Starting phenix.real_space_refine on Sat Jul 4 00:20:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vs5_65297/07_2026/9vs5_65297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vs5_65297/07_2026/9vs5_65297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vs5_65297/07_2026/9vs5_65297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vs5_65297/07_2026/9vs5_65297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vs5_65297/07_2026/9vs5_65297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vs5_65297/07_2026/9vs5_65297.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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 23 5.49 5 S 106 5.16 5 C 10639 2.51 5 N 2772 2.21 5 O 3170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16710 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 16230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1997, 16230 Classifications: {'peptide': 1997} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 68, 'TRANS': 1927} Chain breaks: 12 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'TRP:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "P" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 10} Link IDs: {'rna3p': 12} Time building chain proxies: 3.44, per 1000 atoms: 0.21 Number of scatterers: 16710 At special positions: 0 Unit cell: (104.5, 132.05, 143.45, 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 106 16.00 P 23 15.00 O 3170 8.00 N 2772 7.00 C 10639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 706.8 milliseconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3874 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 17 sheets defined 53.5% alpha, 8.0% beta 8 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 18 through 45 removed outlier: 3.674A pdb=" N ALA A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 114 through 120 removed outlier: 3.824A pdb=" N GLN A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.506A pdb=" N LEU A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.585A pdb=" N ILE A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.647A pdb=" N ASP A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 removed outlier: 5.038A pdb=" N GLU A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.579A pdb=" N LYS A 300 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 332 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 360 through 367 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.531A pdb=" N THR A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 Processing helix chain 'A' and resid 489 through 501 removed outlier: 3.553A pdb=" N ALA A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 523 removed outlier: 3.919A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.742A pdb=" N SER A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.625A pdb=" N PHE A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 651 removed outlier: 3.629A pdb=" N LEU A 647 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.924A pdb=" N MET A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN A 659 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 660 " --> pdb=" O MET A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 675 removed outlier: 4.051A pdb=" N PHE A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 697 removed outlier: 3.517A pdb=" N VAL A 685 " --> pdb=" O THR A 681 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.904A pdb=" N GLN A 701 " --> pdb=" O THR A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 738 through 753 Proline residue: A 749 - end of helix removed outlier: 3.720A pdb=" N ASN A 753 " --> pdb=" O PRO A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 781 removed outlier: 4.330A pdb=" N ILE A 765 " --> pdb=" O HIS A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.149A pdb=" N THR A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 900 " --> pdb=" O GLN A 896 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 901 " --> pdb=" O LEU A 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 901' Processing helix chain 'A' and resid 911 through 922 Processing helix chain 'A' and resid 929 through 941 removed outlier: 3.815A pdb=" N LYS A 939 " --> pdb=" O MET A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 986 removed outlier: 4.174A pdb=" N CYS A 971 " --> pdb=" O GLU A 967 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 974 " --> pdb=" O MET A 970 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1023 removed outlier: 4.233A pdb=" N ARG A1000 " --> pdb=" O ASP A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 Processing helix chain 'A' and resid 1061 through 1076 removed outlier: 3.568A pdb=" N ARG A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1093 Processing helix chain 'A' and resid 1100 through 1106 Processing helix chain 'A' and resid 1107 through 1110 Processing helix chain 'A' and resid 1126 through 1151 removed outlier: 3.965A pdb=" N VAL A1132 " --> pdb=" O MET A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1197 removed outlier: 4.189A pdb=" N ILE A1183 " --> pdb=" O ASP A1179 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR A1185 " --> pdb=" O MET A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1237 removed outlier: 4.437A pdb=" N LEU A1234 " --> pdb=" O ARG A1231 " (cutoff:3.500A) Proline residue: A1235 - end of helix Processing helix chain 'A' and resid 1249 through 1262 removed outlier: 3.825A pdb=" N ALA A1255 " --> pdb=" O SER A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1284 removed outlier: 4.118A pdb=" N TYR A1284 " --> pdb=" O THR A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1324 Processing helix chain 'A' and resid 1327 through 1342 removed outlier: 3.697A pdb=" N ASN A1336 " --> pdb=" O TRP A1332 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1357 removed outlier: 3.808A pdb=" N THR A1356 " --> pdb=" O GLN A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1365 removed outlier: 3.554A pdb=" N LYS A1364 " --> pdb=" O ASN A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1379 Processing helix chain 'A' and resid 1412 through 1416 removed outlier: 4.056A pdb=" N ASN A1415 " --> pdb=" O GLY A1412 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A1416 " --> pdb=" O SER A1413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1412 through 1416' Processing helix chain 'A' and resid 1417 through 1425 Processing helix chain 'A' and resid 1430 through 1442 Processing helix chain 'A' and resid 1443 through 1447 removed outlier: 4.029A pdb=" N LEU A1446 " --> pdb=" O PRO A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1464 removed outlier: 3.910A pdb=" N TYR A1464 " --> pdb=" O ILE A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1473 Processing helix chain 'A' and resid 1477 through 1488 removed outlier: 3.522A pdb=" N LEU A1487 " --> pdb=" O VAL A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1536 removed outlier: 4.014A pdb=" N TYR A1528 " --> pdb=" O TYR A1524 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN A1529 " --> pdb=" O PRO A1525 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET A1530 " --> pdb=" O GLN A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1543 through 1553 removed outlier: 3.583A pdb=" N TYR A1551 " --> pdb=" O ILE A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1569 Processing helix chain 'A' and resid 1597 through 1608 Processing helix chain 'A' and resid 1616 through 1635 removed outlier: 3.522A pdb=" N LEU A1620 " --> pdb=" O ASP A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1645 removed outlier: 4.994A pdb=" N MET A1642 " --> pdb=" O GLU A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1654 through 1677 removed outlier: 3.945A pdb=" N VAL A1670 " --> pdb=" O LYS A1666 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A1671 " --> pdb=" O LEU A1667 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A1677 " --> pdb=" O ASP A1673 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1705 removed outlier: 3.512A pdb=" N THR A1705 " --> pdb=" O ILE A1701 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1753 removed outlier: 4.360A pdb=" N PHE A1744 " --> pdb=" O ALA A1740 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A1745 " --> pdb=" O ALA A1741 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS A1749 " --> pdb=" O ARG A1745 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A1753 " --> pdb=" O HIS A1749 " (cutoff:3.500A) Processing helix chain 'A' and resid 1761 through 1771 removed outlier: 4.090A pdb=" N ASP A1769 " --> pdb=" O ASN A1765 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A1770 " --> pdb=" O GLU A1766 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1787 Processing helix chain 'A' and resid 1794 through 1801 Processing helix chain 'A' and resid 1805 through 1815 removed outlier: 3.577A pdb=" N LEU A1809 " --> pdb=" O THR A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1816 through 1818 No H-bonds generated for 'chain 'A' and resid 1816 through 1818' Processing helix chain 'A' and resid 1868 through 1880 Processing helix chain 'A' and resid 1887 through 1891 removed outlier: 3.504A pdb=" N TYR A1890 " --> pdb=" O LYS A1887 " (cutoff:3.500A) Processing helix chain 'A' and resid 1921 through 1927 Processing helix chain 'A' and resid 1960 through 1968 Processing helix chain 'A' and resid 1991 through 1995 Processing helix chain 'A' and resid 2024 through 2029 Processing helix chain 'A' and resid 2034 through 2038 removed outlier: 3.601A pdb=" N ARG A2037 " --> pdb=" O PRO A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2103 removed outlier: 4.052A pdb=" N ASP A2098 " --> pdb=" O ALA A2094 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A2099 " --> pdb=" O ASN A2095 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A2103 " --> pdb=" O GLU A2099 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2130 Processing helix chain 'A' and resid 2145 through 2149 removed outlier: 3.983A pdb=" N LEU A2148 " --> pdb=" O ILE A2145 " (cutoff:3.500A) Processing helix chain 'A' and resid 2180 through 2185 Processing helix chain 'A' and resid 2198 through 2215 removed outlier: 4.084A pdb=" N LYS A2204 " --> pdb=" O ARG A2200 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A2213 " --> pdb=" O ILE A2209 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A2214 " --> pdb=" O GLU A2210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.027A pdb=" N ILE A 90 " --> pdb=" O CYS A 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 removed outlier: 6.338A pdb=" N GLU A 293 " --> pdb=" O ILE A 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 388 removed outlier: 4.438A pdb=" N LEU A 392 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.718A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE A 561 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.718A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 664 through 665 Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 712 removed outlier: 6.248A pdb=" N TYR A 711 " --> pdb=" O THR A 718 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 728 through 729 Processing sheet with id=AA9, first strand: chain 'A' and resid 846 through 848 removed outlier: 3.843A pdb=" N LYS A 846 " --> pdb=" O ILE A 908 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 908 " --> pdb=" O LYS A 846 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 848 " --> pdb=" O ASP A 906 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 906 " --> pdb=" O GLY A 848 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 960 through 964 removed outlier: 6.520A pdb=" N PHE A 946 " --> pdb=" O ILE A1081 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1219 through 1221 removed outlier: 3.727A pdb=" N GLU A1224 " --> pdb=" O LEU A1221 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1574 through 1575 Processing sheet with id=AB4, first strand: chain 'A' and resid 1581 through 1583 Processing sheet with id=AB5, first strand: chain 'A' and resid 1776 through 1777 Processing sheet with id=AB6, first strand: chain 'A' and resid 1820 through 1822 removed outlier: 3.890A pdb=" N VAL A1851 " --> pdb=" O ILE A1859 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A1859 " --> pdb=" O VAL A1851 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLU A1853 " --> pdb=" O LEU A1857 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A1857 " --> pdb=" O GLU A1853 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LYS A1856 " --> pdb=" O VAL A1945 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS A1858 " --> pdb=" O PRO A1947 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A1949 " --> pdb=" O LYS A1858 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA A1860 " --> pdb=" O VAL A1949 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A1943 " --> pdb=" O TYR A1906 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A1906 " --> pdb=" O VAL A1943 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A1904 " --> pdb=" O VAL A1945 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A1902 " --> pdb=" O PRO A1947 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1976 through 1977 Processing sheet with id=AB8, first strand: chain 'A' and resid 2058 through 2062 removed outlier: 3.779A pdb=" N TYR A2075 " --> pdb=" O ILE A2061 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2694 1.29 - 1.42: 4435 1.42 - 1.56: 9735 1.56 - 1.69: 46 1.69 - 1.82: 179 Bond restraints: 17089 Sorted by residual: bond pdb=" C PHE A1685 " pdb=" O PHE A1685 " ideal model delta sigma weight residual 1.235 1.153 0.082 1.14e-02 7.69e+03 5.21e+01 bond pdb=" N PRO A 652 " pdb=" CD PRO A 652 " ideal model delta sigma weight residual 1.473 1.388 0.085 1.40e-02 5.10e+03 3.66e+01 bond pdb=" C THR A2072 " pdb=" O THR A2072 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.14e-02 7.69e+03 2.16e+01 bond pdb=" C VAL A1682 " pdb=" O VAL A1682 " ideal model delta sigma weight residual 1.238 1.193 0.044 1.06e-02 8.90e+03 1.75e+01 bond pdb=" C LYS A2077 " pdb=" O LYS A2077 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.14e-02 7.69e+03 1.56e+01 ... (remaining 17084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 23072 4.44 - 8.88: 112 8.88 - 13.32: 10 13.32 - 17.76: 0 17.76 - 22.20: 3 Bond angle restraints: 23197 Sorted by residual: angle pdb=" CA PRO A 652 " pdb=" N PRO A 652 " pdb=" CD PRO A 652 " ideal model delta sigma weight residual 112.00 89.80 22.20 1.40e+00 5.10e-01 2.51e+02 angle pdb=" CA PHE A1685 " pdb=" C PHE A1685 " pdb=" O PHE A1685 " ideal model delta sigma weight residual 120.32 112.89 7.43 1.11e+00 8.12e-01 4.48e+01 angle pdb=" CB PRO A 652 " pdb=" CG PRO A 652 " pdb=" CD PRO A 652 " ideal model delta sigma weight residual 106.10 88.15 17.95 3.20e+00 9.77e-02 3.15e+01 angle pdb=" C THR A2060 " pdb=" CA THR A2060 " pdb=" CB THR A2060 " ideal model delta sigma weight residual 109.46 99.51 9.95 1.84e+00 2.95e-01 2.92e+01 angle pdb=" CA PHE A1685 " pdb=" C PHE A1685 " pdb=" N ILE A1686 " ideal model delta sigma weight residual 116.32 123.40 -7.08 1.38e+00 5.25e-01 2.63e+01 ... (remaining 23192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.55: 8902 19.55 - 39.10: 1187 39.10 - 58.66: 270 58.66 - 78.21: 41 78.21 - 97.76: 10 Dihedral angle restraints: 10410 sinusoidal: 4466 harmonic: 5944 Sorted by residual: dihedral pdb=" C PHE A1685 " pdb=" N PHE A1685 " pdb=" CA PHE A1685 " pdb=" CB PHE A1685 " ideal model delta harmonic sigma weight residual -122.60 -106.95 -15.65 0 2.50e+00 1.60e-01 3.92e+01 dihedral pdb=" C TYR A2075 " pdb=" N TYR A2075 " pdb=" CA TYR A2075 " pdb=" CB TYR A2075 " ideal model delta harmonic sigma weight residual -122.60 -107.46 -15.14 0 2.50e+00 1.60e-01 3.67e+01 dihedral pdb=" CA MET A2198 " pdb=" C MET A2198 " pdb=" N GLU A2199 " pdb=" CA GLU A2199 " ideal model delta harmonic sigma weight residual 180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 10407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2483 0.093 - 0.186: 148 0.186 - 0.278: 19 0.278 - 0.371: 6 0.371 - 0.464: 3 Chirality restraints: 2659 Sorted by residual: chirality pdb=" CA PHE A1685 " pdb=" N PHE A1685 " pdb=" C PHE A1685 " pdb=" CB PHE A1685 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA VAL A1682 " pdb=" N VAL A1682 " pdb=" C VAL A1682 " pdb=" CB VAL A1682 " both_signs ideal model delta sigma weight residual False 2.44 2.84 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA TYR A2075 " pdb=" N TYR A2075 " pdb=" C TYR A2075 " pdb=" CB TYR A2075 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 2656 not shown) Planarity restraints: 2846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 77 " -0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO A 78 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A2067 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C SER A2067 " 0.067 2.00e-02 2.50e+03 pdb=" O SER A2067 " -0.025 2.00e-02 2.50e+03 pdb=" N MET A2068 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A1946 " 0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO A1947 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A1947 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A1947 " 0.047 5.00e-02 4.00e+02 ... (remaining 2843 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 1 2.19 - 2.87: 6168 2.87 - 3.55: 23739 3.55 - 4.22: 38075 4.22 - 4.90: 67572 Nonbonded interactions: 135555 Sorted by model distance: nonbonded pdb=" CG2 VAL A2097 " pdb=" CB ALA A2146 " model vdw 1.515 3.880 nonbonded pdb=" O ASN A 659 " pdb=" OG SER A 665 " model vdw 2.194 3.040 nonbonded pdb=" OD1 ASN A1311 " pdb=" OH TYR A1528 " model vdw 2.244 3.040 nonbonded pdb=" OE1 GLU A1444 " pdb=" OG SER A1606 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR A 481 " pdb=" O LEU A1314 " model vdw 2.279 3.040 ... (remaining 135550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 : 0.004 0.101 17089 Z= 0.252 Angle : 0.830 22.196 23197 Z= 0.474 Chirality : 0.053 0.464 2659 Planarity : 0.005 0.099 2846 Dihedral : 17.974 97.759 6536 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.42 % Allowed : 27.74 % Favored : 70.84 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.19), residues: 1971 helix: 0.17 (0.17), residues: 930 sheet: -0.98 (0.40), residues: 174 loop : -1.43 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1468 TYR 0.037 0.001 TYR A2085 PHE 0.025 0.001 PHE A2071 TRP 0.024 0.001 TRP A1826 HIS 0.006 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.25 (17089) covalent geometry : angle 0.83013 / 0.47 (23197) hydrogen bonds : bond 0.15365 / 10.57 ( 743) hydrogen bonds : angle 5.85493 / 4.05 ( 2108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 TYR cc_start: 0.6829 (m-80) cc_final: 0.6461 (m-80) REVERT: A 993 GLU cc_start: 0.6345 (mt-10) cc_final: 0.6061 (mt-10) REVERT: A 1591 MET cc_start: 0.4242 (mtt) cc_final: 0.4004 (mtp) REVERT: A 1683 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8193 (mtmm) REVERT: A 2058 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7919 (mt-10) outliers start: 26 outliers final: 14 residues processed: 248 average time/residue: 0.1132 time to fit residues: 43.1486 Evaluate side-chains 234 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1681 LYS Chi-restraints excluded: chain A residue 1683 LYS Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 2058 GLU Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2070 ILE Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2077 LYS Chi-restraints excluded: chain A residue 2089 ILE Chi-restraints excluded: chain A residue 2092 LEU Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2100 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 761 HIS A 945 ASN A1079 ASN A1089 ASN ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 HIS A2095 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.187433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143102 restraints weight = 18587.055| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.60 r_work: 0.3232 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17089 Z= 0.167 Angle : 0.598 7.569 23197 Z= 0.314 Chirality : 0.042 0.156 2659 Planarity : 0.005 0.071 2846 Dihedral : 9.550 96.854 2509 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.66 % Allowed : 25.51 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 1971 helix: 0.44 (0.17), residues: 956 sheet: -0.98 (0.37), residues: 195 loop : -1.46 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1468 TYR 0.035 0.001 TYR A2085 PHE 0.017 0.001 PHE A2059 TRP 0.015 0.001 TRP A1120 HIS 0.003 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (17089) covalent geometry : angle 0.59826 / 0.31 (23197) hydrogen bonds : bond 0.05088 / 3.43 ( 743) hydrogen bonds : angle 4.65770 / 3.16 ( 2108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 238 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.6745 (ppp) cc_final: 0.6206 (ptt) REVERT: A 329 ASN cc_start: 0.7934 (m-40) cc_final: 0.7545 (m-40) REVERT: A 654 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8269 (mtm110) REVERT: A 1009 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: A 1019 ASP cc_start: 0.7841 (t0) cc_final: 0.7610 (t0) REVERT: A 1049 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8285 (pttp) REVERT: A 1406 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7352 (mmm160) REVERT: A 1619 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: A 1832 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6290 (pp) REVERT: A 1988 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7818 (mmtt) REVERT: A 2074 ARG cc_start: 0.7814 (mtt-85) cc_final: 0.7469 (mtp-110) outliers start: 67 outliers final: 31 residues processed: 290 average time/residue: 0.1089 time to fit residues: 48.8480 Evaluate side-chains 262 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1406 ARG Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1596 HIS Chi-restraints excluded: chain A residue 1619 GLU Chi-restraints excluded: chain A residue 1681 LYS Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1832 LEU Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 2058 GLU Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2070 ILE Chi-restraints excluded: chain A residue 2073 ILE Chi-restraints excluded: chain A residue 2077 LYS Chi-restraints excluded: chain A residue 2089 ILE Chi-restraints excluded: chain A residue 2141 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 80 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 65 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.189612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145060 restraints weight = 18887.304| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.63 r_work: 0.3250 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17089 Z= 0.118 Angle : 0.554 8.813 23197 Z= 0.287 Chirality : 0.041 0.145 2659 Planarity : 0.004 0.070 2846 Dihedral : 9.193 98.502 2494 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.04 % Allowed : 25.72 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1971 helix: 0.63 (0.17), residues: 958 sheet: -0.83 (0.39), residues: 183 loop : -1.40 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.017 0.001 TYR A2085 PHE 0.018 0.001 PHE A 578 TRP 0.013 0.001 TRP A1120 HIS 0.007 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17089) covalent geometry : angle 0.55383 / 0.29 (23197) hydrogen bonds : bond 0.04338 / 2.92 ( 743) hydrogen bonds : angle 4.35951 / 2.96 ( 2108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 234 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.6711 (ppp) cc_final: 0.6223 (ptt) REVERT: A 275 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7072 (p0) REVERT: A 329 ASN cc_start: 0.7949 (m-40) cc_final: 0.7622 (m-40) REVERT: A 989 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 1009 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: A 1019 ASP cc_start: 0.7865 (t0) cc_final: 0.7640 (t0) REVERT: A 1049 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8228 (pttp) REVERT: A 1406 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7305 (mmm160) REVERT: A 1619 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: A 1988 LYS cc_start: 0.8265 (mmtp) cc_final: 0.7900 (mmtt) REVERT: A 2074 ARG cc_start: 0.7846 (mtt-85) cc_final: 0.7593 (mtp-110) REVERT: A 2198 MET cc_start: 0.5354 (pmm) cc_final: 0.5094 (pmm) outliers start: 74 outliers final: 37 residues processed: 291 average time/residue: 0.1002 time to fit residues: 45.8876 Evaluate side-chains 262 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1169 SER Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1257 GLN Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1297 TYR Chi-restraints excluded: chain A residue 1406 ARG Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1596 HIS Chi-restraints excluded: chain A residue 1619 GLU Chi-restraints excluded: chain A residue 1681 LYS Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2058 GLU Chi-restraints excluded: chain A residue 2059 PHE Chi-restraints excluded: chain A residue 2070 ILE Chi-restraints excluded: chain A residue 2089 ILE Chi-restraints excluded: chain A residue 2100 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 HIS A1643 ASN A2080 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.187095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142967 restraints weight = 18821.802| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.71 r_work: 0.3222 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17089 Z= 0.143 Angle : 0.564 11.220 23197 Z= 0.290 Chirality : 0.042 0.145 2659 Planarity : 0.004 0.066 2846 Dihedral : 9.039 97.924 2487 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.66 % Allowed : 25.94 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 1971 helix: 0.73 (0.17), residues: 958 sheet: -0.77 (0.37), residues: 191 loop : -1.35 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.011 0.001 TYR A 629 PHE 0.013 0.001 PHE A1750 TRP 0.013 0.001 TRP A1120 HIS 0.005 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (17089) covalent geometry : angle 0.56436 / 0.29 (23197) hydrogen bonds : bond 0.04294 / 2.88 ( 743) hydrogen bonds : angle 4.24686 / 2.89 ( 2108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 232 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 167 MET cc_start: 0.6658 (ppp) cc_final: 0.6228 (ptt) REVERT: A 275 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7122 (p0) REVERT: A 329 ASN cc_start: 0.7927 (m-40) cc_final: 0.7572 (m-40) REVERT: A 1009 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: A 1049 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8231 (pttp) REVERT: A 1291 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8078 (m) REVERT: A 1406 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7263 (mmm160) REVERT: A 1543 ASP cc_start: 0.7163 (t0) cc_final: 0.6905 (t0) REVERT: A 1619 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: A 1965 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: A 1988 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7871 (mmtt) REVERT: A 2074 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7614 (mtp-110) REVERT: A 2100 ILE cc_start: 0.5864 (OUTLIER) cc_final: 0.5531 (tt) REVERT: A 2144 HIS cc_start: 0.6900 (OUTLIER) cc_final: 0.6476 (t-90) REVERT: A 2198 MET cc_start: 0.5520 (pmm) cc_final: 0.5234 (pmm) outliers start: 67 outliers final: 44 residues processed: 283 average time/residue: 0.1130 time to fit residues: 49.7903 Evaluate side-chains 276 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1169 SER Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1257 GLN Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1297 TYR Chi-restraints excluded: chain A residue 1406 ARG Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1596 HIS Chi-restraints excluded: chain A residue 1619 GLU Chi-restraints excluded: chain A residue 1681 LYS Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain A residue 1846 ARG Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1949 VAL Chi-restraints excluded: chain A residue 1965 PHE Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2070 ILE Chi-restraints excluded: chain A residue 2100 ILE Chi-restraints excluded: chain A residue 2144 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 158 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1537 GLN A1596 HIS A2080 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.189083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144008 restraints weight = 18523.114| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.43 r_work: 0.3235 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17089 Z= 0.128 Angle : 0.546 9.221 23197 Z= 0.282 Chirality : 0.041 0.145 2659 Planarity : 0.004 0.068 2846 Dihedral : 8.895 98.220 2480 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.10 % Allowed : 25.78 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1971 helix: 0.81 (0.17), residues: 958 sheet: -0.72 (0.38), residues: 189 loop : -1.33 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.010 0.001 TYR A 629 PHE 0.011 0.001 PHE A 9 TRP 0.013 0.001 TRP A1120 HIS 0.006 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (17089) covalent geometry : angle 0.54645 / 0.28 (23197) hydrogen bonds : bond 0.04114 / 2.76 ( 743) hydrogen bonds : angle 4.15760 / 2.82 ( 2108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 233 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 167 MET cc_start: 0.6681 (ppp) cc_final: 0.6294 (ptt) REVERT: A 275 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7050 (p0) REVERT: A 329 ASN cc_start: 0.7937 (m-40) cc_final: 0.7597 (m-40) REVERT: A 534 MET cc_start: 0.8208 (mmp) cc_final: 0.7911 (mmp) REVERT: A 1009 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: A 1049 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8190 (pttp) REVERT: A 1072 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7845 (mmt) REVERT: A 1291 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8099 (m) REVERT: A 1439 MET cc_start: 0.8073 (mmt) cc_final: 0.7762 (mmt) REVERT: A 1444 GLU cc_start: 0.7410 (pm20) cc_final: 0.6931 (pm20) REVERT: A 1543 ASP cc_start: 0.7179 (t0) cc_final: 0.6903 (t0) REVERT: A 1619 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: A 1626 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.7213 (t-90) REVERT: A 1809 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6449 (mp) REVERT: A 1853 GLU cc_start: 0.8170 (tt0) cc_final: 0.7934 (tt0) REVERT: A 1884 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7203 (p90) REVERT: A 1965 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: A 1988 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7898 (mmtt) REVERT: A 2100 ILE cc_start: 0.5699 (OUTLIER) cc_final: 0.5382 (tt) REVERT: A 2144 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.6536 (t-90) REVERT: A 2198 MET cc_start: 0.5541 (pmm) cc_final: 0.5254 (pmm) outliers start: 75 outliers final: 43 residues processed: 291 average time/residue: 0.1022 time to fit residues: 46.8353 Evaluate side-chains 280 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1169 SER Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1257 GLN Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1297 TYR Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1596 HIS Chi-restraints excluded: chain A residue 1619 GLU Chi-restraints excluded: chain A residue 1626 HIS Chi-restraints excluded: chain A residue 1681 LYS Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1949 VAL Chi-restraints excluded: chain A residue 1965 PHE Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2100 ILE Chi-restraints excluded: chain A residue 2144 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 54 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 138 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A1421 ASN ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.190347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144806 restraints weight = 18501.238| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.45 r_work: 0.3292 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17089 Z= 0.115 Angle : 0.534 9.084 23197 Z= 0.276 Chirality : 0.041 0.157 2659 Planarity : 0.004 0.068 2846 Dihedral : 8.869 98.526 2478 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.77 % Allowed : 26.60 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 1971 helix: 0.86 (0.17), residues: 963 sheet: -0.71 (0.38), residues: 187 loop : -1.35 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.009 0.001 TYR A 629 PHE 0.015 0.001 PHE A 9 TRP 0.012 0.001 TRP A1120 HIS 0.006 0.001 HIS A1595 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (17089) covalent geometry : angle 0.53438 / 0.28 (23197) hydrogen bonds : bond 0.03900 / 2.62 ( 743) hydrogen bonds : angle 4.08398 / 2.77 ( 2108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 240 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 167 MET cc_start: 0.6693 (ppp) cc_final: 0.6193 (ptt) REVERT: A 275 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7175 (p0) REVERT: A 329 ASN cc_start: 0.7919 (m-40) cc_final: 0.7558 (m-40) REVERT: A 534 MET cc_start: 0.8216 (mmp) cc_final: 0.7983 (mmp) REVERT: A 1009 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: A 1049 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8307 (pttp) REVERT: A 1072 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7660 (mmt) REVERT: A 1089 ASN cc_start: 0.7350 (OUTLIER) cc_final: 0.7008 (m110) REVERT: A 1291 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8055 (m) REVERT: A 1444 GLU cc_start: 0.7553 (pm20) cc_final: 0.7014 (pm20) REVERT: A 1543 ASP cc_start: 0.7185 (t0) cc_final: 0.6948 (t0) REVERT: A 1619 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: A 1809 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6433 (mp) REVERT: A 1853 GLU cc_start: 0.8324 (tt0) cc_final: 0.8050 (tt0) REVERT: A 1894 TYR cc_start: 0.6767 (t80) cc_final: 0.6555 (t80) REVERT: A 1965 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: A 1988 LYS cc_start: 0.8300 (mmtp) cc_final: 0.7885 (mmtt) REVERT: A 2100 ILE cc_start: 0.5614 (OUTLIER) cc_final: 0.5295 (tt) REVERT: A 2144 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6563 (t-90) REVERT: A 2198 MET cc_start: 0.5450 (pmm) cc_final: 0.5161 (pmm) outliers start: 69 outliers final: 43 residues processed: 292 average time/residue: 0.1052 time to fit residues: 48.4349 Evaluate side-chains 280 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1169 SER Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1257 GLN Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1297 TYR Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1596 HIS Chi-restraints excluded: chain A residue 1619 GLU Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1949 VAL Chi-restraints excluded: chain A residue 1965 PHE Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2100 ILE Chi-restraints excluded: chain A residue 2139 LEU Chi-restraints excluded: chain A residue 2144 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 1 optimal weight: 0.3980 chunk 176 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A1222 HIS A1421 ASN ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.187893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142756 restraints weight = 18673.442| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.67 r_work: 0.3210 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17089 Z= 0.133 Angle : 0.546 8.867 23197 Z= 0.282 Chirality : 0.041 0.148 2659 Planarity : 0.004 0.068 2846 Dihedral : 8.806 98.235 2474 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.10 % Allowed : 26.60 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 1971 helix: 0.85 (0.17), residues: 969 sheet: -0.68 (0.38), residues: 187 loop : -1.37 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.027 0.001 TYR A2085 PHE 0.018 0.001 PHE A 578 TRP 0.012 0.001 TRP A1120 HIS 0.007 0.001 HIS A1595 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (17089) covalent geometry : angle 0.54645 / 0.28 (23197) hydrogen bonds : bond 0.03998 / 2.69 ( 743) hydrogen bonds : angle 4.06863 / 2.77 ( 2108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.6648 (ppp) cc_final: 0.6209 (ptt) REVERT: A 255 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 275 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6981 (p0) REVERT: A 329 ASN cc_start: 0.7936 (m-40) cc_final: 0.7637 (m-40) REVERT: A 336 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6719 (mt-10) REVERT: A 534 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7929 (mmp) REVERT: A 646 MET cc_start: 0.7543 (tpt) cc_final: 0.7237 (tpt) REVERT: A 1009 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: A 1049 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8232 (pttp) REVERT: A 1072 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7516 (mmt) REVERT: A 1076 MET cc_start: 0.8743 (mtm) cc_final: 0.8507 (mtm) REVERT: A 1089 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7086 (m110) REVERT: A 1291 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8082 (m) REVERT: A 1444 GLU cc_start: 0.7517 (pm20) cc_final: 0.6894 (pm20) REVERT: A 1543 ASP cc_start: 0.7149 (t0) cc_final: 0.6889 (t0) REVERT: A 1619 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: A 1809 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6479 (mp) REVERT: A 1853 GLU cc_start: 0.8209 (tt0) cc_final: 0.7946 (tt0) REVERT: A 1883 ARG cc_start: 0.7279 (tmt-80) cc_final: 0.6964 (tmt-80) REVERT: A 1884 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.7181 (p90) REVERT: A 1894 TYR cc_start: 0.6654 (t80) cc_final: 0.6444 (t80) REVERT: A 1965 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: A 1988 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7876 (mmtt) REVERT: A 2100 ILE cc_start: 0.5673 (OUTLIER) cc_final: 0.5340 (tt) REVERT: A 2144 HIS cc_start: 0.6822 (OUTLIER) cc_final: 0.6571 (t-90) REVERT: A 2198 MET cc_start: 0.5443 (pmm) cc_final: 0.5149 (pmm) outliers start: 75 outliers final: 47 residues processed: 291 average time/residue: 0.1097 time to fit residues: 49.8165 Evaluate side-chains 291 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1169 SER Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1257 GLN Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1297 TYR Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1619 GLU Chi-restraints excluded: chain A residue 1681 LYS Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1884 HIS Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1949 VAL Chi-restraints excluded: chain A residue 1965 PHE Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2092 LEU Chi-restraints excluded: chain A residue 2100 ILE Chi-restraints excluded: chain A residue 2139 LEU Chi-restraints excluded: chain A residue 2144 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 121 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 0.0470 chunk 40 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 134 optimal weight: 3.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A1421 ASN A1596 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.189902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145866 restraints weight = 18612.960| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.47 r_work: 0.3279 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17089 Z= 0.119 Angle : 0.546 8.581 23197 Z= 0.281 Chirality : 0.041 0.154 2659 Planarity : 0.004 0.067 2846 Dihedral : 8.782 98.508 2474 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.77 % Allowed : 26.93 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.19), residues: 1971 helix: 0.90 (0.17), residues: 970 sheet: -0.63 (0.38), residues: 187 loop : -1.34 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1468 TYR 0.021 0.001 TYR A2085 PHE 0.015 0.001 PHE A1371 TRP 0.013 0.001 TRP A1120 HIS 0.003 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (17089) covalent geometry : angle 0.54621 / 0.28 (23197) hydrogen bonds : bond 0.03839 / 2.58 ( 743) hydrogen bonds : angle 4.01986 / 2.74 ( 2108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 241 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.6657 (ppp) cc_final: 0.6194 (ptt) REVERT: A 255 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8270 (mp) REVERT: A 275 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6965 (p0) REVERT: A 290 GLN cc_start: 0.8555 (tm-30) cc_final: 0.7947 (mt0) REVERT: A 329 ASN cc_start: 0.7926 (m-40) cc_final: 0.7618 (m-40) REVERT: A 336 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6769 (mt-10) REVERT: A 534 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7950 (mmp) REVERT: A 1009 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: A 1049 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8212 (pttp) REVERT: A 1072 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7665 (mmt) REVERT: A 1076 MET cc_start: 0.8731 (mtm) cc_final: 0.8475 (mtm) REVERT: A 1089 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7011 (m110) REVERT: A 1291 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.8042 (m) REVERT: A 1444 GLU cc_start: 0.7515 (pm20) cc_final: 0.6888 (pm20) REVERT: A 1619 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: A 1809 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6422 (mp) REVERT: A 1853 GLU cc_start: 0.8121 (tt0) cc_final: 0.7848 (tt0) REVERT: A 1883 ARG cc_start: 0.7271 (tmt-80) cc_final: 0.7010 (tmt-80) REVERT: A 1894 TYR cc_start: 0.6589 (t80) cc_final: 0.6348 (t80) REVERT: A 1965 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: A 1968 ASN cc_start: 0.7323 (m-40) cc_final: 0.7055 (m-40) REVERT: A 1988 LYS cc_start: 0.8302 (mmtp) cc_final: 0.7847 (mmtt) REVERT: A 2144 HIS cc_start: 0.6820 (OUTLIER) cc_final: 0.6494 (t-90) REVERT: A 2198 MET cc_start: 0.5381 (pmm) cc_final: 0.5106 (pmm) outliers start: 69 outliers final: 49 residues processed: 292 average time/residue: 0.1304 time to fit residues: 59.2718 Evaluate side-chains 296 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1169 SER Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1257 GLN Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1297 TYR Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1596 HIS Chi-restraints excluded: chain A residue 1619 GLU Chi-restraints excluded: chain A residue 1681 LYS Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain A residue 1846 ARG Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1949 VAL Chi-restraints excluded: chain A residue 1965 PHE Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2092 LEU Chi-restraints excluded: chain A residue 2139 LEU Chi-restraints excluded: chain A residue 2144 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 21 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A1421 ASN A1596 HIS A1626 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.190350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145582 restraints weight = 18501.249| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.60 r_work: 0.3254 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17089 Z= 0.115 Angle : 0.549 9.417 23197 Z= 0.283 Chirality : 0.041 0.149 2659 Planarity : 0.004 0.067 2846 Dihedral : 8.771 98.576 2474 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.66 % Allowed : 27.31 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 1971 helix: 0.93 (0.17), residues: 970 sheet: -0.62 (0.38), residues: 187 loop : -1.34 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1468 TYR 0.023 0.001 TYR A2085 PHE 0.023 0.001 PHE A 578 TRP 0.012 0.001 TRP A1120 HIS 0.015 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (17089) covalent geometry : angle 0.54850 / 0.28 (23197) hydrogen bonds : bond 0.03744 / 2.52 ( 743) hydrogen bonds : angle 3.99894 / 2.72 ( 2108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 234 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.6668 (ppp) cc_final: 0.6209 (ptt) REVERT: A 255 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8282 (mp) REVERT: A 275 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6911 (p0) REVERT: A 329 ASN cc_start: 0.7931 (m-40) cc_final: 0.7638 (m-40) REVERT: A 336 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 534 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7890 (mmp) REVERT: A 1009 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: A 1049 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8246 (pttp) REVERT: A 1072 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7429 (mmt) REVERT: A 1076 MET cc_start: 0.8709 (mtm) cc_final: 0.8470 (mtm) REVERT: A 1089 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.6972 (m110) REVERT: A 1291 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.8045 (m) REVERT: A 1439 MET cc_start: 0.8044 (mmt) cc_final: 0.7762 (mmt) REVERT: A 1444 GLU cc_start: 0.7526 (pm20) cc_final: 0.6907 (pm20) REVERT: A 1619 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: A 1809 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6433 (mp) REVERT: A 1853 GLU cc_start: 0.8128 (tt0) cc_final: 0.7868 (tt0) REVERT: A 1883 ARG cc_start: 0.7304 (tmt-80) cc_final: 0.7073 (tmt-80) REVERT: A 1894 TYR cc_start: 0.6588 (t80) cc_final: 0.6365 (t80) REVERT: A 1965 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: A 1968 ASN cc_start: 0.7345 (m-40) cc_final: 0.7075 (m-40) REVERT: A 1988 LYS cc_start: 0.8321 (mmtp) cc_final: 0.7874 (mmtt) REVERT: A 2144 HIS cc_start: 0.6706 (OUTLIER) cc_final: 0.6427 (t-90) REVERT: A 2198 MET cc_start: 0.5411 (pmm) cc_final: 0.5117 (pmm) outliers start: 67 outliers final: 47 residues processed: 285 average time/residue: 0.1306 time to fit residues: 57.7361 Evaluate side-chains 287 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 228 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1169 SER Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1257 GLN Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1297 TYR Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1596 HIS Chi-restraints excluded: chain A residue 1619 GLU Chi-restraints excluded: chain A residue 1681 LYS Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1949 VAL Chi-restraints excluded: chain A residue 1965 PHE Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2092 LEU Chi-restraints excluded: chain A residue 2139 LEU Chi-restraints excluded: chain A residue 2144 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 193 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 179 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A1421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.188971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144309 restraints weight = 18501.448| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.56 r_work: 0.3251 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17089 Z= 0.127 Angle : 0.558 10.229 23197 Z= 0.288 Chirality : 0.041 0.191 2659 Planarity : 0.004 0.067 2846 Dihedral : 8.754 98.381 2474 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.33 % Allowed : 27.58 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 1971 helix: 0.93 (0.17), residues: 967 sheet: -0.59 (0.38), residues: 187 loop : -1.34 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1468 TYR 0.024 0.001 TYR A2085 PHE 0.015 0.001 PHE A1371 TRP 0.012 0.001 TRP A1120 HIS 0.009 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (17089) covalent geometry : angle 0.55832 / 0.29 (23197) hydrogen bonds : bond 0.03810 / 2.56 ( 743) hydrogen bonds : angle 4.00061 / 2.73 ( 2108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 233 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.6680 (ppp) cc_final: 0.6221 (ptt) REVERT: A 255 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 275 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6914 (p0) REVERT: A 329 ASN cc_start: 0.7933 (m-40) cc_final: 0.7640 (m-40) REVERT: A 336 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6791 (mt-10) REVERT: A 534 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7922 (mmp) REVERT: A 715 TYR cc_start: 0.7303 (p90) cc_final: 0.6995 (m-80) REVERT: A 1009 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: A 1049 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8210 (pttp) REVERT: A 1076 MET cc_start: 0.8721 (mtm) cc_final: 0.8496 (mtm) REVERT: A 1291 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.8063 (m) REVERT: A 1407 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7089 (mmtt) REVERT: A 1444 GLU cc_start: 0.7556 (pm20) cc_final: 0.6927 (pm20) REVERT: A 1619 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: A 1745 ARG cc_start: 0.7194 (ttp80) cc_final: 0.6814 (ttp80) REVERT: A 1809 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6432 (mp) REVERT: A 1853 GLU cc_start: 0.8139 (tt0) cc_final: 0.7885 (tt0) REVERT: A 1883 ARG cc_start: 0.7323 (tmt-80) cc_final: 0.7114 (tmt-80) REVERT: A 1894 TYR cc_start: 0.6586 (t80) cc_final: 0.6380 (t80) REVERT: A 1965 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: A 1968 ASN cc_start: 0.7354 (m-40) cc_final: 0.7084 (m-40) REVERT: A 1988 LYS cc_start: 0.8307 (mmtp) cc_final: 0.7863 (mmtt) REVERT: A 2144 HIS cc_start: 0.6726 (OUTLIER) cc_final: 0.6377 (t-90) REVERT: A 2198 MET cc_start: 0.5370 (pmm) cc_final: 0.5083 (pmm) outliers start: 61 outliers final: 48 residues processed: 281 average time/residue: 0.1246 time to fit residues: 54.1569 Evaluate side-chains 287 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 229 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1134 SER Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1169 SER Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1257 GLN Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1297 TYR Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1619 GLU Chi-restraints excluded: chain A residue 1681 LYS Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1862 LEU Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1949 VAL Chi-restraints excluded: chain A residue 1965 PHE Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2092 LEU Chi-restraints excluded: chain A residue 2139 LEU Chi-restraints excluded: chain A residue 2144 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 56 optimal weight: 0.1980 chunk 94 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A1421 ASN A1596 HIS A2080 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.189906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145588 restraints weight = 18505.365| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.62 r_work: 0.3279 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17089 Z= 0.119 Angle : 0.557 10.137 23197 Z= 0.287 Chirality : 0.041 0.197 2659 Planarity : 0.004 0.067 2846 Dihedral : 8.734 98.511 2474 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.66 % Allowed : 27.14 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 1971 helix: 0.95 (0.17), residues: 969 sheet: -0.58 (0.38), residues: 189 loop : -1.31 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1468 TYR 0.024 0.001 TYR A2085 PHE 0.032 0.001 PHE A 578 TRP 0.012 0.001 TRP A1120 HIS 0.006 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (17089) covalent geometry : angle 0.55692 / 0.29 (23197) hydrogen bonds : bond 0.03719 / 2.50 ( 743) hydrogen bonds : angle 3.97950 / 2.72 ( 2108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3421.43 seconds wall clock time: 59 minutes 42.85 seconds (3582.85 seconds total)