Starting phenix.real_space_refine on Sat Sep 12 21:21:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6z6g_11093/09_2026/6z6g_11093.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z6g_11093/09_2026/6z6g_11093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6z6g_11093/09_2026/6z6g_11093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z6g_11093/09_2026/6z6g_11093.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z6g_11093/09_2026/6z6g_11093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z6g_11093/09_2026/6z6g_11093.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6z6g_11093/09_2026/6z6g_11093.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6z6g_11093/09_2026/6z6g_11093.cif" } resolution = 3.06 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 27 5.49 5 Mg 1 5.21 5 S 111 5.16 5 C 11450 2.51 5 N 3028 2.21 5 O 3450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.14s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18068 Number of models: 1 Model: "" Number of chains: 5 Chain: "U" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 216 Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "X" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 101 Classifications: {'RNAv2': 5} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 274 Classifications: {'RNAv2': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "A" Number of atoms: 17475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2142, 17475 Classifications: {'peptide': 2142} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 2073} Chain breaks: 12 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16596 SG CYS A2064 87.218 100.954 88.526 1.00 77.50 S Time building chain proxies: 3.39, per 1000 atoms: 0.19 Number of scatterers: 18068 At special positions: 0 Unit cell: (120.596, 132.986, 147.854, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 111 16.00 P 27 15.00 Mg 1 11.99 O 3450 8.00 N 3028 7.00 C 11450 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: 1.62 Conformation dependent library (CDL) restraints added in 778.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2182 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2064 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2169 " 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4130 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 18 sheets defined 55.4% alpha, 9.5% beta 7 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.676A pdb=" N TYR A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN A 8 " --> pdb=" O GLN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 46 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 99 through 121 removed outlier: 4.779A pdb=" N GLU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.570A pdb=" N MET A 214 " --> pdb=" O PHE A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 237 through 261 removed outlier: 5.185A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.760A pdb=" N ASP A 300 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.653A pdb=" N SER A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 447 through 466 removed outlier: 3.739A pdb=" N TYR A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 6.276A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 removed outlier: 3.833A pdb=" N THR A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 522 Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 606 through 620 removed outlier: 3.661A pdb=" N LEU A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 639 removed outlier: 4.132A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 661 removed outlier: 4.125A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.420A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 680 through 700 removed outlier: 3.573A pdb=" N VAL A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 704 removed outlier: 3.816A pdb=" N VAL A 704 " --> pdb=" O ARG A 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 704' Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 748 through 752 removed outlier: 3.520A pdb=" N ASN A 752 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 removed outlier: 4.281A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 814 removed outlier: 3.554A pdb=" N HIS A 814 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 849 through 870 removed outlier: 4.011A pdb=" N LYS A 853 " --> pdb=" O PHE A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 910 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.924A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 983 Processing helix chain 'A' and resid 996 through 1020 Processing helix chain 'A' and resid 1020 through 1031 Processing helix chain 'A' and resid 1040 through 1047 removed outlier: 4.074A pdb=" N LYS A1044 " --> pdb=" O GLY A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1079 removed outlier: 3.890A pdb=" N TRP A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.561A pdb=" N ASP A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 Processing helix chain 'A' and resid 1148 through 1174 removed outlier: 3.502A pdb=" N LEU A1174 " --> pdb=" O ALA A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1219 removed outlier: 3.653A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1259 Processing helix chain 'A' and resid 1267 through 1285 Processing helix chain 'A' and resid 1288 through 1307 removed outlier: 3.594A pdb=" N TYR A1307 " --> pdb=" O THR A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1320 removed outlier: 4.439A pdb=" N ASP A1319 " --> pdb=" O ASP A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1329 removed outlier: 3.621A pdb=" N ILE A1329 " --> pdb=" O ARG A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1334 Processing helix chain 'A' and resid 1340 through 1347 Processing helix chain 'A' and resid 1350 through 1365 Processing helix chain 'A' and resid 1366 through 1370 removed outlier: 3.817A pdb=" N LYS A1370 " --> pdb=" O VAL A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1379 Processing helix chain 'A' and resid 1380 through 1384 removed outlier: 3.530A pdb=" N ASN A1383 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1403 Processing helix chain 'A' and resid 1441 through 1452 removed outlier: 3.719A pdb=" N SER A1445 " --> pdb=" O LEU A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1466 Processing helix chain 'A' and resid 1467 through 1472 removed outlier: 3.842A pdb=" N LEU A1470 " --> pdb=" O LYS A1467 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1471 " --> pdb=" O PRO A1468 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A1472 " --> pdb=" O GLU A1469 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1467 through 1472' Processing helix chain 'A' and resid 1477 through 1488 Processing helix chain 'A' and resid 1491 through 1498 Processing helix chain 'A' and resid 1502 through 1513 removed outlier: 3.625A pdb=" N LEU A1506 " --> pdb=" O ASN A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1526 Processing helix chain 'A' and resid 1548 through 1561 removed outlier: 3.692A pdb=" N SER A1561 " --> pdb=" O MET A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1578 Processing helix chain 'A' and resid 1581 through 1593 Processing helix chain 'A' and resid 1623 through 1633 Processing helix chain 'A' and resid 1647 through 1658 Processing helix chain 'A' and resid 1662 through 1677 removed outlier: 3.910A pdb=" N LYS A1666 " --> pdb=" O GLU A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1700 removed outlier: 3.757A pdb=" N TYR A1698 " --> pdb=" O VAL A1694 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1729 removed outlier: 3.718A pdb=" N PHE A1721 " --> pdb=" O THR A1717 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A1729 " --> pdb=" O MET A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1752 through 1779 Processing helix chain 'A' and resid 1784 through 1794 removed outlier: 3.703A pdb=" N GLU A1794 " --> pdb=" O LEU A1790 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1812 Processing helix chain 'A' and resid 1814 through 1817 Processing helix chain 'A' and resid 1818 through 1826 Processing helix chain 'A' and resid 1829 through 1840 Processing helix chain 'A' and resid 1892 through 1904 removed outlier: 3.692A pdb=" N THR A1897 " --> pdb=" O PRO A1893 " (cutoff:3.500A) Processing helix chain 'A' and resid 1944 through 1955 Processing helix chain 'A' and resid 2014 through 2019 removed outlier: 3.562A pdb=" N LYS A2017 " --> pdb=" O HIS A2014 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2038 Processing helix chain 'A' and resid 2047 through 2052 Processing helix chain 'A' and resid 2054 through 2059 Processing helix chain 'A' and resid 2069 through 2074 Processing helix chain 'A' and resid 2109 through 2129 removed outlier: 3.866A pdb=" N ALA A2113 " --> pdb=" O THR A2109 " (cutoff:3.500A) Processing helix chain 'A' and resid 2138 through 2153 removed outlier: 3.719A pdb=" N ALA A2147 " --> pdb=" O GLY A2143 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A2148 " --> pdb=" O CYS A2144 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2175 Processing helix chain 'A' and resid 2177 through 2183 Processing helix chain 'A' and resid 2200 through 2210 Processing helix chain 'A' and resid 2218 through 2238 removed outlier: 3.985A pdb=" N MET A2222 " --> pdb=" O PRO A2218 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A2238 " --> pdb=" O ILE A2234 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2251 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.417A pdb=" N LEU A 88 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A 127 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE A 90 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE A 129 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP A 92 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE A 131 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS A 94 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 130 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 387 removed outlier: 5.140A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 586 " --> pdb=" O CYS A 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 387 removed outlier: 5.140A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 716 through 718 removed outlier: 6.417A pdb=" N TYR A 710 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A2096 " --> pdb=" O ILE A2090 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA7, first strand: chain 'A' and resid 785 through 786 Processing sheet with id=AA8, first strand: chain 'A' and resid 845 through 847 removed outlier: 4.264A pdb=" N ASP A 905 " --> pdb=" O GLY A 847 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 959 through 963 removed outlier: 3.584A pdb=" N ILE A 960 " --> pdb=" O PHE A 948 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 948 " --> pdb=" O ILE A 960 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1177 through 1184 Processing sheet with id=AB2, first strand: chain 'A' and resid 1236 through 1238 removed outlier: 3.510A pdb=" N PHE A1249 " --> pdb=" O PHE A1242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1594 through 1596 Processing sheet with id=AB4, first strand: chain 'A' and resid 1606 through 1609 Processing sheet with id=AB5, first strand: chain 'A' and resid 1800 through 1801 Processing sheet with id=AB6, first strand: chain 'A' and resid 1862 through 1867 removed outlier: 3.617A pdb=" N TYR A1883 " --> pdb=" O ILE A1875 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR A1882 " --> pdb=" O VAL A1970 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ASN A1972 " --> pdb=" O THR A1882 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A1884 " --> pdb=" O ASN A1972 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA A1974 " --> pdb=" O ALA A1884 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU A1886 " --> pdb=" O ALA A1974 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL A1970 " --> pdb=" O TYR A1925 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR A1925 " --> pdb=" O VAL A1970 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1930 through 1932 removed outlier: 3.773A pdb=" N ARG A1930 " --> pdb=" O VAL A1938 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A1938 " --> pdb=" O ARG A1930 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1999 through 2001 Processing sheet with id=AB9, first strand: chain 'A' and resid 2027 through 2028 894 hydrogen bonds defined for protein. 2577 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4145 1.33 - 1.45: 4018 1.45 - 1.57: 10084 1.57 - 1.69: 52 1.69 - 1.81: 183 Bond restraints: 18482 Sorted by residual: bond pdb=" CB VAL A 558 " pdb=" CG2 VAL A 558 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.62e+00 bond pdb=" CG1 ILE A 571 " pdb=" CD1 ILE A 571 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.31e+00 bond pdb=" CB ARG A 653 " pdb=" CG ARG A 653 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.67e+00 bond pdb=" CA ARG A1958 " pdb=" C ARG A1958 " ideal model delta sigma weight residual 1.525 1.496 0.029 1.34e-02 5.57e+03 4.82e+00 bond pdb=" CB ASN A 469 " pdb=" CG ASN A 469 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.72e+00 ... (remaining 18477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 23914 2.17 - 4.34: 993 4.34 - 6.51: 107 6.51 - 8.68: 23 8.68 - 10.85: 5 Bond angle restraints: 25042 Sorted by residual: angle pdb=" C ASN A 85 " pdb=" N ASN A 86 " pdb=" CA ASN A 86 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C LYS A 759 " pdb=" N HIS A 760 " pdb=" CA HIS A 760 " ideal model delta sigma weight residual 120.82 128.61 -7.79 1.50e+00 4.44e-01 2.70e+01 angle pdb=" N SER A1841 " pdb=" CA SER A1841 " pdb=" C SER A1841 " ideal model delta sigma weight residual 108.74 115.61 -6.87 1.38e+00 5.25e-01 2.48e+01 angle pdb=" N CYS A1969 " pdb=" CA CYS A1969 " pdb=" C CYS A1969 " ideal model delta sigma weight residual 110.80 120.96 -10.16 2.13e+00 2.20e-01 2.28e+01 angle pdb=" C ILE A 84 " pdb=" N ASN A 85 " pdb=" CA ASN A 85 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.01e+01 ... (remaining 25037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 10477 16.53 - 33.06: 524 33.06 - 49.58: 142 49.58 - 66.11: 51 66.11 - 82.64: 13 Dihedral angle restraints: 11207 sinusoidal: 4851 harmonic: 6356 Sorted by residual: dihedral pdb=" C4' A H 9 " pdb=" C3' A H 9 " pdb=" C2' A H 9 " pdb=" C1' A H 9 " ideal model delta sinusoidal sigma weight residual 36.34 -36.92 73.26 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' U H 16 " pdb=" C3' U H 16 " pdb=" C2' U H 16 " pdb=" C1' U H 16 " ideal model delta sinusoidal sigma weight residual 36.34 -35.89 72.24 1 3.10e+00 1.04e-01 6.94e+02 dihedral pdb=" C4' G U 7 " pdb=" C3' G U 7 " pdb=" C2' G U 7 " pdb=" C1' G U 7 " ideal model delta sinusoidal sigma weight residual 36.34 -33.27 69.61 1 3.10e+00 1.04e-01 6.51e+02 ... (remaining 11204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2629 0.117 - 0.233: 159 0.233 - 0.350: 22 0.350 - 0.467: 1 0.467 - 0.583: 1 Chirality restraints: 2812 Sorted by residual: chirality pdb=" CB VAL A 521 " pdb=" CA VAL A 521 " pdb=" CG1 VAL A 521 " pdb=" CG2 VAL A 521 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.51e+00 chirality pdb=" CB VAL A 736 " pdb=" CA VAL A 736 " pdb=" CG1 VAL A 736 " pdb=" CG2 VAL A 736 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CB ILE A1918 " pdb=" CA ILE A1918 " pdb=" CG1 ILE A1918 " pdb=" CG2 ILE A1918 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2809 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 511 " 0.032 2.00e-02 2.50e+03 2.88e-02 1.45e+01 pdb=" CG PHE A 511 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE A 511 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 511 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 511 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 511 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 511 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1709 " -0.018 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE A1709 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A1709 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A1709 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A1709 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A1709 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A1709 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1220 " -0.017 2.00e-02 2.50e+03 2.17e-02 8.28e+00 pdb=" CG PHE A1220 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A1220 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A1220 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A1220 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A1220 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A1220 " -0.003 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 12 2.27 - 2.92: 7301 2.92 - 3.58: 25779 3.58 - 4.24: 44157 4.24 - 4.90: 73041 Nonbonded interactions: 150290 Sorted by model distance: nonbonded pdb=" O ARG A1829 " pdb=" OD1 ASP A1832 " model vdw 1.608 3.040 nonbonded pdb=" O HIS A1185 " pdb=" OG SER A1186 " model vdw 1.869 3.040 nonbonded pdb=" CD1 LEU A2151 " pdb=" CE2 PHE A2204 " model vdw 1.985 3.760 nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2301 " model vdw 2.097 2.230 nonbonded pdb=" C ARG A1829 " pdb=" OD1 ASP A1832 " model vdw 2.218 3.270 ... (remaining 150285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.760 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.011 0.566 18485 Z= 0.448 Angle : 0.998 10.853 25042 Z= 0.547 Chirality : 0.067 0.583 2812 Planarity : 0.007 0.068 3066 Dihedral : 11.952 82.639 7077 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.57 % Favored : 93.29 % Rotamer: Outliers : 1.47 % Allowed : 2.59 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -3.39 (0.15), residues: 2116 helix: -1.96 (0.12), residues: 1121 sheet: -1.39 (0.38), residues: 168 loop : -2.70 (0.18), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 531 TYR 0.039 0.004 TYR A 677 PHE 0.066 0.004 PHE A 511 TRP 0.030 0.004 TRP A1735 HIS 0.010 0.003 HIS A2169 Details of bonding type rmsd/Z covalent geometry : bond 0.01007 / 0.42 (18482) covalent geometry : angle 0.99837 / 0.55 (25042) hydrogen bonds : bond 0.16099 / 9.14 ( 897) hydrogen bonds : angle 6.85959 / 4.21 ( 2603) metal coordination : bond 0.37913 / 18.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 312 time to evaluate : 0.525 Fit side-chains REVERT: A 57 ASP cc_start: 0.6941 (m-30) cc_final: 0.6622 (t0) REVERT: A 61 ASP cc_start: 0.6792 (m-30) cc_final: 0.5242 (m-30) REVERT: A 91 ILE cc_start: 0.8956 (mt) cc_final: 0.8738 (mm) REVERT: A 862 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6823 (tttm) REVERT: A 934 MET cc_start: 0.8894 (mmp) cc_final: 0.8479 (mmt) REVERT: A 1177 SER cc_start: 0.8712 (m) cc_final: 0.8458 (p) REVERT: A 1385 LYS cc_start: 0.7667 (mppt) cc_final: 0.7452 (mmtm) REVERT: A 1470 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8177 (pp) REVERT: A 1633 ASN cc_start: 0.7240 (m-40) cc_final: 0.6888 (m-40) REVERT: A 1645 MET cc_start: 0.5503 (tpt) cc_final: 0.4291 (ttm) REVERT: A 1756 ASN cc_start: 0.8376 (m110) cc_final: 0.8115 (m110) REVERT: A 1814 ASN cc_start: 0.7863 (p0) cc_final: 0.7292 (p0) REVERT: A 1829 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6258 (mtt90) REVERT: A 1835 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8007 (tptp) REVERT: A 1918 ILE cc_start: 0.0868 (OUTLIER) cc_final: -0.0129 (pt) REVERT: A 1983 LEU cc_start: 0.5492 (OUTLIER) cc_final: 0.5268 (mp) REVERT: A 2012 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7438 (tptm) REVERT: A 2251 MET cc_start: 0.2227 (mmm) cc_final: 0.1762 (mmt) outliers start: 29 outliers final: 8 residues processed: 333 average time/residue: 0.1623 time to fit residues: 77.9740 Evaluate side-chains 198 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1829 ARG Chi-restraints excluded: chain A residue 1835 LYS Chi-restraints excluded: chain A residue 1918 ILE Chi-restraints excluded: chain A residue 1958 ARG Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2011 LYS Chi-restraints excluded: chain A residue 2012 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.0870 chunk 212 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 389 ASN A 489 ASN A 539 ASN A 565 HIS A 602 GLN A 718 GLN A 902 ASN A1058 ASN A1112 ASN A1181 ASN A1243 ASN A1392 ASN A1693 GLN A1754 GLN A1755 HIS A1924 ASN A1944 HIS A2091 HIS ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2175 ASN A2209 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100421 restraints weight = 29616.189| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.15 r_work: 0.2960 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18485 Z= 0.132 Angle : 0.642 14.834 25042 Z= 0.328 Chirality : 0.049 0.692 2812 Planarity : 0.005 0.060 3066 Dihedral : 9.944 164.694 2691 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 1.32 % Allowed : 6.20 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.43 (0.17), residues: 2116 helix: -0.08 (0.15), residues: 1127 sheet: -0.56 (0.39), residues: 171 loop : -2.24 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 707 TYR 0.018 0.001 TYR A 677 PHE 0.033 0.001 PHE A2204 TRP 0.009 0.001 TRP A 193 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (18482) covalent geometry : angle 0.64161 / 0.33 (25042) hydrogen bonds : bond 0.04795 / 2.69 ( 897) hydrogen bonds : angle 4.71327 / 2.88 ( 2603) metal coordination : bond 0.00073 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.640 Fit side-chains REVERT: A 46 ASN cc_start: 0.8491 (t0) cc_final: 0.8240 (t0) REVERT: A 57 ASP cc_start: 0.7439 (m-30) cc_final: 0.6784 (t0) REVERT: A 61 ASP cc_start: 0.6708 (m-30) cc_final: 0.4945 (m-30) REVERT: A 91 ILE cc_start: 0.8855 (mt) cc_final: 0.8646 (mm) REVERT: A 144 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.7955 (mmm-85) REVERT: A 162 PHE cc_start: 0.8547 (m-10) cc_final: 0.7751 (m-80) REVERT: A 190 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8878 (p) REVERT: A 726 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: A 1177 SER cc_start: 0.8859 (m) cc_final: 0.8509 (p) REVERT: A 1371 ARG cc_start: 0.8277 (ptp-110) cc_final: 0.7564 (mmm160) REVERT: A 1385 LYS cc_start: 0.7721 (mppt) cc_final: 0.7431 (mmtm) REVERT: A 1391 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: A 1470 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8380 (pp) REVERT: A 1633 ASN cc_start: 0.7593 (m-40) cc_final: 0.7224 (m-40) REVERT: A 1645 MET cc_start: 0.5682 (tpt) cc_final: 0.4296 (ttm) REVERT: A 1666 LYS cc_start: 0.8030 (ptpt) cc_final: 0.7545 (tptt) REVERT: A 1688 MET cc_start: 0.8289 (tpp) cc_final: 0.7812 (tpt) REVERT: A 1756 ASN cc_start: 0.8285 (m110) cc_final: 0.8066 (m110) REVERT: A 1835 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7767 (tptp) REVERT: A 1918 ILE cc_start: 0.1865 (OUTLIER) cc_final: 0.1614 (tp) REVERT: A 2012 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7323 (tptt) outliers start: 26 outliers final: 8 residues processed: 233 average time/residue: 0.1497 time to fit residues: 52.2345 Evaluate side-chains 186 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1918 ILE Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2108 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 8 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 188 optimal weight: 40.0000 chunk 199 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A 312 HIS A 752 ASN A2141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.136221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099645 restraints weight = 29631.229| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.00 r_work: 0.2962 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18485 Z= 0.147 Angle : 0.578 9.537 25042 Z= 0.300 Chirality : 0.045 0.430 2812 Planarity : 0.004 0.056 3066 Dihedral : 9.435 172.395 2663 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 1.68 % Allowed : 7.52 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.65 (0.18), residues: 2116 helix: 0.57 (0.15), residues: 1137 sheet: -0.23 (0.39), residues: 171 loop : -1.93 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 531 TYR 0.019 0.001 TYR A 677 PHE 0.021 0.001 PHE A1768 TRP 0.008 0.001 TRP A1847 HIS 0.005 0.001 HIS A1739 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (18482) covalent geometry : angle 0.57844 / 0.30 (25042) hydrogen bonds : bond 0.04405 / 2.43 ( 897) hydrogen bonds : angle 4.37933 / 2.66 ( 2603) metal coordination : bond 0.00150 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.8542 (t0) cc_final: 0.8342 (t0) REVERT: A 57 ASP cc_start: 0.7484 (m-30) cc_final: 0.6876 (t0) REVERT: A 61 ASP cc_start: 0.6688 (m-30) cc_final: 0.4915 (m-30) REVERT: A 144 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8024 (mmm-85) REVERT: A 162 PHE cc_start: 0.8535 (m-10) cc_final: 0.7931 (m-80) REVERT: A 726 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: A 1177 SER cc_start: 0.8920 (m) cc_final: 0.8619 (p) REVERT: A 1371 ARG cc_start: 0.8444 (ptp-110) cc_final: 0.7642 (mmm160) REVERT: A 1385 LYS cc_start: 0.7834 (mppt) cc_final: 0.7552 (mmtm) REVERT: A 1391 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: A 1476 GLU cc_start: 0.7322 (pt0) cc_final: 0.6906 (pm20) REVERT: A 1633 ASN cc_start: 0.7552 (m-40) cc_final: 0.7138 (m-40) REVERT: A 1645 MET cc_start: 0.5793 (tpt) cc_final: 0.4403 (ttm) REVERT: A 1666 LYS cc_start: 0.8032 (ptpt) cc_final: 0.7629 (tptt) REVERT: A 1688 MET cc_start: 0.8463 (tpp) cc_final: 0.8006 (tpt) REVERT: A 1756 ASN cc_start: 0.8339 (m110) cc_final: 0.8092 (m110) REVERT: A 1794 GLU cc_start: 0.8304 (pm20) cc_final: 0.8092 (mp0) REVERT: A 1835 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7772 (tptp) REVERT: A 1918 ILE cc_start: 0.1918 (OUTLIER) cc_final: 0.1496 (tp) REVERT: A 1984 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7344 (mm) REVERT: A 2007 PHE cc_start: 0.6998 (m-10) cc_final: 0.6714 (m-10) REVERT: A 2012 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7400 (tptt) REVERT: A 2204 PHE cc_start: 0.5668 (OUTLIER) cc_final: 0.4954 (t80) outliers start: 33 outliers final: 11 residues processed: 214 average time/residue: 0.1398 time to fit residues: 45.9391 Evaluate side-chains 195 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1369 GLN Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1915 MET Chi-restraints excluded: chain A residue 1918 ILE Chi-restraints excluded: chain A residue 1984 ILE Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 82 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 86 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A 469 ASN A1133 ASN A1285 HIS A1924 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100039 restraints weight = 29580.000| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.05 r_work: 0.2961 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18485 Z= 0.127 Angle : 0.548 8.395 25042 Z= 0.283 Chirality : 0.044 0.345 2812 Planarity : 0.004 0.056 3066 Dihedral : 9.216 172.744 2661 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.08 % Rotamer: Outliers : 1.58 % Allowed : 8.03 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.28 (0.18), residues: 2116 helix: 0.87 (0.16), residues: 1141 sheet: 0.21 (0.40), residues: 163 loop : -1.84 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 531 TYR 0.017 0.001 TYR A 677 PHE 0.024 0.001 PHE A2204 TRP 0.007 0.001 TRP A1143 HIS 0.005 0.001 HIS A1739 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (18482) covalent geometry : angle 0.54782 / 0.28 (25042) hydrogen bonds : bond 0.04043 / 2.23 ( 897) hydrogen bonds : angle 4.22303 / 2.55 ( 2603) metal coordination : bond 0.00127 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.8549 (t0) cc_final: 0.8074 (t0) REVERT: A 57 ASP cc_start: 0.7513 (m-30) cc_final: 0.6891 (t0) REVERT: A 61 ASP cc_start: 0.6636 (m-30) cc_final: 0.4947 (m-30) REVERT: A 144 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8072 (mmm-85) REVERT: A 162 PHE cc_start: 0.8471 (m-10) cc_final: 0.8012 (m-80) REVERT: A 190 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8680 (p) REVERT: A 726 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: A 855 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7265 (mm) REVERT: A 1177 SER cc_start: 0.8929 (m) cc_final: 0.8616 (p) REVERT: A 1371 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.7626 (mmm160) REVERT: A 1385 LYS cc_start: 0.7808 (mppt) cc_final: 0.7497 (mmtm) REVERT: A 1391 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8183 (m-30) REVERT: A 1476 GLU cc_start: 0.7369 (pt0) cc_final: 0.6948 (pm20) REVERT: A 1633 ASN cc_start: 0.7600 (m-40) cc_final: 0.7202 (m-40) REVERT: A 1645 MET cc_start: 0.5764 (tpt) cc_final: 0.4272 (ttm) REVERT: A 1688 MET cc_start: 0.8430 (tpp) cc_final: 0.8017 (tpt) REVERT: A 1756 ASN cc_start: 0.8287 (m110) cc_final: 0.8060 (m110) REVERT: A 1835 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7803 (tptp) REVERT: A 1918 ILE cc_start: 0.1969 (OUTLIER) cc_final: 0.1624 (tp) REVERT: A 2012 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7381 (tptt) REVERT: A 2204 PHE cc_start: 0.5366 (OUTLIER) cc_final: 0.5048 (t80) outliers start: 31 outliers final: 12 residues processed: 209 average time/residue: 0.1387 time to fit residues: 44.5573 Evaluate side-chains 186 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1918 ILE Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2082 MET Chi-restraints excluded: chain A residue 2108 MET Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 90 optimal weight: 0.0470 chunk 194 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A 469 ASN A1133 ASN A1190 GLN A2071 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.137614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.093453 restraints weight = 29536.419| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.06 r_work: 0.3014 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18485 Z= 0.102 Angle : 0.518 7.929 25042 Z= 0.267 Chirality : 0.043 0.282 2812 Planarity : 0.004 0.054 3066 Dihedral : 9.106 174.829 2661 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.08 % Rotamer: Outliers : 1.22 % Allowed : 8.89 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.03 (0.18), residues: 2116 helix: 1.12 (0.16), residues: 1142 sheet: 0.50 (0.41), residues: 160 loop : -1.71 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 707 TYR 0.019 0.001 TYR A1576 PHE 0.025 0.001 PHE A2204 TRP 0.007 0.001 TRP A1143 HIS 0.004 0.001 HIS A1755 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (18482) covalent geometry : angle 0.51816 / 0.27 (25042) hydrogen bonds : bond 0.03663 / 2.02 ( 897) hydrogen bonds : angle 4.07211 / 2.45 ( 2603) metal coordination : bond 0.00091 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8321 (mtp180) cc_final: 0.7992 (ttp80) REVERT: A 46 ASN cc_start: 0.8527 (t0) cc_final: 0.8038 (t0) REVERT: A 57 ASP cc_start: 0.7526 (m-30) cc_final: 0.6902 (t0) REVERT: A 61 ASP cc_start: 0.6484 (m-30) cc_final: 0.4812 (m-30) REVERT: A 144 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8036 (mmm-85) REVERT: A 162 PHE cc_start: 0.8467 (m-10) cc_final: 0.8043 (m-80) REVERT: A 190 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8663 (p) REVERT: A 855 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7234 (mm) REVERT: A 1177 SER cc_start: 0.8932 (m) cc_final: 0.8604 (p) REVERT: A 1371 ARG cc_start: 0.8357 (ptp-110) cc_final: 0.7546 (mmm160) REVERT: A 1385 LYS cc_start: 0.7752 (mppt) cc_final: 0.7504 (mmtm) REVERT: A 1470 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8340 (pt) REVERT: A 1633 ASN cc_start: 0.7756 (m-40) cc_final: 0.7312 (m-40) REVERT: A 1645 MET cc_start: 0.5772 (tpt) cc_final: 0.4157 (ttm) REVERT: A 1756 ASN cc_start: 0.8245 (m110) cc_final: 0.8040 (m110) REVERT: A 1835 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7767 (tptp) REVERT: A 2012 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7302 (tptp) REVERT: A 2204 PHE cc_start: 0.5214 (OUTLIER) cc_final: 0.4818 (t80) REVERT: A 2250 LEU cc_start: 0.1517 (OUTLIER) cc_final: 0.1220 (pt) outliers start: 24 outliers final: 10 residues processed: 203 average time/residue: 0.1361 time to fit residues: 42.3613 Evaluate side-chains 182 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2250 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 120 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 143 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A 469 ASN A1133 ASN A1755 HIS A2071 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.089562 restraints weight = 29238.703| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.08 r_work: 0.2938 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18485 Z= 0.185 Angle : 0.592 8.611 25042 Z= 0.303 Chirality : 0.046 0.386 2812 Planarity : 0.004 0.055 3066 Dihedral : 9.064 171.547 2656 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 1.47 % Allowed : 10.21 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.03 (0.18), residues: 2116 helix: 1.10 (0.16), residues: 1142 sheet: 0.45 (0.41), residues: 161 loop : -1.65 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 595 TYR 0.022 0.002 TYR A 677 PHE 0.029 0.002 PHE A2204 TRP 0.011 0.001 TRP A 395 HIS 0.005 0.001 HIS A1591 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (18482) covalent geometry : angle 0.59201 / 0.30 (25042) hydrogen bonds : bond 0.04475 / 2.46 ( 897) hydrogen bonds : angle 4.20511 / 2.51 ( 2603) metal coordination : bond 0.00227 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8305 (mtp180) cc_final: 0.7985 (ttp80) REVERT: A 28 ASP cc_start: 0.8023 (m-30) cc_final: 0.7582 (m-30) REVERT: A 46 ASN cc_start: 0.8551 (t0) cc_final: 0.7995 (t0) REVERT: A 57 ASP cc_start: 0.7573 (m-30) cc_final: 0.6926 (t0) REVERT: A 61 ASP cc_start: 0.6516 (m-30) cc_final: 0.4780 (m-30) REVERT: A 144 ARG cc_start: 0.8466 (mmm-85) cc_final: 0.8040 (mmm-85) REVERT: A 162 PHE cc_start: 0.8446 (m-10) cc_final: 0.7948 (m-80) REVERT: A 726 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: A 854 GLU cc_start: 0.8141 (pp20) cc_final: 0.7620 (mm-30) REVERT: A 1177 SER cc_start: 0.8946 (m) cc_final: 0.8633 (p) REVERT: A 1371 ARG cc_start: 0.8435 (ptp-110) cc_final: 0.7546 (mmm160) REVERT: A 1385 LYS cc_start: 0.7809 (mppt) cc_final: 0.7486 (mmtm) REVERT: A 1391 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8221 (m-30) REVERT: A 1470 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8389 (pt) REVERT: A 1633 ASN cc_start: 0.7765 (m-40) cc_final: 0.7323 (m-40) REVERT: A 1645 MET cc_start: 0.5514 (tpt) cc_final: 0.3989 (ttm) REVERT: A 1688 MET cc_start: 0.8477 (tpp) cc_final: 0.8041 (tpt) REVERT: A 1734 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8755 (pt0) REVERT: A 1756 ASN cc_start: 0.8360 (m110) cc_final: 0.8120 (m110) REVERT: A 1835 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7802 (tptp) REVERT: A 2012 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7345 (tptm) REVERT: A 2204 PHE cc_start: 0.5170 (OUTLIER) cc_final: 0.4749 (t80) outliers start: 29 outliers final: 12 residues processed: 198 average time/residue: 0.1316 time to fit residues: 39.7130 Evaluate side-chains 187 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1557 MET Chi-restraints excluded: chain A residue 1734 GLU Chi-restraints excluded: chain A residue 2082 MET Chi-restraints excluded: chain A residue 2118 ILE Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 146 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A 469 ASN A1133 ASN A2071 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.137160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.092784 restraints weight = 29486.935| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.11 r_work: 0.2998 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18485 Z= 0.105 Angle : 0.521 8.969 25042 Z= 0.267 Chirality : 0.043 0.262 2812 Planarity : 0.003 0.054 3066 Dihedral : 8.930 174.517 2656 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 1.32 % Allowed : 10.57 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2116 helix: 1.32 (0.16), residues: 1143 sheet: 0.72 (0.43), residues: 154 loop : -1.54 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1999 TYR 0.020 0.001 TYR A1576 PHE 0.027 0.001 PHE A2204 TRP 0.010 0.001 TRP A1143 HIS 0.004 0.001 HIS A1739 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (18482) covalent geometry : angle 0.52110 / 0.27 (25042) hydrogen bonds : bond 0.03615 / 1.99 ( 897) hydrogen bonds : angle 4.03262 / 2.41 ( 2603) metal coordination : bond 0.00106 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8044 (m-30) cc_final: 0.7601 (m-30) REVERT: A 46 ASN cc_start: 0.8559 (t0) cc_final: 0.8056 (t0) REVERT: A 57 ASP cc_start: 0.7610 (m-30) cc_final: 0.6932 (t0) REVERT: A 61 ASP cc_start: 0.6438 (m-30) cc_final: 0.4688 (m-30) REVERT: A 111 GLU cc_start: 0.7439 (mp0) cc_final: 0.6979 (mp0) REVERT: A 115 ASP cc_start: 0.7121 (t0) cc_final: 0.6884 (m-30) REVERT: A 144 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.7988 (mmm-85) REVERT: A 162 PHE cc_start: 0.8427 (m-10) cc_final: 0.8009 (m-80) REVERT: A 190 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8632 (p) REVERT: A 212 MET cc_start: 0.8066 (pp-130) cc_final: 0.7658 (mmp) REVERT: A 726 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: A 776 GLU cc_start: 0.7939 (tp30) cc_final: 0.7582 (mm-30) REVERT: A 1056 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: A 1177 SER cc_start: 0.9009 (m) cc_final: 0.8614 (p) REVERT: A 1371 ARG cc_start: 0.8369 (ptp-110) cc_final: 0.7478 (mmm160) REVERT: A 1385 LYS cc_start: 0.7820 (mppt) cc_final: 0.7457 (mmtm) REVERT: A 1391 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: A 1470 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8304 (pt) REVERT: A 1633 ASN cc_start: 0.7838 (m-40) cc_final: 0.7366 (m-40) REVERT: A 1645 MET cc_start: 0.5527 (tpt) cc_final: 0.3956 (ttm) REVERT: A 1688 MET cc_start: 0.8437 (tpp) cc_final: 0.8026 (tpt) REVERT: A 1756 ASN cc_start: 0.8247 (m110) cc_final: 0.8042 (m110) REVERT: A 1835 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7812 (tptp) REVERT: A 2012 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7233 (tptm) REVERT: A 2204 PHE cc_start: 0.5184 (OUTLIER) cc_final: 0.4694 (t80) outliers start: 26 outliers final: 11 residues processed: 199 average time/residue: 0.1375 time to fit residues: 42.2514 Evaluate side-chains 189 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1557 MET Chi-restraints excluded: chain A residue 2118 ILE Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 171 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A1133 ASN ** A1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1842 HIS A2071 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.133014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.087810 restraints weight = 29481.140| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.15 r_work: 0.2914 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18485 Z= 0.248 Angle : 0.654 12.019 25042 Z= 0.331 Chirality : 0.049 0.446 2812 Planarity : 0.004 0.054 3066 Dihedral : 9.116 169.400 2656 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 1.47 % Allowed : 10.98 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 (0.18), residues: 2116 helix: 1.16 (0.16), residues: 1130 sheet: 0.35 (0.41), residues: 162 loop : -1.49 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 12 TYR 0.026 0.002 TYR A1736 PHE 0.030 0.002 PHE A2204 TRP 0.013 0.001 TRP A 395 HIS 0.007 0.002 HIS A2169 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.25 (18482) covalent geometry : angle 0.65415 / 0.33 (25042) hydrogen bonds : bond 0.04855 / 2.67 ( 897) hydrogen bonds : angle 4.29466 / 2.54 ( 2603) metal coordination : bond 0.00369 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.479 Fit side-chains REVERT: A 28 ASP cc_start: 0.8106 (m-30) cc_final: 0.7625 (m-30) REVERT: A 46 ASN cc_start: 0.8561 (t0) cc_final: 0.8053 (t0) REVERT: A 57 ASP cc_start: 0.7638 (m-30) cc_final: 0.6962 (t0) REVERT: A 61 ASP cc_start: 0.6425 (m-30) cc_final: 0.4667 (m-30) REVERT: A 144 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.7951 (mmm-85) REVERT: A 162 PHE cc_start: 0.8462 (m-10) cc_final: 0.7954 (m-80) REVERT: A 190 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8632 (p) REVERT: A 726 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: A 854 GLU cc_start: 0.8070 (pp20) cc_final: 0.7578 (mm-30) REVERT: A 1056 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: A 1177 SER cc_start: 0.9046 (m) cc_final: 0.8678 (p) REVERT: A 1371 ARG cc_start: 0.8539 (ptp-110) cc_final: 0.7621 (mmm160) REVERT: A 1385 LYS cc_start: 0.7874 (mppt) cc_final: 0.7484 (mmtm) REVERT: A 1391 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: A 1470 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8404 (pt) REVERT: A 1633 ASN cc_start: 0.7768 (m-40) cc_final: 0.7310 (m-40) REVERT: A 1645 MET cc_start: 0.5585 (tpt) cc_final: 0.3924 (ttm) REVERT: A 1688 MET cc_start: 0.8481 (tpp) cc_final: 0.8042 (tpt) REVERT: A 1734 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8801 (pt0) REVERT: A 1756 ASN cc_start: 0.8376 (m110) cc_final: 0.8122 (m110) REVERT: A 2012 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7322 (tptm) REVERT: A 2204 PHE cc_start: 0.5037 (OUTLIER) cc_final: 0.4748 (t80) outliers start: 29 outliers final: 14 residues processed: 189 average time/residue: 0.1347 time to fit residues: 38.8282 Evaluate side-chains 183 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1557 MET Chi-restraints excluded: chain A residue 1577 ILE Chi-restraints excluded: chain A residue 1734 GLU Chi-restraints excluded: chain A residue 1915 MET Chi-restraints excluded: chain A residue 2082 MET Chi-restraints excluded: chain A residue 2118 ILE Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 143 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A1112 ASN A1133 ASN A2071 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.090831 restraints weight = 29375.246| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.12 r_work: 0.2964 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18485 Z= 0.129 Angle : 0.558 11.492 25042 Z= 0.284 Chirality : 0.045 0.298 2812 Planarity : 0.004 0.054 3066 Dihedral : 9.004 173.191 2656 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.31 % Rotamer: Outliers : 1.42 % Allowed : 11.33 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.28 (0.18), residues: 2116 helix: 1.26 (0.16), residues: 1142 sheet: 0.76 (0.44), residues: 142 loop : -1.48 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 12 TYR 0.019 0.001 TYR A1576 PHE 0.029 0.001 PHE A2204 TRP 0.008 0.001 TRP A1143 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (18482) covalent geometry : angle 0.55815 / 0.28 (25042) hydrogen bonds : bond 0.03937 / 2.17 ( 897) hydrogen bonds : angle 4.11763 / 2.44 ( 2603) metal coordination : bond 0.00107 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.726 Fit side-chains REVERT: A 28 ASP cc_start: 0.8062 (m-30) cc_final: 0.7587 (m-30) REVERT: A 46 ASN cc_start: 0.8584 (t0) cc_final: 0.8131 (t0) REVERT: A 57 ASP cc_start: 0.7610 (m-30) cc_final: 0.7190 (t0) REVERT: A 111 GLU cc_start: 0.7420 (mp0) cc_final: 0.7025 (mp0) REVERT: A 115 ASP cc_start: 0.7129 (t0) cc_final: 0.6861 (m-30) REVERT: A 144 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.7942 (mmm-85) REVERT: A 162 PHE cc_start: 0.8436 (m-10) cc_final: 0.7952 (m-80) REVERT: A 190 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 726 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 776 GLU cc_start: 0.7957 (tp30) cc_final: 0.7618 (mm-30) REVERT: A 1056 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: A 1177 SER cc_start: 0.9005 (m) cc_final: 0.8630 (p) REVERT: A 1371 ARG cc_start: 0.8426 (ptp-110) cc_final: 0.7555 (mmm160) REVERT: A 1385 LYS cc_start: 0.7854 (mppt) cc_final: 0.7460 (mmtm) REVERT: A 1391 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: A 1470 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8378 (pt) REVERT: A 1633 ASN cc_start: 0.7835 (m-40) cc_final: 0.7361 (m-40) REVERT: A 1645 MET cc_start: 0.5530 (tpt) cc_final: 0.3853 (ttm) REVERT: A 1688 MET cc_start: 0.8488 (tpp) cc_final: 0.8092 (tpt) REVERT: A 1756 ASN cc_start: 0.8311 (m110) cc_final: 0.8095 (m110) REVERT: A 2012 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7261 (tptm) REVERT: A 2204 PHE cc_start: 0.4955 (OUTLIER) cc_final: 0.4684 (t80) outliers start: 28 outliers final: 16 residues processed: 191 average time/residue: 0.1362 time to fit residues: 39.8282 Evaluate side-chains 190 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1055 MET Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1557 MET Chi-restraints excluded: chain A residue 1577 ILE Chi-restraints excluded: chain A residue 2095 ILE Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 131 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 173 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 213 optimal weight: 0.0020 chunk 83 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN A 299 HIS A1133 ASN A2071 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093404 restraints weight = 29493.746| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.12 r_work: 0.3013 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18485 Z= 0.102 Angle : 0.524 11.242 25042 Z= 0.267 Chirality : 0.043 0.262 2812 Planarity : 0.004 0.067 3066 Dihedral : 8.887 177.247 2656 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.08 % Rotamer: Outliers : 1.27 % Allowed : 11.38 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 2116 helix: 1.45 (0.16), residues: 1147 sheet: 0.80 (0.44), residues: 147 loop : -1.38 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 12 TYR 0.012 0.001 TYR A 677 PHE 0.026 0.001 PHE A2204 TRP 0.009 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (18482) covalent geometry : angle 0.52372 / 0.27 (25042) hydrogen bonds : bond 0.03474 / 1.92 ( 897) hydrogen bonds : angle 3.94873 / 2.34 ( 2603) metal coordination : bond 0.00132 / 0.07 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8095 (m-30) cc_final: 0.7650 (m-30) REVERT: A 46 ASN cc_start: 0.8541 (t0) cc_final: 0.8169 (t0) REVERT: A 57 ASP cc_start: 0.7581 (m-30) cc_final: 0.7229 (t70) REVERT: A 111 GLU cc_start: 0.7461 (mp0) cc_final: 0.7046 (mp0) REVERT: A 115 ASP cc_start: 0.7089 (t0) cc_final: 0.6874 (m-30) REVERT: A 144 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7926 (mmm-85) REVERT: A 162 PHE cc_start: 0.8441 (m-10) cc_final: 0.8127 (m-80) REVERT: A 190 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8585 (p) REVERT: A 212 MET cc_start: 0.8072 (pp-130) cc_final: 0.7691 (mmp) REVERT: A 726 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: A 864 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7653 (mp) REVERT: A 1056 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: A 1177 SER cc_start: 0.9001 (m) cc_final: 0.8611 (p) REVERT: A 1371 ARG cc_start: 0.8379 (ptp-110) cc_final: 0.7532 (mmm160) REVERT: A 1385 LYS cc_start: 0.7826 (mppt) cc_final: 0.7446 (mmtm) REVERT: A 1391 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8185 (m-30) REVERT: A 1470 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8303 (pt) REVERT: A 1633 ASN cc_start: 0.7804 (m-40) cc_final: 0.7329 (m-40) REVERT: A 1645 MET cc_start: 0.5507 (tpt) cc_final: 0.3869 (ttm) REVERT: A 1688 MET cc_start: 0.8455 (tpp) cc_final: 0.8072 (tpt) REVERT: A 2012 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7264 (tptm) REVERT: A 2204 PHE cc_start: 0.4984 (OUTLIER) cc_final: 0.4754 (t80) outliers start: 25 outliers final: 12 residues processed: 200 average time/residue: 0.1392 time to fit residues: 43.1342 Evaluate side-chains 191 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1557 MET Chi-restraints excluded: chain A residue 1577 ILE Chi-restraints excluded: chain A residue 1915 MET Chi-restraints excluded: chain A residue 2204 PHE Chi-restraints excluded: chain A residue 2250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A1112 ASN A1133 ASN A2071 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090978 restraints weight = 29459.175| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.10 r_work: 0.2970 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18485 Z= 0.142 Angle : 0.553 11.042 25042 Z= 0.281 Chirality : 0.045 0.316 2812 Planarity : 0.004 0.054 3066 Dihedral : 8.897 174.473 2656 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.31 % Rotamer: Outliers : 1.17 % Allowed : 11.59 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 2116 helix: 1.45 (0.16), residues: 1139 sheet: 0.75 (0.44), residues: 147 loop : -1.36 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 12 TYR 0.020 0.001 TYR A1576 PHE 0.028 0.001 PHE A2204 TRP 0.009 0.001 TRP A 395 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (18482) covalent geometry : angle 0.55282 / 0.28 (25042) hydrogen bonds : bond 0.03902 / 2.15 ( 897) hydrogen bonds : angle 4.03964 / 2.40 ( 2603) metal coordination : bond 0.00120 / 0.06 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5313.00 seconds wall clock time: 91 minutes 31.73 seconds (5491.73 seconds total)