296 (ptp) outliers start: 54 outliers final: 36 residues processed: 193 average time/residue: 0.1740 time to fit residues: 60.3761 Evaluate side-chains 190 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2374 GLU Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2470 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1097 PHE Chi-restraints excluded: chain C residue 1232 ILE Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 1338 MET Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1949 LEU Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2205 VAL Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain C residue 2459 MET Chi-restraints excluded: chain C residue 2473 LEU Chi-restraints excluded: chain D residue 158 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 318 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 436 optimal weight: 20.0000 chunk 111 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 412 optimal weight: 0.0010 chunk 105 optimal weight: 10.0000 chunk 371 optimal weight: 0.9980 chunk 312 optimal weight: 3.9990 chunk 150 optimal weight: 0.0870 chunk 288 optimal weight: 3.9990 overall best weight: 0.8566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.089570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.058580 restraints weight = 223862.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.054192 restraints weight = 218209.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.054109 restraints weight = 237234.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.054325 restraints weight = 172596.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.054401 restraints weight = 153903.559| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34361 Z= 0.099 Angle : 0.551 13.008 47107 Z= 0.272 Chirality : 0.040 0.200 5936 Planarity : 0.004 0.050 5925 Dihedral : 5.474 91.861 5076 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.57 % Allowed : 20.07 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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 (0.13), residues: 4692 helix: 0.87 (0.12), residues: 2038 sheet: -2.16 (0.20), residues: 678 loop : -1.64 (0.15), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1968 TYR 0.015 0.001 TYR A1645 PHE 0.011 0.001 PHE C2181 TRP 0.021 0.001 TRP C2104 HIS 0.007 0.001 HIS A2510 Details of bonding type rmsd covalent geometry : bond 0.00220 (34361) covalent geometry : angle 0.55067 (47107) hydrogen bonds : bond 0.02350 ( 1510) hydrogen bonds : angle 4.14971 ( 4236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6348 (mt) REVERT: A 465 MET cc_start: 0.8073 (ptm) cc_final: 0.7758 (tmm) REVERT: A 505 LEU cc_start: 0.7924 (mm) cc_final: 0.7695 (mp) REVERT: A 1702 MET cc_start: 0.8719 (mmm) cc_final: 0.8337 (mmm) REVERT: A 1830 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 1831 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8882 (pmm) REVERT: A 1949 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7515 (mt) REVERT: A 2155 MET cc_start: 0.7947 (ppp) cc_final: 0.6512 (ppp) REVERT: A 2374 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: A 2458 MET cc_start: 0.8951 (ttp) cc_final: 0.8108 (ptt) REVERT: A 2521 MET cc_start: 0.7927 (tmm) cc_final: 0.7389 (tmm) REVERT: B 59 MET cc_start: 0.1959 (ttt) cc_final: 0.1470 (mtp) REVERT: B 139 MET cc_start: 0.2574 (ttt) cc_final: 0.2101 (ptm) REVERT: C 405 MET cc_start: 0.7618 (ppp) cc_final: 0.6924 (ttp) REVERT: C 538 PHE cc_start: 0.3790 (OUTLIER) cc_final: 0.3585 (m-80) REVERT: C 712 MET cc_start: 0.9469 (ttp) cc_final: 0.9188 (ppp) REVERT: C 842 MET cc_start: 0.9347 (mmm) cc_final: 0.8903 (ptm) REVERT: C 1057 MET cc_start: 0.8199 (mmp) cc_final: 0.7947 (mmm) REVERT: C 1097 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7918 (t80) REVERT: C 1175 MET cc_start: 0.8514 (tpp) cc_final: 0.8085 (mmm) REVERT: C 1830 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8287 (tt) REVERT: C 1831 MET cc_start: 0.9195 (pmm) cc_final: 0.8809 (pmm) REVERT: C 1949 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7743 (mt) REVERT: C 2315 MET cc_start: 0.7946 (mmt) cc_final: 0.7680 (mmm) REVERT: C 2458 MET cc_start: 0.8932 (ttp) cc_final: 0.8138 (ptt) outliers start: 48 outliers final: 33 residues processed: 191 average time/residue: 0.1525 time to fit residues: 52.3585 Evaluate side-chains 188 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1252 LEU Chi-restraints excluded: chain A residue 1266 CYS Chi-restraints excluded: chain A residue 1271 THR Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1831 MET Chi-restraints excluded: chain A residue 1839 LEU Chi-restraints excluded: chain A residue 1949 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2374 GLU Chi-restraints excluded: chain A residue 2414 VAL Chi-restraints excluded: chain A residue 2470 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1097 PHE Chi-restraints excluded: chain C residue 1232 ILE Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 1338 MET Chi-restraints excluded: chain C residue 1368 THR Chi-restraints excluded: chain C residue 1830 LEU Chi-restraints excluded: chain C residue 1839 LEU Chi-restraints excluded: chain C residue 1949 LEU Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2205 VAL Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2357 VAL Chi-restraints excluded: chain C residue 2473 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 272 optimal weight: 10.0000 chunk 370 optimal weight: 0.7980 chunk 431 optimal weight: 0.9980 chunk 473 optimal weight: 5.9990 chunk 374 optimal weight: 0.0970 chunk 348 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 413 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 389 optimal weight: 0.0170 chunk 187 optimal weight: 7.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1182 GLN ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1977 HIS ** 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 = 0.4222 r_free = 0.4222 target = 0.089756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.058553 restraints weight = 221149.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.054171 restraints weight = 215330.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.054272 restraints weight = 242663.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.054193 restraints weight = 182783.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.054255 restraints weight = 161898.561| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34361 Z= 0.091 Angle : 0.545 13.663 47107 Z= 0.269 Chirality : 0.040 0.200 5936 Planarity : 0.004 0.049 5925 Dihedral : 5.368 87.826 5076 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.37 % Allowed : 20.20 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % 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: -0.88 (0.13), residues: 4692 helix: 0.92 (0.12), residues: 2050 sheet: -2.05 (0.20), residues: 678 loop : -1.64 (0.15), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 715 TYR 0.014 0.001 TYR A1645 PHE 0.017 0.001 PHE C 415 TRP 0.037 0.001 TRP C 372 HIS 0.007 0.001 HIS C2510 Details of bonding type rmsd covalent geometry : bond 0.00199 (34361) covalent geometry : angle 0.54465 (47107) hydrogen bonds : bond 0.02342 ( 1510) hydrogen bonds : angle 4.08176 ( 4236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5653.29 seconds wall clock time: 98 minutes 12.76 seconds (5892.76 seconds total)