Starting phenix.real_space_refine on Fri Jun 5 02:00:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vs5_65297/06_2026/9vs5_65297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vs5_65297/06_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_65297/06_2026/9vs5_65297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vs5_65297/06_2026/9vs5_65297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vs5_65297/06_2026/9vs5_65297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vs5_65297/06_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-6079/lib/python3.9/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: 3.83, per 1000 atoms: 0.23 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: 1.46 Conformation dependent library (CDL) restraints added in 742.9 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: 2.08 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: 3.69 Time building geometry restraints manager: 1.93 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.990 Find NCS groups from input model: 0.050 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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= 0.251 Angle : 0.830 22.196 23197 Z= 0.464 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 / 0.46 (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 : 0.540 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: 0.1263 time to fit residues: 47.9856 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 : 0.605 ------------------------------------------------------------------------------- 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: 8.9990 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... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 709 ASN A 761 HIS A 945 ASN A1079 ASN A1089 ASN ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1526 GLN A1596 HIS A1680 HIS A2095 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.186699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142353 restraints weight = 18789.844| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.69 r_work: 0.3219 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17089 Z= 0.162 Angle : 0.591 7.350 23197 Z= 0.306 Chirality : 0.042 0.150 2659 Planarity : 0.005 0.071 2846 Dihedral : 9.441 97.045 2509 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.99 % Allowed : 25.34 % Favored : 70.67 % 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: -0.72 (0.19), residues: 1971 helix: 0.48 (0.17), residues: 958 sheet: -1.00 (0.36), residues: 193 loop : -1.45 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1468 TYR 0.029 0.001 TYR A2085 PHE 0.016 0.001 PHE A 9 TRP 0.015 0.001 TRP A1120 HIS 0.004 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (17089) covalent geometry : angle 0.59083 / 0.31 (23197) hydrogen bonds : bond 0.04683 / 3.13 ( 743) hydrogen bonds : angle 4.51928 / 3.07 ( 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 310 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 237 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.6602 (ppp) cc_final: 0.6131 (ptt) REVERT: A 275 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7170 (p0) REVERT: A 314 ASP cc_start: 0.7792 (t0) cc_final: 0.7588 (t0) REVERT: A 329 ASN cc_start: 0.7943 (m-40) cc_final: 0.7563 (m-40) REVERT: A 336 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6435 (mt-10) REVERT: A 654 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8315 (mtm110) REVERT: A 1009 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: A 1049 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8192 (pttt) REVERT: A 1406 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7293 (mmm160) REVERT: A 1619 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: A 1988 LYS cc_start: 0.8242 (mmtp) cc_final: 0.7859 (mmtt) REVERT: A 2074 ARG cc_start: 0.7864 (mtt-85) cc_final: 0.7587 (mtp-110) outliers start: 73 outliers final: 29 residues processed: 296 average time/residue: 0.1225 time to fit residues: 55.9230 Evaluate side-chains 254 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 624 THR Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 832 ILE 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 1156 LEU Chi-restraints excluded: chain A residue 1169 SER 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 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 1684 VAL Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain A residue 1848 ILE 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 2073 ILE Chi-restraints excluded: chain A residue 2089 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 80 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A1089 ASN ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 HIS A1643 ASN A2080 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.187937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143346 restraints weight = 18928.393| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.69 r_work: 0.3244 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1069 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= 0.135 Angle : 0.565 10.336 23197 Z= 0.290 Chirality : 0.041 0.147 2659 Planarity : 0.004 0.068 2846 Dihedral : 9.041 97.953 2488 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.88 % Allowed : 25.67 % Favored : 70.45 % 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: -0.51 (0.19), residues: 1971 helix: 0.67 (0.17), residues: 958 sheet: -0.81 (0.37), residues: 191 loop : -1.39 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1468 TYR 0.019 0.001 TYR A2085 PHE 0.012 0.001 PHE A 9 TRP 0.014 0.001 TRP A1120 HIS 0.005 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (17089) covalent geometry : angle 0.56518 / 0.29 (23197) hydrogen bonds : bond 0.04175 / 2.80 ( 743) hydrogen bonds : angle 4.30140 / 2.92 ( 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 301 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 230 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.6667 (ppp) cc_final: 0.6212 (ptt) REVERT: A 275 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7149 (p0) REVERT: A 314 ASP cc_start: 0.7812 (t0) cc_final: 0.7611 (t0) REVERT: A 329 ASN cc_start: 0.7927 (m-40) cc_final: 0.7585 (m-40) REVERT: A 654 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8318 (mtm110) REVERT: A 1009 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: A 1019 ASP cc_start: 0.7740 (t0) cc_final: 0.7529 (t0) REVERT: A 1049 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8129 (pttt) REVERT: A 1072 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7971 (mmt) REVERT: A 1291 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8070 (m) REVERT: A 1406 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7245 (mmm160) REVERT: A 1619 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: A 1626 HIS cc_start: 0.7503 (OUTLIER) cc_final: 0.7272 (t-90) REVERT: A 1853 GLU cc_start: 0.8200 (tt0) cc_final: 0.7922 (tt0) REVERT: A 1988 LYS cc_start: 0.8260 (mmtp) cc_final: 0.7859 (mmtt) REVERT: A 2074 ARG cc_start: 0.7864 (mtt-85) cc_final: 0.7614 (mtp-110) REVERT: A 2100 ILE cc_start: 0.5757 (OUTLIER) cc_final: 0.5449 (tt) REVERT: A 2144 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6431 (t-90) REVERT: A 2198 MET cc_start: 0.5313 (pmm) cc_final: 0.5022 (pmm) outliers start: 71 outliers final: 33 residues processed: 287 average time/residue: 0.1176 time to fit residues: 53.1499 Evaluate side-chains 263 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 126 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 SER 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 654 ARG 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 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 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 1797 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 1896 LEU Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2092 LEU Chi-restraints excluded: chain A residue 2100 ILE Chi-restraints excluded: chain A residue 2144 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 104 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 131 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1537 GLN 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 = 0.4072 r_free = 0.4072 target = 0.189200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144954 restraints weight = 18753.205| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.56 r_work: 0.3287 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17089 Z= 0.107 Angle : 0.539 11.718 23197 Z= 0.275 Chirality : 0.040 0.146 2659 Planarity : 0.004 0.066 2846 Dihedral : 8.868 98.605 2478 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.55 % Allowed : 26.49 % Favored : 69.96 % 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: 0.83 (0.17), residues: 961 sheet: -0.69 (0.39), residues: 177 loop : -1.31 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.010 0.001 TYR A2085 PHE 0.025 0.001 PHE A 578 TRP 0.012 0.001 TRP A1120 HIS 0.011 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (17089) covalent geometry : angle 0.53937 / 0.27 (23197) hydrogen bonds : bond 0.03704 / 2.49 ( 743) hydrogen bonds : angle 4.10621 / 2.79 ( 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 300 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 167 MET cc_start: 0.6630 (ppp) cc_final: 0.6228 (ptt) REVERT: A 275 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6913 (p0) REVERT: A 329 ASN cc_start: 0.7913 (m-40) cc_final: 0.7571 (m-40) REVERT: A 534 MET cc_start: 0.8134 (mmp) cc_final: 0.7846 (mmp) REVERT: A 654 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8254 (mtm110) REVERT: A 1009 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: A 1049 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8160 (pttp) REVERT: A 1072 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.7796 (mmt) REVERT: A 1291 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.8039 (m) REVERT: A 1444 GLU cc_start: 0.7297 (pm20) cc_final: 0.6297 (pm20) REVERT: A 1619 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: A 1809 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6439 (mp) REVERT: A 1853 GLU cc_start: 0.8107 (tt0) cc_final: 0.7842 (tt0) REVERT: A 1965 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: A 1968 ASN cc_start: 0.7338 (m-40) cc_final: 0.7085 (m-40) REVERT: A 1988 LYS cc_start: 0.8273 (mmtp) cc_final: 0.7848 (mmtt) REVERT: A 2074 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.7658 (mtp-110) REVERT: A 2100 ILE cc_start: 0.5755 (OUTLIER) cc_final: 0.5434 (tt) REVERT: A 2144 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6473 (t-90) REVERT: A 2198 MET cc_start: 0.5556 (pmm) cc_final: 0.5275 (pmm) outliers start: 65 outliers final: 35 residues processed: 283 average time/residue: 0.1255 time to fit residues: 55.0784 Evaluate side-chains 269 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 162 PHE 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 654 ARG 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 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 1434 GLU Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1545 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 1949 VAL Chi-restraints excluded: chain A residue 1965 PHE Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2056 VAL 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 2144 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 158 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 GLN A 761 HIS A 953 GLN A1089 ASN A1222 HIS A1421 ASN ** A1480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.188531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143209 restraints weight = 18567.043| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.52 r_work: 0.3265 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1368 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= 0.144 Angle : 0.555 8.854 23197 Z= 0.284 Chirality : 0.041 0.155 2659 Planarity : 0.004 0.067 2846 Dihedral : 8.787 97.781 2474 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.75 % Allowed : 25.51 % Favored : 69.74 % 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: -0.29 (0.19), residues: 1971 helix: 0.85 (0.17), residues: 964 sheet: -0.68 (0.38), residues: 189 loop : -1.30 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 814 TYR 0.011 0.001 TYR A 629 PHE 0.016 0.001 PHE A 9 TRP 0.012 0.001 TRP A1120 HIS 0.008 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (17089) covalent geometry : angle 0.55481 / 0.28 (23197) hydrogen bonds : bond 0.03977 / 2.67 ( 743) hydrogen bonds : angle 4.08919 / 2.77 ( 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 321 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 234 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.8066 (mmm) cc_final: 0.7839 (mmt) REVERT: A 167 MET cc_start: 0.6569 (ppp) cc_final: 0.6163 (ptt) REVERT: A 255 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 275 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7082 (p0) REVERT: A 329 ASN cc_start: 0.7931 (m-40) cc_final: 0.7573 (m-40) REVERT: A 654 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8299 (mtm110) REVERT: A 715 TYR cc_start: 0.7371 (p90) cc_final: 0.6966 (m-80) REVERT: A 1009 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: A 1049 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8173 (pttp) REVERT: A 1291 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8077 (m) REVERT: A 1439 MET cc_start: 0.8120 (mmt) cc_final: 0.7819 (mmt) REVERT: A 1444 GLU cc_start: 0.7369 (pm20) cc_final: 0.6294 (pm20) REVERT: A 1619 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: A 1809 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6429 (mp) REVERT: A 1853 GLU cc_start: 0.8195 (tt0) cc_final: 0.7922 (tt0) REVERT: A 1883 ARG cc_start: 0.7251 (tmt-80) cc_final: 0.6991 (tmt-80) REVERT: A 1884 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7146 (p90) REVERT: A 1965 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: A 1988 LYS cc_start: 0.8292 (mmtp) cc_final: 0.7863 (mmtt) REVERT: A 2074 ARG cc_start: 0.7901 (mtt-85) cc_final: 0.7655 (mtp-110) REVERT: A 2100 ILE cc_start: 0.5699 (OUTLIER) cc_final: 0.5368 (tt) REVERT: A 2144 HIS cc_start: 0.6752 (OUTLIER) cc_final: 0.6499 (t-90) REVERT: A 2198 MET cc_start: 0.5524 (pmm) cc_final: 0.5222 (pmm) outliers start: 87 outliers final: 55 residues processed: 300 average time/residue: 0.1226 time to fit residues: 57.3055 Evaluate side-chains 293 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 226 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 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 654 ARG 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 850 PHE 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 1156 LEU 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 1259 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1297 TYR Chi-restraints excluded: chain A residue 1356 THR 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 1545 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 1797 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 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 2056 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 54 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 159 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.0270 chunk 139 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN 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 = 0.4083 r_free = 0.4083 target = 0.190217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145264 restraints weight = 18569.058| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.74 r_work: 0.3295 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17089 Z= 0.104 Angle : 0.524 8.720 23197 Z= 0.270 Chirality : 0.040 0.148 2659 Planarity : 0.004 0.066 2846 Dihedral : 8.765 98.811 2474 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.10 % Allowed : 26.32 % Favored : 69.58 % 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: -0.18 (0.19), residues: 1971 helix: 0.94 (0.17), residues: 974 sheet: -0.58 (0.39), residues: 177 loop : -1.29 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 814 TYR 0.008 0.001 TYR A1773 PHE 0.021 0.001 PHE A 578 TRP 0.012 0.001 TRP A1120 HIS 0.006 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (17089) covalent geometry : angle 0.52448 / 0.27 (23197) hydrogen bonds : bond 0.03492 / 2.36 ( 743) hydrogen bonds : angle 3.95880 / 2.69 ( 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 312 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 237 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 167 MET cc_start: 0.6628 (ppp) cc_final: 0.6151 (ptt) REVERT: A 255 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8269 (mp) REVERT: A 275 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6888 (p0) REVERT: A 329 ASN cc_start: 0.7921 (m-40) cc_final: 0.7564 (m-40) REVERT: A 336 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6765 (mt-10) REVERT: A 1009 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: A 1049 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8185 (pttp) REVERT: A 1072 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.7324 (mmt) REVERT: A 1291 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.8024 (m) REVERT: A 1444 GLU cc_start: 0.7323 (pm20) cc_final: 0.6240 (pm20) REVERT: A 1619 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: A 1745 ARG cc_start: 0.7163 (ttp80) cc_final: 0.6846 (ttp80) REVERT: A 1809 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6418 (mp) REVERT: A 1853 GLU cc_start: 0.8079 (tt0) cc_final: 0.7810 (tt0) REVERT: A 1883 ARG cc_start: 0.7311 (tmt-80) cc_final: 0.7085 (tmt-80) REVERT: A 1965 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: A 1968 ASN cc_start: 0.7299 (m-40) cc_final: 0.7063 (m-40) REVERT: A 1978 PHE cc_start: 0.7788 (m-80) cc_final: 0.7521 (m-10) REVERT: A 1988 LYS cc_start: 0.8310 (mmtp) cc_final: 0.7825 (mmtt) REVERT: A 2074 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7721 (mtp-110) REVERT: A 2100 ILE cc_start: 0.5692 (OUTLIER) cc_final: 0.5335 (tt) REVERT: A 2144 HIS cc_start: 0.6666 (OUTLIER) cc_final: 0.6447 (t-90) REVERT: A 2198 MET cc_start: 0.5414 (pmm) cc_final: 0.5090 (pmm) outliers start: 75 outliers final: 45 residues processed: 295 average time/residue: 0.1274 time to fit residues: 58.1407 Evaluate side-chains 281 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 589 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 643 THR 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 850 PHE Chi-restraints excluded: chain A residue 961 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 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 1259 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1297 TYR 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 1949 VAL Chi-restraints excluded: chain A residue 1965 PHE Chi-restraints excluded: chain A residue 1987 ILE Chi-restraints excluded: chain A residue 2056 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 1 optimal weight: 0.0770 chunk 176 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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 = 0.4049 r_free = 0.4049 target = 0.186500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141830 restraints weight = 18538.772| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.62 r_work: 0.3183 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17089 Z= 0.184 Angle : 0.586 8.235 23197 Z= 0.302 Chirality : 0.043 0.157 2659 Planarity : 0.004 0.066 2846 Dihedral : 8.720 97.104 2474 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.88 % Allowed : 27.14 % Favored : 68.98 % 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: -0.33 (0.19), residues: 1971 helix: 0.84 (0.17), residues: 972 sheet: -0.67 (0.38), residues: 190 loop : -1.41 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1577 TYR 0.014 0.001 TYR A 629 PHE 0.014 0.001 PHE A 9 TRP 0.012 0.001 TRP A1120 HIS 0.006 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (17089) covalent geometry : angle 0.58624 / 0.30 (23197) hydrogen bonds : bond 0.04288 / 2.87 ( 743) hydrogen bonds : angle 4.08678 / 2.78 ( 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 294 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 223 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.8142 (mmm) cc_final: 0.7927 (mmp) REVERT: A 167 MET cc_start: 0.6721 (ppp) cc_final: 0.6278 (ptt) REVERT: A 255 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 275 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7209 (p0) REVERT: A 329 ASN cc_start: 0.7965 (m-40) cc_final: 0.7593 (m-40) REVERT: A 336 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6818 (mt-10) REVERT: A 715 TYR cc_start: 0.7332 (p90) cc_final: 0.7028 (m-80) REVERT: A 1009 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: A 1072 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7519 (mmt) REVERT: A 1076 MET cc_start: 0.8792 (mtm) cc_final: 0.8588 (mtm) REVERT: A 1128 MET cc_start: 0.8661 (ttt) cc_final: 0.8438 (ttt) REVERT: A 1291 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8097 (m) REVERT: A 1444 GLU cc_start: 0.7461 (pm20) cc_final: 0.6290 (pm20) REVERT: A 1619 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: A 1809 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6480 (mp) REVERT: A 1853 GLU cc_start: 0.8215 (tt0) cc_final: 0.7965 (tt0) REVERT: A 1894 TYR cc_start: 0.6666 (t80) cc_final: 0.6427 (t80) REVERT: A 1965 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: A 1988 LYS cc_start: 0.8328 (mmtp) cc_final: 0.7883 (mmtt) REVERT: A 2074 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7707 (mtp-110) REVERT: A 2144 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.6477 (t-90) REVERT: A 2198 MET cc_start: 0.5339 (pmm) cc_final: 0.5057 (pmm) outliers start: 71 outliers final: 53 residues processed: 280 average time/residue: 0.1218 time to fit residues: 53.3809 Evaluate side-chains 280 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 218 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 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 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 653 SER 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 850 PHE Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1009 GLU 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 1156 LEU 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 1259 SER Chi-restraints excluded: chain A residue 1291 VAL 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 1797 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 2056 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 121 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 132 optimal weight: 0.0060 chunk 40 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A1595 HIS A1596 HIS 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 = 0.189103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144447 restraints weight = 18718.519| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.69 r_work: 0.3251 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17089 Z= 0.108 Angle : 0.541 8.421 23197 Z= 0.279 Chirality : 0.041 0.149 2659 Planarity : 0.004 0.067 2846 Dihedral : 8.713 98.834 2474 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.77 % Allowed : 27.09 % Favored : 69.14 % 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: -0.14 (0.19), residues: 1971 helix: 1.01 (0.17), residues: 970 sheet: -0.57 (0.37), residues: 189 loop : -1.31 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1468 TYR 0.025 0.001 TYR A2085 PHE 0.022 0.001 PHE A1355 TRP 0.019 0.001 TRP A1826 HIS 0.011 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (17089) covalent geometry : angle 0.54132 / 0.28 (23197) hydrogen bonds : bond 0.03535 / 2.38 ( 743) hydrogen bonds : angle 3.94402 / 2.68 ( 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 301 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 232 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 167 MET cc_start: 0.6702 (ppp) cc_final: 0.6232 (ptt) REVERT: A 255 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8287 (mp) REVERT: A 275 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6968 (p0) REVERT: A 329 ASN cc_start: 0.7936 (m-40) cc_final: 0.7584 (m-40) REVERT: A 336 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 1009 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: A 1049 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8227 (pttp) REVERT: A 1072 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7062 (mmt) REVERT: A 1076 MET cc_start: 0.8713 (mtm) cc_final: 0.8470 (mtm) REVERT: A 1444 GLU cc_start: 0.7411 (pm20) cc_final: 0.6291 (pm20) REVERT: A 1619 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: A 1809 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6522 (mp) REVERT: A 1853 GLU cc_start: 0.8157 (tt0) cc_final: 0.7910 (tt0) REVERT: A 1868 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 1894 TYR cc_start: 0.6564 (t80) cc_final: 0.6332 (t80) REVERT: A 1965 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: A 1968 ASN cc_start: 0.7347 (m-40) cc_final: 0.7081 (m-40) REVERT: A 2074 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7761 (mtp-110) REVERT: A 2198 MET cc_start: 0.5165 (pmm) cc_final: 0.4832 (pmm) outliers start: 69 outliers final: 46 residues processed: 284 average time/residue: 0.1158 time to fit residues: 51.8298 Evaluate side-chains 277 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 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 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 589 VAL Chi-restraints excluded: chain A residue 613 ILE 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 850 PHE Chi-restraints excluded: chain A residue 989 GLU 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 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 1259 SER 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 1587 GLU 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 1797 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 2056 VAL Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2092 LEU Chi-restraints excluded: chain A residue 2139 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 21 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN A1421 ASN A1596 HIS A2144 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.189208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144502 restraints weight = 18573.284| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.75 r_work: 0.3258 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1685 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= 0.133 Angle : 0.556 9.551 23197 Z= 0.287 Chirality : 0.041 0.168 2659 Planarity : 0.004 0.067 2846 Dihedral : 8.673 98.093 2474 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.44 % Allowed : 27.36 % 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: -0.18 (0.19), residues: 1971 helix: 0.99 (0.17), residues: 972 sheet: -0.57 (0.37), residues: 189 loop : -1.36 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1468 TYR 0.021 0.001 TYR A2085 PHE 0.028 0.001 PHE A1432 TRP 0.017 0.001 TRP A1826 HIS 0.003 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (17089) covalent geometry : angle 0.55648 / 0.29 (23197) hydrogen bonds : bond 0.03768 / 2.53 ( 743) hydrogen bonds : angle 3.95873 / 2.69 ( 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 290 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 227 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 167 MET cc_start: 0.6644 (ppp) cc_final: 0.6186 (ptt) REVERT: A 255 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8287 (mp) REVERT: A 275 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.7002 (p0) REVERT: A 329 ASN cc_start: 0.7929 (m-40) cc_final: 0.7563 (m-40) REVERT: A 336 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6764 (mt-10) REVERT: A 1009 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: A 1049 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8186 (pttp) REVERT: A 1072 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.7253 (mmt) REVERT: A 1076 MET cc_start: 0.8776 (mtm) cc_final: 0.8534 (mtm) REVERT: A 1436 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7827 (mm) REVERT: A 1444 GLU cc_start: 0.7427 (pm20) cc_final: 0.6303 (pm20) REVERT: A 1619 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: A 1745 ARG cc_start: 0.7204 (ttp80) cc_final: 0.6880 (ttp80) REVERT: A 1809 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6499 (mp) REVERT: A 1853 GLU cc_start: 0.8160 (tt0) cc_final: 0.7878 (tt0) REVERT: A 1868 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 1884 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7094 (p90) REVERT: A 1894 TYR cc_start: 0.6544 (t80) cc_final: 0.6241 (t80) REVERT: A 1965 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: A 1968 ASN cc_start: 0.7318 (m-40) cc_final: 0.7045 (m-40) REVERT: A 2074 ARG cc_start: 0.8020 (mtt-85) cc_final: 0.7759 (mtp-110) REVERT: A 2198 MET cc_start: 0.5106 (pmm) cc_final: 0.4771 (pmm) outliers start: 63 outliers final: 47 residues processed: 278 average time/residue: 0.1149 time to fit residues: 50.9103 Evaluate side-chains 278 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 220 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 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 589 VAL Chi-restraints excluded: chain A residue 613 ILE 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 843 SER Chi-restraints excluded: chain A residue 961 ILE 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 1155 CYS Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1169 SER Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1480 GLN 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 1681 LYS Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1797 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 2056 VAL 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: 9.9990 chunk 161 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A1596 HIS A2144 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.181990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123116 restraints weight = 19072.567| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.35 r_work: 0.3207 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17089 Z= 0.230 Angle : 0.638 10.357 23197 Z= 0.328 Chirality : 0.045 0.197 2659 Planarity : 0.004 0.068 2846 Dihedral : 8.661 96.537 2472 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.71 % Allowed : 27.09 % 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: -0.45 (0.19), residues: 1971 helix: 0.79 (0.17), residues: 969 sheet: -0.73 (0.38), residues: 190 loop : -1.53 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1468 TYR 0.023 0.002 TYR A2085 PHE 0.024 0.002 PHE A1355 TRP 0.019 0.002 TRP A1826 HIS 0.012 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 (17089) covalent geometry : angle 0.63789 / 0.33 (23197) hydrogen bonds : bond 0.04637 / 3.11 ( 743) hydrogen bonds : angle 4.17300 / 2.83 ( 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 290 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 167 MET cc_start: 0.6372 (ppp) cc_final: 0.5904 (ptt) REVERT: A 255 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8149 (mp) REVERT: A 275 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7042 (p0) REVERT: A 329 ASN cc_start: 0.7800 (m-40) cc_final: 0.7396 (m-40) REVERT: A 336 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6667 (mt-10) REVERT: A 1009 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: A 1076 MET cc_start: 0.8911 (mtm) cc_final: 0.8701 (mtm) REVERT: A 1436 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7161 (mm) REVERT: A 1444 GLU cc_start: 0.7452 (pm20) cc_final: 0.6244 (pm20) REVERT: A 1619 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: A 1853 GLU cc_start: 0.8066 (tt0) cc_final: 0.7707 (tt0) REVERT: A 1884 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.7063 (p90) REVERT: A 1965 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: A 2018 GLU cc_start: 0.7602 (mp0) cc_final: 0.7203 (mp0) REVERT: A 2074 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7581 (mtp180) REVERT: A 2198 MET cc_start: 0.5070 (pmm) cc_final: 0.4776 (pmm) outliers start: 68 outliers final: 51 residues processed: 278 average time/residue: 0.1153 time to fit residues: 50.7259 Evaluate side-chains 271 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET 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 152 ILE 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 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 733 PHE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 990 MET Chi-restraints excluded: chain A residue 1009 GLU Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1155 CYS Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1168 THR Chi-restraints excluded: chain A residue 1169 SER Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1259 SER Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1447 VAL Chi-restraints excluded: chain A residue 1480 GLN 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 1700 LEU Chi-restraints excluded: chain A residue 1797 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 2056 VAL Chi-restraints excluded: chain A residue 2087 ASN Chi-restraints excluded: chain A residue 2092 LEU Chi-restraints excluded: chain A residue 2139 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 174 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 153 optimal weight: 0.0870 chunk 155 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A1596 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.187274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125388 restraints weight = 18849.368| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.26 r_work: 0.3270 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17089 Z= 0.110 Angle : 0.562 10.877 23197 Z= 0.289 Chirality : 0.041 0.197 2659 Planarity : 0.004 0.067 2846 Dihedral : 8.650 98.978 2472 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.57 % Allowed : 28.18 % Favored : 69.25 % 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: -0.17 (0.19), residues: 1971 helix: 1.01 (0.17), residues: 970 sheet: -0.59 (0.38), residues: 189 loop : -1.37 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1468 TYR 0.024 0.001 TYR A2085 PHE 0.021 0.001 PHE A1355 TRP 0.015 0.001 TRP A1826 HIS 0.009 0.001 HIS A1596 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17089) covalent geometry : angle 0.56160 / 0.29 (23197) hydrogen bonds : bond 0.03556 / 2.41 ( 743) hydrogen bonds : angle 3.96404 / 2.70 ( 2108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4060.30 seconds wall clock time: 70 minutes 29.06 seconds (4229.06 seconds total)