Starting phenix.real_space_refine on Wed Feb 21 02:14:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh8_11216/02_2024/6zh8_11216.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh8_11216/02_2024/6zh8_11216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh8_11216/02_2024/6zh8_11216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh8_11216/02_2024/6zh8_11216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh8_11216/02_2024/6zh8_11216.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh8_11216/02_2024/6zh8_11216.pdb" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 19 5.49 5 S 193 5.16 5 C 18852 2.51 5 N 4995 2.21 5 O 5447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3013": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29506 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 29120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3694, 29120 Classifications: {'peptide': 3694} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'CIS': 1, 'PTRANS': 160, 'TRANS': 3532} Chain breaks: 18 Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 382 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'UNK:plan-1': 26, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 272 Chain: "B" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 222 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Time building chain proxies: 15.22, per 1000 atoms: 0.52 Number of scatterers: 29506 At special positions: 0 Unit cell: (122.85, 145.95, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 193 16.00 P 19 15.00 O 5447 8.00 N 4995 7.00 C 18852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.90 Conformation dependent library (CDL) restraints added in 5.5 seconds 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7086 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 6 sheets defined 72.7% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 33 through 45 removed outlier: 4.065A pdb=" N GLY A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 73 removed outlier: 4.120A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 96 Processing helix chain 'A' and resid 103 through 118 removed outlier: 4.051A pdb=" N ILE A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 146 removed outlier: 3.656A pdb=" N LYS A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.687A pdb=" N GLU A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 207 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 224 through 232 removed outlier: 4.359A pdb=" N SER A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.616A pdb=" N SER A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.798A pdb=" N LEU A 286 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 307 through 328 Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 380 through 397 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.910A pdb=" N TYR A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 removed outlier: 3.728A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 450 through 469 removed outlier: 3.954A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 3.809A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.899A pdb=" N ASP A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 559 through 579 Processing helix chain 'A' and resid 616 through 637 removed outlier: 3.578A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Proline residue: A 635 - end of helix Processing helix chain 'A' and resid 644 through 660 removed outlier: 4.680A pdb=" N SER A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 removed outlier: 3.998A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 744 through 747 removed outlier: 3.638A pdb=" N ALA A 747 " --> pdb=" O ASP A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 744 through 747' Processing helix chain 'A' and resid 748 through 760 removed outlier: 3.681A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.522A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 793 Proline residue: A 787 - end of helix removed outlier: 4.183A pdb=" N LYS A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP A 791 " --> pdb=" O PRO A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 800 removed outlier: 3.577A pdb=" N ASP A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY A 798 " --> pdb=" O CYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 862 Processing helix chain 'A' and resid 863 through 868 removed outlier: 3.587A pdb=" N LYS A 868 " --> pdb=" O GLY A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 872 through 877 Processing helix chain 'A' and resid 910 through 921 Processing helix chain 'A' and resid 925 through 948 Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.763A pdb=" N TYR A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 977 through 996 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1002 through 1005 Processing helix chain 'A' and resid 1006 through 1013 removed outlier: 4.057A pdb=" N LEU A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 removed outlier: 4.127A pdb=" N ILE A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1044 Processing helix chain 'A' and resid 1045 through 1051 removed outlier: 3.510A pdb=" N GLU A1050 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1086 Processing helix chain 'A' and resid 1088 through 1091 Processing helix chain 'A' and resid 1092 through 1115 removed outlier: 6.200A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1142 Processing helix chain 'A' and resid 1143 through 1146 removed outlier: 3.802A pdb=" N ASN A1146 " --> pdb=" O VAL A1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1143 through 1146' Processing helix chain 'A' and resid 1164 through 1174 removed outlier: 3.654A pdb=" N LEU A1168 " --> pdb=" O CYS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1203 through 1215 Processing helix chain 'A' and resid 1216 through 1226 removed outlier: 4.151A pdb=" N LEU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1273 removed outlier: 3.572A pdb=" N CYS A1255 " --> pdb=" O GLN A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.756A pdb=" N LEU A1282 " --> pdb=" O LEU A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1303 removed outlier: 3.916A pdb=" N ALA A1302 " --> pdb=" O LEU A1298 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET A1303 " --> pdb=" O GLU A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1351 Processing helix chain 'A' and resid 1354 through 1361 Processing helix chain 'A' and resid 1364 through 1378 Processing helix chain 'A' and resid 1379 through 1382 Processing helix chain 'A' and resid 1390 through 1409 Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.848A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1434 removed outlier: 3.592A pdb=" N VAL A1434 " --> pdb=" O GLU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1462 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1476 through 1485 removed outlier: 3.503A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1521 Processing helix chain 'A' and resid 1524 through 1533 Processing helix chain 'A' and resid 1554 through 1563 Processing helix chain 'A' and resid 1564 through 1574 Processing helix chain 'A' and resid 1574 through 1585 removed outlier: 3.522A pdb=" N ALA A1578 " --> pdb=" O ASN A1574 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 Processing helix chain 'A' and resid 1612 through 1626 removed outlier: 3.986A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.798A pdb=" N LYS A1642 " --> pdb=" O PRO A1638 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 Processing helix chain 'A' and resid 1685 through 1694 Processing helix chain 'A' and resid 1695 through 1702 removed outlier: 4.429A pdb=" N SER A1701 " --> pdb=" O PHE A1698 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1702 " --> pdb=" O PHE A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1722 removed outlier: 3.900A pdb=" N LEU A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1767 Processing helix chain 'A' and resid 1774 through 1788 removed outlier: 3.720A pdb=" N PHE A1778 " --> pdb=" O MET A1774 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 4.113A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1829 removed outlier: 3.575A pdb=" N LEU A1827 " --> pdb=" O SER A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1851 removed outlier: 4.003A pdb=" N LEU A1836 " --> pdb=" O SER A1832 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1882 Processing helix chain 'A' and resid 1885 through 1890 Processing helix chain 'A' and resid 1909 through 1924 Processing helix chain 'A' and resid 1933 through 1956 removed outlier: 3.870A pdb=" N ARG A1937 " --> pdb=" O LEU A1933 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A1956 " --> pdb=" O ILE A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1976 removed outlier: 3.562A pdb=" N ASN A1974 " --> pdb=" O LYS A1970 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1976 " --> pdb=" O GLU A1972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2108 Processing helix chain 'A' and resid 2123 through 2135 removed outlier: 3.627A pdb=" N ASN A2135 " --> pdb=" O GLY A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2140 through 2152 removed outlier: 3.900A pdb=" N LEU A2144 " --> pdb=" O LEU A2140 " (cutoff:3.500A) Processing helix chain 'A' and resid 2157 through 2159 No H-bonds generated for 'chain 'A' and resid 2157 through 2159' Processing helix chain 'A' and resid 2160 through 2172 removed outlier: 3.607A pdb=" N TRP A2164 " --> pdb=" O TYR A2160 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2183 through 2195 Processing helix chain 'A' and resid 2205 through 2222 removed outlier: 4.037A pdb=" N GLU A2209 " --> pdb=" O VAL A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2246 removed outlier: 5.346A pdb=" N CYS A2244 " --> pdb=" O THR A2240 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP A2245 " --> pdb=" O LEU A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2247 through 2249 No H-bonds generated for 'chain 'A' and resid 2247 through 2249' Processing helix chain 'A' and resid 2253 through 2261 removed outlier: 3.665A pdb=" N GLU A2258 " --> pdb=" O ARG A2254 " (cutoff:3.500A) Processing helix chain 'A' and resid 2270 through 2283 Processing helix chain 'A' and resid 2298 through 2306 removed outlier: 4.048A pdb=" N ALA A2302 " --> pdb=" O GLU A2298 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A2303 " --> pdb=" O TYR A2299 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2309 No H-bonds generated for 'chain 'A' and resid 2307 through 2309' Processing helix chain 'A' and resid 2315 through 2333 Processing helix chain 'A' and resid 2337 through 2353 removed outlier: 3.549A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2371 removed outlier: 3.638A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2377 removed outlier: 4.325A pdb=" N ASP A2376 " --> pdb=" O PRO A2373 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2391 through 2406 removed outlier: 4.061A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A2406 " --> pdb=" O LEU A2402 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2418 Processing helix chain 'A' and resid 2420 through 2426 removed outlier: 3.854A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2443 removed outlier: 3.664A pdb=" N VAL A2434 " --> pdb=" O GLU A2430 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS A2435 " --> pdb=" O ARG A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2460 removed outlier: 4.096A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix removed outlier: 3.776A pdb=" N GLU A2460 " --> pdb=" O ASN A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2468 through 2485 Processing helix chain 'A' and resid 2494 through 2509 Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2527 Processing helix chain 'A' and resid 2534 through 2545 removed outlier: 3.623A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2557 through 2565 Processing helix chain 'A' and resid 2566 through 2569 Processing helix chain 'A' and resid 2786 through 2799 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2824 removed outlier: 3.834A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYS A2822 " --> pdb=" O LYS A2818 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE A2823 " --> pdb=" O GLU A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2846 Processing helix chain 'A' and resid 2851 through 2865 removed outlier: 4.254A pdb=" N HIS A2865 " --> pdb=" O ILE A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2884 Processing helix chain 'A' and resid 2885 through 2900 removed outlier: 3.708A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2934 Processing helix chain 'A' and resid 2935 through 2946 Processing helix chain 'A' and resid 2950 through 2963 removed outlier: 4.109A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2978 Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3007 through 3014 removed outlier: 3.641A pdb=" N CYS A3014 " --> pdb=" O SER A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3039 through 3054 removed outlier: 4.418A pdb=" N TYR A3043 " --> pdb=" O THR A3039 " (cutoff:3.500A) Processing helix chain 'A' and resid 3058 through 3071 removed outlier: 4.209A pdb=" N LEU A3062 " --> pdb=" O ASP A3058 " (cutoff:3.500A) Processing helix chain 'A' and resid 3073 through 3094 removed outlier: 4.135A pdb=" N ILE A3077 " --> pdb=" O LEU A3073 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A3078 " --> pdb=" O GLN A3074 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A3083 " --> pdb=" O GLU A3079 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLN A3084 " --> pdb=" O LEU A3080 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU A3085 " --> pdb=" O HIS A3081 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3117 Processing helix chain 'A' and resid 3121 through 3131 removed outlier: 4.005A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 3.858A pdb=" N LEU A3135 " --> pdb=" O SER A3131 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3148 through 3153 removed outlier: 3.584A pdb=" N SER A3152 " --> pdb=" O GLN A3148 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A3153 " --> pdb=" O GLY A3149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3148 through 3153' Processing helix chain 'A' and resid 3154 through 3167 Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 3.634A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3228 through 3249 Processing helix chain 'A' and resid 3251 through 3266 removed outlier: 3.974A pdb=" N LYS A3264 " --> pdb=" O LYS A3260 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU A3265 " --> pdb=" O GLU A3261 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3288 removed outlier: 3.780A pdb=" N VAL A3274 " --> pdb=" O ASP A3270 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3307 Processing helix chain 'A' and resid 3322 through 3344 Processing helix chain 'A' and resid 3346 through 3352 Processing helix chain 'A' and resid 3353 through 3364 Processing helix chain 'A' and resid 3369 through 3394 removed outlier: 4.877A pdb=" N ALA A3375 " --> pdb=" O GLU A3371 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A3394 " --> pdb=" O GLN A3390 " (cutoff:3.500A) Processing helix chain 'A' and resid 3407 through 3428 Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 4.144A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3474 Proline residue: A3466 - end of helix removed outlier: 4.228A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG A3474 " --> pdb=" O GLN A3470 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3485 removed outlier: 3.649A pdb=" N LYS A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3505 Processing helix chain 'A' and resid 3514 through 3525 Processing helix chain 'A' and resid 3529 through 3538 Processing helix chain 'A' and resid 3547 through 3563 removed outlier: 3.985A pdb=" N ASN A3551 " --> pdb=" O THR A3547 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3576 removed outlier: 3.747A pdb=" N ASP A3570 " --> pdb=" O GLY A3566 " (cutoff:3.500A) Processing helix chain 'A' and resid 3577 through 3579 No H-bonds generated for 'chain 'A' and resid 3577 through 3579' Processing helix chain 'A' and resid 3580 through 3595 removed outlier: 3.748A pdb=" N ALA A3594 " --> pdb=" O ASN A3590 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A3595 " --> pdb=" O ASP A3591 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3617 removed outlier: 3.594A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) Processing helix chain 'A' and resid 3627 through 3634 removed outlier: 3.856A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A3634 " --> pdb=" O ARG A3630 " (cutoff:3.500A) Processing helix chain 'A' and resid 3639 through 3644 Processing helix chain 'A' and resid 3647 through 3651 Processing helix chain 'A' and resid 3657 through 3673 Processing helix chain 'A' and resid 3686 through 3690 Processing helix chain 'A' and resid 3758 through 3777 removed outlier: 3.894A pdb=" N GLN A3777 " --> pdb=" O GLY A3773 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3785 Processing helix chain 'A' and resid 3812 through 3818 Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3846 Processing helix chain 'A' and resid 3851 through 3862 removed outlier: 4.221A pdb=" N TYR A3855 " --> pdb=" O ASP A3851 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET A3856 " --> pdb=" O VAL A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3877 Processing helix chain 'A' and resid 3881 through 3891 Processing helix chain 'A' and resid 3893 through 3919 Processing helix chain 'A' and resid 3947 through 3953 removed outlier: 3.831A pdb=" N PHE A3952 " --> pdb=" O SER A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3971 removed outlier: 3.570A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 4.206A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4007 removed outlier: 4.092A pdb=" N LEU A3998 " --> pdb=" O ASP A3994 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A4005 " --> pdb=" O THR A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4022 Processing helix chain 'A' and resid 4039 through 4054 removed outlier: 3.786A pdb=" N LYS A4043 " --> pdb=" O TYR A4039 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A4054 " --> pdb=" O LYS A4050 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4069 Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4121 through 4125 Processing helix chain 'A' and resid 5012 through 5016 removed outlier: 3.824A pdb=" N UNK A5015 " --> pdb=" O UNK A5012 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N UNK A5016 " --> pdb=" O UNK A5013 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5012 through 5016' Processing helix chain 'A' and resid 6005 through 6019 Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 2586 through 2588 Processing sheet with id=AA4, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.503A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.960A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A3753 " --> pdb=" O GLY A3801 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3809 through 3811 1723 hydrogen bonds defined for protein. 5085 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: 16.04 Time building geometry restraints manager: 13.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9226 1.33 - 1.46: 4906 1.46 - 1.58: 15673 1.58 - 1.70: 36 1.70 - 1.82: 301 Bond restraints: 30142 Sorted by residual: bond pdb=" CA TYR A3475 " pdb=" CB TYR A3475 " ideal model delta sigma weight residual 1.522 1.533 -0.010 7.00e-03 2.04e+04 2.24e+00 bond pdb=" N ILE A4089 " pdb=" CA ILE A4089 " ideal model delta sigma weight residual 1.474 1.452 0.022 1.57e-02 4.06e+03 2.05e+00 bond pdb=" C ILE A 633 " pdb=" N LEU A 634 " ideal model delta sigma weight residual 1.341 1.318 0.022 1.65e-02 3.67e+03 1.85e+00 bond pdb=" CB TRP A2525 " pdb=" CG TRP A2525 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.84e+00 bond pdb=" C HIS A2464 " pdb=" N PRO A2465 " ideal model delta sigma weight residual 1.334 1.304 0.030 2.34e-02 1.83e+03 1.62e+00 ... (remaining 30137 not shown) Histogram of bond angle deviations from ideal: 95.47 - 103.20: 331 103.20 - 110.92: 11574 110.92 - 118.65: 12574 118.65 - 126.37: 15915 126.37 - 134.09: 471 Bond angle restraints: 40865 Sorted by residual: angle pdb=" N ILE A3030 " pdb=" CA ILE A3030 " pdb=" C ILE A3030 " ideal model delta sigma weight residual 113.71 108.42 5.29 9.50e-01 1.11e+00 3.10e+01 angle pdb=" N VAL A 553 " pdb=" CA VAL A 553 " pdb=" C VAL A 553 " ideal model delta sigma weight residual 111.91 107.26 4.65 8.90e-01 1.26e+00 2.73e+01 angle pdb=" C ASN A4088 " pdb=" N ILE A4089 " pdb=" CA ILE A4089 " ideal model delta sigma weight residual 121.65 117.46 4.19 9.40e-01 1.13e+00 1.99e+01 angle pdb=" C GLU A1893 " pdb=" N SER A1894 " pdb=" CA SER A1894 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 angle pdb=" N ILE A1382 " pdb=" CA ILE A1382 " pdb=" C ILE A1382 " ideal model delta sigma weight residual 112.98 107.99 4.99 1.25e+00 6.40e-01 1.59e+01 ... (remaining 40860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 16364 17.90 - 35.79: 1565 35.79 - 53.69: 285 53.69 - 71.59: 76 71.59 - 89.48: 47 Dihedral angle restraints: 18337 sinusoidal: 7468 harmonic: 10869 Sorted by residual: dihedral pdb=" CA SER A2296 " pdb=" C SER A2296 " pdb=" N SER A2297 " pdb=" CA SER A2297 " ideal model delta harmonic sigma weight residual 180.00 152.14 27.86 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA TYR A3315 " pdb=" C TYR A3315 " pdb=" N LEU A3316 " pdb=" CA LEU A3316 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ALA A 378 " pdb=" C ALA A 378 " pdb=" N LYS A 379 " pdb=" CA LYS A 379 " ideal model delta harmonic sigma weight residual 180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 18334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3357 0.043 - 0.086: 1057 0.086 - 0.129: 234 0.129 - 0.171: 18 0.171 - 0.214: 4 Chirality restraints: 4670 Sorted by residual: chirality pdb=" CB ILE A1386 " pdb=" CA ILE A1386 " pdb=" CG1 ILE A1386 " pdb=" CG2 ILE A1386 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA THR A2792 " pdb=" N THR A2792 " pdb=" C THR A2792 " pdb=" CB THR A2792 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CG LEU A2411 " pdb=" CB LEU A2411 " pdb=" CD1 LEU A2411 " pdb=" CD2 LEU A2411 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 4667 not shown) Planarity restraints: 5136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 723 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ASP A 723 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP A 723 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 724 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1356 " -0.017 2.00e-02 2.50e+03 1.85e-02 8.56e+00 pdb=" CG TRP A1356 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A1356 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A1356 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1356 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1356 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1356 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1356 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1356 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1356 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 911 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO A 912 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 912 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 912 " -0.040 5.00e-02 4.00e+02 ... (remaining 5133 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3726 2.74 - 3.28: 36976 3.28 - 3.82: 53319 3.82 - 4.36: 62617 4.36 - 4.90: 94870 Nonbonded interactions: 251508 Sorted by model distance: nonbonded pdb=" O VAL A1021 " pdb=" NH2 ARG A1026 " model vdw 2.198 2.520 nonbonded pdb=" OG1 THR A2987 " pdb=" OE1 GLU A2988 " model vdw 2.201 2.440 nonbonded pdb=" O LYS A1591 " pdb=" OG SER A1594 " model vdw 2.203 2.440 nonbonded pdb=" O ASP A1305 " pdb=" OH TYR A1330 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR A1802 " pdb=" OD2 ASP A1846 " model vdw 2.206 2.440 ... (remaining 251503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.880 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 86.410 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 : 0.005 0.047 30142 Z= 0.328 Angle : 0.770 10.640 40865 Z= 0.420 Chirality : 0.042 0.214 4670 Planarity : 0.005 0.073 5136 Dihedral : 15.358 89.484 11251 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.65 % Favored : 89.32 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3634 helix: -0.18 (0.10), residues: 2311 sheet: -2.27 (0.65), residues: 46 loop : -2.31 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A1356 HIS 0.010 0.002 HIS A3549 PHE 0.039 0.002 PHE A2943 TYR 0.043 0.002 TYR A1739 ARG 0.006 0.001 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8200 (ppp) cc_final: 0.7968 (ppp) REVERT: A 410 MET cc_start: 0.9609 (mmp) cc_final: 0.9032 (mmm) REVERT: A 785 MET cc_start: 0.9344 (mmp) cc_final: 0.8790 (mmm) REVERT: A 901 MET cc_start: 0.8942 (pmm) cc_final: 0.8712 (pmm) REVERT: A 1583 MET cc_start: 0.9342 (ttt) cc_final: 0.8912 (ttt) REVERT: A 1600 MET cc_start: 0.9659 (mmp) cc_final: 0.9252 (mmm) REVERT: A 1762 MET cc_start: 0.9344 (mtt) cc_final: 0.9112 (mtt) REVERT: A 1774 MET cc_start: 0.9536 (tpt) cc_final: 0.9240 (tpt) REVERT: A 2576 MET cc_start: 0.8982 (mpp) cc_final: 0.8695 (mpp) REVERT: A 3242 MET cc_start: 0.9587 (ttm) cc_final: 0.9348 (ttm) REVERT: A 3256 MET cc_start: 0.9612 (ppp) cc_final: 0.9390 (ppp) REVERT: A 3450 MET cc_start: 0.9729 (mmp) cc_final: 0.9400 (mmm) REVERT: A 3609 MET cc_start: 0.9295 (pmm) cc_final: 0.8757 (pmm) REVERT: A 3771 MET cc_start: 0.9603 (mmp) cc_final: 0.9340 (mmp) REVERT: A 3820 MET cc_start: 0.8959 (pmm) cc_final: 0.8721 (pmm) REVERT: A 4020 MET cc_start: 0.9556 (mmp) cc_final: 0.9303 (mmm) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.4083 time to fit residues: 84.5058 Evaluate side-chains 113 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 290 optimal weight: 40.0000 chunk 112 optimal weight: 0.8980 chunk 176 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 336 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN A 485 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3166 ASN ** A3379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4015 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30142 Z= 0.203 Angle : 0.654 9.896 40865 Z= 0.342 Chirality : 0.040 0.186 4670 Planarity : 0.005 0.053 5136 Dihedral : 10.437 88.096 4169 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.31 % Favored : 91.66 % Rotamer: Outliers : 0.06 % Allowed : 6.34 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3634 helix: 0.37 (0.11), residues: 2395 sheet: -1.94 (0.79), residues: 38 loop : -2.19 (0.19), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A3686 HIS 0.007 0.001 HIS A1721 PHE 0.018 0.001 PHE A2943 TYR 0.032 0.002 TYR A1739 ARG 0.003 0.000 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8170 (ppp) cc_final: 0.7819 (ppp) REVERT: A 410 MET cc_start: 0.9598 (mmp) cc_final: 0.9175 (mmm) REVERT: A 628 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8706 (tp30) REVERT: A 785 MET cc_start: 0.9310 (mmp) cc_final: 0.8724 (mmm) REVERT: A 901 MET cc_start: 0.9079 (pmm) cc_final: 0.8841 (pmm) REVERT: A 1583 MET cc_start: 0.9246 (ttt) cc_final: 0.8788 (ttt) REVERT: A 1600 MET cc_start: 0.9593 (mmp) cc_final: 0.9236 (mmm) REVERT: A 1774 MET cc_start: 0.9533 (tpt) cc_final: 0.9211 (tpp) REVERT: A 1880 MET cc_start: 0.9397 (tmm) cc_final: 0.9153 (tmm) REVERT: A 2379 MET cc_start: 0.9503 (mmp) cc_final: 0.9264 (mmm) REVERT: A 2576 MET cc_start: 0.8979 (mpp) cc_final: 0.8694 (mpp) REVERT: A 3238 MET cc_start: 0.9708 (pmm) cc_final: 0.9438 (pmm) REVERT: A 3242 MET cc_start: 0.9574 (ttm) cc_final: 0.9371 (tpp) REVERT: A 3256 MET cc_start: 0.9584 (ppp) cc_final: 0.9317 (ppp) REVERT: A 3450 MET cc_start: 0.9730 (mmp) cc_final: 0.9399 (mmm) REVERT: A 3609 MET cc_start: 0.9261 (pmm) cc_final: 0.8663 (pmm) REVERT: A 3820 MET cc_start: 0.8930 (pmm) cc_final: 0.8663 (pmm) REVERT: A 3929 MET cc_start: 0.8612 (tpp) cc_final: 0.8354 (tpp) REVERT: A 4020 MET cc_start: 0.9493 (mmp) cc_final: 0.9284 (mmm) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.4123 time to fit residues: 88.1727 Evaluate side-chains 115 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 336 optimal weight: 0.5980 chunk 363 optimal weight: 0.0970 chunk 299 optimal weight: 5.9990 chunk 333 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 195 ASN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1426 GLN A1435 ASN ** A1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1598 ASN ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1754 GLN ** A2130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3166 ASN A3327 ASN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS ** A3772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4015 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30142 Z= 0.206 Angle : 0.630 10.289 40865 Z= 0.327 Chirality : 0.040 0.187 4670 Planarity : 0.004 0.051 5136 Dihedral : 10.273 88.771 4169 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3634 helix: 0.59 (0.11), residues: 2391 sheet: -1.82 (0.79), residues: 38 loop : -2.15 (0.19), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1356 HIS 0.005 0.001 HIS A1721 PHE 0.025 0.001 PHE A2851 TYR 0.030 0.001 TYR A1739 ARG 0.004 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8193 (ppp) cc_final: 0.7747 (ppp) REVERT: A 410 MET cc_start: 0.9492 (mmp) cc_final: 0.8912 (mmm) REVERT: A 785 MET cc_start: 0.9331 (mmp) cc_final: 0.8712 (mmm) REVERT: A 939 MET cc_start: 0.9411 (mmt) cc_final: 0.8919 (tpp) REVERT: A 1600 MET cc_start: 0.9505 (mmp) cc_final: 0.9182 (mmm) REVERT: A 1774 MET cc_start: 0.9523 (tpt) cc_final: 0.9202 (tpp) REVERT: A 1871 MET cc_start: 0.9736 (ptp) cc_final: 0.9498 (ptt) REVERT: A 2379 MET cc_start: 0.9504 (mmp) cc_final: 0.9189 (mmm) REVERT: A 2576 MET cc_start: 0.8966 (mpp) cc_final: 0.8686 (mpp) REVERT: A 3238 MET cc_start: 0.9684 (pmm) cc_final: 0.9470 (pmm) REVERT: A 3240 MET cc_start: 0.9480 (ppp) cc_final: 0.9269 (ppp) REVERT: A 3256 MET cc_start: 0.9584 (ppp) cc_final: 0.9316 (ppp) REVERT: A 3450 MET cc_start: 0.9700 (mmp) cc_final: 0.9458 (mmm) REVERT: A 3609 MET cc_start: 0.9295 (pmm) cc_final: 0.8666 (pmm) REVERT: A 3929 MET cc_start: 0.8639 (tpp) cc_final: 0.8254 (tpp) REVERT: A 4020 MET cc_start: 0.9499 (mmp) cc_final: 0.9291 (mmm) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.4020 time to fit residues: 84.8296 Evaluate side-chains 115 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 0.0370 chunk 253 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 160 optimal weight: 0.4980 chunk 226 optimal weight: 9.9990 chunk 337 optimal weight: 20.0000 chunk 357 optimal weight: 0.0970 chunk 176 optimal weight: 1.9990 chunk 320 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2130 HIS A2301 GLN A2365 ASN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3105 ASN A3166 ASN ** A3379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3569 GLN A3573 ASN A4015 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30142 Z= 0.159 Angle : 0.617 8.847 40865 Z= 0.313 Chirality : 0.040 0.202 4670 Planarity : 0.004 0.051 5136 Dihedral : 10.115 89.071 4169 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3634 helix: 0.80 (0.11), residues: 2402 sheet: -1.49 (0.69), residues: 43 loop : -2.14 (0.19), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1356 HIS 0.005 0.001 HIS A 935 PHE 0.021 0.001 PHE A2851 TYR 0.030 0.001 TYR A1739 ARG 0.005 0.000 ARG A1445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 TYR cc_start: 0.9572 (t80) cc_final: 0.9342 (t80) REVERT: A 410 MET cc_start: 0.9486 (mmp) cc_final: 0.8967 (mmm) REVERT: A 785 MET cc_start: 0.9286 (mmp) cc_final: 0.8652 (mmm) REVERT: A 901 MET cc_start: 0.9130 (pmm) cc_final: 0.8885 (pmm) REVERT: A 1600 MET cc_start: 0.9434 (mmp) cc_final: 0.9154 (mmm) REVERT: A 1774 MET cc_start: 0.9556 (tpt) cc_final: 0.9221 (tpp) REVERT: A 1871 MET cc_start: 0.9714 (ptp) cc_final: 0.9478 (ptt) REVERT: A 2576 MET cc_start: 0.8874 (mpp) cc_final: 0.8615 (mpp) REVERT: A 3256 MET cc_start: 0.9560 (ppp) cc_final: 0.9296 (ppp) REVERT: A 3450 MET cc_start: 0.9678 (mmp) cc_final: 0.9433 (mmm) REVERT: A 3609 MET cc_start: 0.9285 (pmm) cc_final: 0.8881 (pmm) REVERT: A 3771 MET cc_start: 0.9518 (mmp) cc_final: 0.9278 (mmp) REVERT: A 3820 MET cc_start: 0.8931 (pmm) cc_final: 0.8614 (pmm) REVERT: A 3929 MET cc_start: 0.8523 (tpp) cc_final: 0.8107 (tpp) REVERT: A 3932 MET cc_start: 0.9140 (mpp) cc_final: 0.8940 (mpp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.3986 time to fit residues: 87.9757 Evaluate side-chains 118 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 182 optimal weight: 5.9990 chunk 321 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3105 ASN A3166 ASN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3569 GLN A4015 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30142 Z= 0.186 Angle : 0.610 8.993 40865 Z= 0.310 Chirality : 0.039 0.229 4670 Planarity : 0.004 0.048 5136 Dihedral : 10.024 89.990 4169 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3634 helix: 0.90 (0.11), residues: 2405 sheet: -1.63 (0.69), residues: 43 loop : -2.13 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1356 HIS 0.006 0.001 HIS A 935 PHE 0.016 0.001 PHE A 620 TYR 0.030 0.001 TYR A1739 ARG 0.007 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8311 (ppp) cc_final: 0.7693 (ppp) REVERT: A 385 TYR cc_start: 0.9586 (t80) cc_final: 0.9336 (t80) REVERT: A 410 MET cc_start: 0.9505 (mmp) cc_final: 0.9001 (mmm) REVERT: A 785 MET cc_start: 0.9334 (mmp) cc_final: 0.8841 (mmm) REVERT: A 901 MET cc_start: 0.9189 (pmm) cc_final: 0.8899 (pmm) REVERT: A 939 MET cc_start: 0.9406 (mmt) cc_final: 0.8849 (tpp) REVERT: A 1600 MET cc_start: 0.9375 (mmp) cc_final: 0.9133 (mmm) REVERT: A 1774 MET cc_start: 0.9575 (tpt) cc_final: 0.9233 (tpp) REVERT: A 1871 MET cc_start: 0.9721 (ptp) cc_final: 0.9476 (ptt) REVERT: A 2576 MET cc_start: 0.8880 (mpp) cc_final: 0.8533 (mpp) REVERT: A 3238 MET cc_start: 0.9668 (pmm) cc_final: 0.9439 (pmm) REVERT: A 3256 MET cc_start: 0.9575 (ppp) cc_final: 0.9329 (ppp) REVERT: A 3450 MET cc_start: 0.9663 (mmp) cc_final: 0.9456 (mmm) REVERT: A 3609 MET cc_start: 0.9316 (pmm) cc_final: 0.8900 (pmm) REVERT: A 3820 MET cc_start: 0.8946 (pmm) cc_final: 0.8562 (pmm) REVERT: A 3929 MET cc_start: 0.8600 (tpp) cc_final: 0.8178 (tpp) REVERT: A 3932 MET cc_start: 0.9141 (mpp) cc_final: 0.8901 (mpp) REVERT: A 4020 MET cc_start: 0.9494 (mmp) cc_final: 0.9165 (mmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.4204 time to fit residues: 90.1682 Evaluate side-chains 118 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 0.9980 chunk 322 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 357 optimal weight: 3.9990 chunk 297 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 GLN ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3105 ASN A3166 ASN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4015 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30142 Z= 0.187 Angle : 0.610 9.081 40865 Z= 0.310 Chirality : 0.039 0.205 4670 Planarity : 0.004 0.048 5136 Dihedral : 9.970 89.577 4169 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3634 helix: 0.94 (0.11), residues: 2413 sheet: -1.41 (0.70), residues: 41 loop : -2.13 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1356 HIS 0.006 0.001 HIS A 935 PHE 0.014 0.001 PHE A 620 TYR 0.029 0.001 TYR A1739 ARG 0.006 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8308 (ppp) cc_final: 0.7727 (ppp) REVERT: A 385 TYR cc_start: 0.9597 (t80) cc_final: 0.9336 (t80) REVERT: A 410 MET cc_start: 0.9510 (mmp) cc_final: 0.9026 (mmm) REVERT: A 785 MET cc_start: 0.9292 (mmp) cc_final: 0.8791 (mmm) REVERT: A 901 MET cc_start: 0.9189 (pmm) cc_final: 0.8933 (pmm) REVERT: A 939 MET cc_start: 0.9395 (mmt) cc_final: 0.8825 (tpp) REVERT: A 1600 MET cc_start: 0.9314 (mmp) cc_final: 0.9101 (mmm) REVERT: A 1774 MET cc_start: 0.9602 (tpt) cc_final: 0.9270 (tpp) REVERT: A 1871 MET cc_start: 0.9720 (ptp) cc_final: 0.9473 (ptt) REVERT: A 2576 MET cc_start: 0.8887 (mpp) cc_final: 0.8544 (mpp) REVERT: A 3238 MET cc_start: 0.9676 (pmm) cc_final: 0.9463 (pmm) REVERT: A 3256 MET cc_start: 0.9572 (ppp) cc_final: 0.9314 (ppp) REVERT: A 3609 MET cc_start: 0.9330 (pmm) cc_final: 0.8889 (pmm) REVERT: A 3820 MET cc_start: 0.8950 (pmm) cc_final: 0.8538 (pmm) REVERT: A 3929 MET cc_start: 0.8658 (tpp) cc_final: 0.8225 (tpp) REVERT: A 3932 MET cc_start: 0.9147 (mpp) cc_final: 0.8900 (mpp) REVERT: A 4020 MET cc_start: 0.9493 (mmp) cc_final: 0.9240 (mmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.4042 time to fit residues: 87.9334 Evaluate side-chains 118 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 261 optimal weight: 0.0370 chunk 202 optimal weight: 2.9990 chunk 301 optimal weight: 0.0010 chunk 199 optimal weight: 4.9990 chunk 356 optimal weight: 20.0000 chunk 223 optimal weight: 0.0980 chunk 217 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 overall best weight: 1.0268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 ASN ** A1738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3105 ASN A3166 ASN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4015 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30142 Z= 0.153 Angle : 0.608 11.045 40865 Z= 0.303 Chirality : 0.039 0.211 4670 Planarity : 0.004 0.048 5136 Dihedral : 9.905 89.535 4169 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3634 helix: 1.01 (0.11), residues: 2410 sheet: -1.36 (0.68), residues: 43 loop : -2.12 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A3686 HIS 0.008 0.001 HIS A 437 PHE 0.016 0.001 PHE A 620 TYR 0.030 0.001 TYR A1739 ARG 0.004 0.000 ARG A1445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 3.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8239 (ppp) cc_final: 0.7955 (ppp) REVERT: A 385 TYR cc_start: 0.9591 (t80) cc_final: 0.9327 (t80) REVERT: A 410 MET cc_start: 0.9481 (mmp) cc_final: 0.8991 (mmm) REVERT: A 785 MET cc_start: 0.9261 (mmp) cc_final: 0.8713 (mmm) REVERT: A 901 MET cc_start: 0.9206 (pmm) cc_final: 0.8945 (pmm) REVERT: A 937 MET cc_start: 0.9787 (mmm) cc_final: 0.9289 (mmm) REVERT: A 939 MET cc_start: 0.9394 (mmt) cc_final: 0.8808 (tpp) REVERT: A 1774 MET cc_start: 0.9608 (tpt) cc_final: 0.9258 (tpp) REVERT: A 1880 MET cc_start: 0.9414 (tmm) cc_final: 0.9202 (tmm) REVERT: A 2576 MET cc_start: 0.8825 (mpp) cc_final: 0.8491 (mpp) REVERT: A 3256 MET cc_start: 0.9556 (ppp) cc_final: 0.9274 (ppp) REVERT: A 3450 MET cc_start: 0.9692 (mmp) cc_final: 0.9408 (mmm) REVERT: A 3609 MET cc_start: 0.9324 (pmm) cc_final: 0.8894 (pmm) REVERT: A 3771 MET cc_start: 0.9544 (mmp) cc_final: 0.9341 (mmp) REVERT: A 3820 MET cc_start: 0.8899 (pmm) cc_final: 0.8511 (pmm) REVERT: A 3929 MET cc_start: 0.8694 (tpp) cc_final: 0.8260 (tpp) REVERT: A 3932 MET cc_start: 0.9173 (mpp) cc_final: 0.8904 (mpp) REVERT: A 4002 MET cc_start: 0.9715 (ptt) cc_final: 0.9460 (ppp) REVERT: A 4020 MET cc_start: 0.9482 (mmp) cc_final: 0.9158 (mmm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4112 time to fit residues: 89.7148 Evaluate side-chains 117 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 3.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 4.9990 chunk 142 optimal weight: 0.2980 chunk 212 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 242 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 280 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2141 ASN A2365 ASN A2523 ASN ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3105 ASN A3166 ASN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4015 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30142 Z= 0.153 Angle : 0.612 9.626 40865 Z= 0.305 Chirality : 0.039 0.222 4670 Planarity : 0.004 0.049 5136 Dihedral : 9.834 89.549 4169 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3634 helix: 1.09 (0.11), residues: 2395 sheet: -1.38 (0.64), residues: 49 loop : -2.11 (0.19), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A3686 HIS 0.006 0.001 HIS A 437 PHE 0.036 0.001 PHE A1746 TYR 0.031 0.001 TYR A1739 ARG 0.008 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8239 (ppp) cc_final: 0.7920 (ppp) REVERT: A 385 TYR cc_start: 0.9600 (t80) cc_final: 0.9311 (t80) REVERT: A 410 MET cc_start: 0.9453 (mmp) cc_final: 0.8985 (mmm) REVERT: A 785 MET cc_start: 0.9262 (mmp) cc_final: 0.8725 (mmm) REVERT: A 901 MET cc_start: 0.9223 (pmm) cc_final: 0.8953 (pmm) REVERT: A 939 MET cc_start: 0.9398 (mmt) cc_final: 0.8799 (tpp) REVERT: A 1600 MET cc_start: 0.9529 (mmp) cc_final: 0.9133 (mmm) REVERT: A 1774 MET cc_start: 0.9535 (tpt) cc_final: 0.9180 (tpp) REVERT: A 1871 MET cc_start: 0.9732 (ptt) cc_final: 0.9469 (ppp) REVERT: A 2576 MET cc_start: 0.8783 (mpp) cc_final: 0.8469 (mpp) REVERT: A 3238 MET cc_start: 0.9670 (pmm) cc_final: 0.9435 (pmm) REVERT: A 3256 MET cc_start: 0.9556 (ppp) cc_final: 0.9276 (ppp) REVERT: A 3450 MET cc_start: 0.9700 (mmp) cc_final: 0.9394 (mmm) REVERT: A 3609 MET cc_start: 0.9337 (pmm) cc_final: 0.8907 (pmm) REVERT: A 3771 MET cc_start: 0.9513 (mmp) cc_final: 0.9273 (mmp) REVERT: A 3929 MET cc_start: 0.8707 (tpp) cc_final: 0.8266 (tpp) REVERT: A 3932 MET cc_start: 0.9228 (mpp) cc_final: 0.9006 (mpp) REVERT: A 4002 MET cc_start: 0.9721 (ptt) cc_final: 0.9474 (ppp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4029 time to fit residues: 88.1694 Evaluate side-chains 118 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 0.9980 chunk 341 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 332 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3105 ASN A3108 GLN A3166 ASN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4015 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30142 Z= 0.185 Angle : 0.607 9.900 40865 Z= 0.307 Chirality : 0.039 0.225 4670 Planarity : 0.004 0.049 5136 Dihedral : 9.796 89.502 4169 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3634 helix: 1.15 (0.11), residues: 2402 sheet: -1.40 (0.63), residues: 49 loop : -2.10 (0.19), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A3686 HIS 0.005 0.001 HIS A 437 PHE 0.023 0.001 PHE A1746 TYR 0.028 0.001 TYR A1739 ARG 0.008 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 3.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8183 (ppp) cc_final: 0.7864 (ppp) REVERT: A 385 TYR cc_start: 0.9627 (t80) cc_final: 0.9320 (t80) REVERT: A 410 MET cc_start: 0.9490 (mmp) cc_final: 0.9029 (mmm) REVERT: A 785 MET cc_start: 0.9302 (mmp) cc_final: 0.8635 (mmm) REVERT: A 901 MET cc_start: 0.9230 (pmm) cc_final: 0.8965 (pmm) REVERT: A 939 MET cc_start: 0.9383 (mmt) cc_final: 0.8746 (tpp) REVERT: A 1600 MET cc_start: 0.9539 (mmp) cc_final: 0.9173 (mmm) REVERT: A 1762 MET cc_start: 0.9474 (mmm) cc_final: 0.9214 (mmm) REVERT: A 1774 MET cc_start: 0.9553 (tpt) cc_final: 0.9227 (tpp) REVERT: A 1871 MET cc_start: 0.9736 (ptt) cc_final: 0.9455 (ppp) REVERT: A 2576 MET cc_start: 0.8814 (mpp) cc_final: 0.8491 (mpp) REVERT: A 3256 MET cc_start: 0.9570 (ppp) cc_final: 0.9315 (ppp) REVERT: A 3450 MET cc_start: 0.9706 (mmp) cc_final: 0.9429 (mmm) REVERT: A 3609 MET cc_start: 0.9379 (pmm) cc_final: 0.8814 (pmm) REVERT: A 3771 MET cc_start: 0.9519 (mmp) cc_final: 0.9293 (mmp) REVERT: A 3820 MET cc_start: 0.8829 (pmm) cc_final: 0.8034 (pmm) REVERT: A 3929 MET cc_start: 0.8716 (tpp) cc_final: 0.8286 (tpp) REVERT: A 3932 MET cc_start: 0.9215 (mpp) cc_final: 0.8963 (mpp) REVERT: A 4020 MET cc_start: 0.9471 (mmp) cc_final: 0.9265 (mmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.4665 time to fit residues: 100.7172 Evaluate side-chains 117 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 4.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 8.9990 chunk 351 optimal weight: 5.9990 chunk 214 optimal weight: 0.0670 chunk 166 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 339 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 226 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 overall best weight: 2.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3105 ASN A3166 ASN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4015 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30142 Z= 0.184 Angle : 0.613 9.873 40865 Z= 0.310 Chirality : 0.039 0.220 4670 Planarity : 0.004 0.048 5136 Dihedral : 9.790 89.578 4169 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3634 helix: 1.18 (0.11), residues: 2394 sheet: -1.41 (0.63), residues: 49 loop : -2.11 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A3686 HIS 0.005 0.001 HIS A 935 PHE 0.022 0.001 PHE A1746 TYR 0.031 0.001 TYR A1739 ARG 0.007 0.000 ARG A 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 4.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8184 (ppp) cc_final: 0.7842 (ppp) REVERT: A 385 TYR cc_start: 0.9630 (t80) cc_final: 0.9286 (t80) REVERT: A 410 MET cc_start: 0.9492 (mmp) cc_final: 0.9028 (mmm) REVERT: A 785 MET cc_start: 0.9300 (mmp) cc_final: 0.8634 (mmm) REVERT: A 901 MET cc_start: 0.9226 (pmm) cc_final: 0.8965 (pmm) REVERT: A 939 MET cc_start: 0.9375 (mmt) cc_final: 0.8736 (tpp) REVERT: A 1583 MET cc_start: 0.9562 (ttm) cc_final: 0.9246 (ttt) REVERT: A 1600 MET cc_start: 0.9535 (mmp) cc_final: 0.9164 (mmm) REVERT: A 1762 MET cc_start: 0.9506 (mmm) cc_final: 0.9230 (mmm) REVERT: A 1774 MET cc_start: 0.9430 (tpp) cc_final: 0.9151 (tpp) REVERT: A 1871 MET cc_start: 0.9735 (ptt) cc_final: 0.9444 (ppp) REVERT: A 2576 MET cc_start: 0.8876 (mpp) cc_final: 0.8528 (mpp) REVERT: A 3238 MET cc_start: 0.9659 (pmm) cc_final: 0.9433 (pmm) REVERT: A 3450 MET cc_start: 0.9701 (mmp) cc_final: 0.9460 (mmm) REVERT: A 3609 MET cc_start: 0.9369 (pmm) cc_final: 0.8745 (pmm) REVERT: A 3771 MET cc_start: 0.9520 (mmp) cc_final: 0.9275 (mmp) REVERT: A 3820 MET cc_start: 0.8849 (pmm) cc_final: 0.8037 (pmm) REVERT: A 3929 MET cc_start: 0.8717 (tpp) cc_final: 0.8287 (tpp) REVERT: A 3932 MET cc_start: 0.9232 (mpp) cc_final: 0.8970 (mpp) REVERT: A 4020 MET cc_start: 0.9473 (mmp) cc_final: 0.9256 (mmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.4276 time to fit residues: 92.7991 Evaluate side-chains 118 residues out of total 3281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 0.6980 chunk 312 optimal weight: 10.0000 chunk 89 optimal weight: 0.0980 chunk 270 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 293 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3105 ASN A3166 ASN ** A3494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4015 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.031502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.024259 restraints weight = 382327.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.024961 restraints weight = 253115.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.025485 restraints weight = 185679.355| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30142 Z= 0.149 Angle : 0.622 11.889 40865 Z= 0.308 Chirality : 0.040 0.225 4670 Planarity : 0.004 0.051 5136 Dihedral : 9.763 89.966 4169 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3634 helix: 1.15 (0.11), residues: 2405 sheet: -1.30 (0.64), residues: 49 loop : -2.14 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A3686 HIS 0.005 0.001 HIS A 935 PHE 0.019 0.001 PHE A1746 TYR 0.029 0.001 TYR A1739 ARG 0.007 0.000 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4368.74 seconds wall clock time: 82 minutes 40.40 seconds (4960.40 seconds total)