Starting phenix.real_space_refine on Thu Mar 5 02:43:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z6g_11093/03_2026/6z6g_11093.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z6g_11093/03_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_11093/03_2026/6z6g_11093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z6g_11093/03_2026/6z6g_11093.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z6g_11093/03_2026/6z6g_11093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z6g_11093/03_2026/6z6g_11093.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: {'RNA': 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: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 274 Classifications: {'RNA': 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: 4.01, per 1000 atoms: 0.22 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: 1.29 Conformation dependent library (CDL) restraints added in 640.3 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: 2.44 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: 4.84 Time building geometry restraints manager: 1.73 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: 23984 2.17 - 4.34: 937 4.34 - 6.51: 93 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 - 20.47: 10815 20.47 - 40.94: 361 40.94 - 61.42: 99 61.42 - 81.89: 27 81.89 - 102.36: 1 Dihedral angle restraints: 11303 sinusoidal: 4947 harmonic: 6356 Sorted by residual: dihedral pdb=" O4' U U 8 " pdb=" C1' U U 8 " pdb=" N1 U U 8 " pdb=" C2 U U 8 " ideal model delta sinusoidal sigma weight residual -128.00 -25.64 -102.36 1 1.70e+01 3.46e-03 4.03e+01 dihedral pdb=" CA ILE A 116 " pdb=" C ILE A 116 " pdb=" N SER A 117 " pdb=" CA SER A 117 " ideal model delta harmonic sigma weight residual -180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA THR A1846 " pdb=" C THR A1846 " pdb=" N TRP A1847 " pdb=" CA TRP A1847 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 11300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2667 0.117 - 0.233: 135 0.233 - 0.350: 8 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: 1.750 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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= 0.449 Angle : 0.978 10.853 25042 Z= 0.544 Chirality : 0.061 0.583 2812 Planarity : 0.007 0.068 3066 Dihedral : 12.173 102.361 7173 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 covalent geometry : bond 0.01006 (18482) covalent geometry : angle 0.97827 (25042) hydrogen bonds : bond 0.16099 ( 897) hydrogen bonds : angle 6.85959 ( 2603) metal coordination : bond 0.37913 ( 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 : 0.683 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: 0.1691 time to fit residues: 80.8623 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 : 0.604 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 312 HIS A 332 GLN A 389 ASN A 489 ASN A 539 ASN A 565 HIS A 602 GLN A 718 GLN A 752 ASN A 902 ASN A1058 ASN A1181 ASN A1243 ASN A1392 ASN A1693 GLN A1754 GLN A1755 HIS A1944 HIS A2091 HIS ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2209 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100169 restraints weight = 29577.196| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.21 r_work: 0.2955 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18485 Z= 0.124 Angle : 0.567 8.263 25042 Z= 0.307 Chirality : 0.041 0.166 2812 Planarity : 0.005 0.058 3066 Dihedral : 10.905 100.837 2787 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 1.42 % Allowed : 5.84 % Favored : 92.73 % 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: -1.36 (0.17), residues: 2116 helix: -0.02 (0.15), residues: 1127 sheet: -0.52 (0.39), residues: 171 loop : -2.22 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 144 TYR 0.018 0.001 TYR A 677 PHE 0.033 0.001 PHE A2204 TRP 0.009 0.001 TRP A 193 HIS 0.007 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00262 (18482) covalent geometry : angle 0.56718 (25042) hydrogen bonds : bond 0.04579 ( 897) hydrogen bonds : angle 4.64985 ( 2603) metal coordination : bond 0.01315 ( 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 245 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.576 Fit side-chains REVERT: A 46 ASN cc_start: 0.8507 (t0) cc_final: 0.8252 (t0) REVERT: A 57 ASP cc_start: 0.7416 (m-30) cc_final: 0.6780 (t0) REVERT: A 61 ASP cc_start: 0.6739 (m-30) cc_final: 0.5004 (m-30) REVERT: A 91 ILE cc_start: 0.8824 (mt) cc_final: 0.8617 (mm) REVERT: A 144 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.7960 (mmm-85) REVERT: A 162 PHE cc_start: 0.8522 (m-10) cc_final: 0.7743 (m-80) REVERT: A 190 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8857 (p) REVERT: A 726 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: A 1177 SER cc_start: 0.8859 (m) cc_final: 0.8510 (p) REVERT: A 1371 ARG cc_start: 0.8229 (ptp-110) cc_final: 0.7570 (mmm160) REVERT: A 1385 LYS cc_start: 0.7756 (mppt) cc_final: 0.7423 (mmtm) REVERT: A 1391 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8113 (m-30) REVERT: A 1470 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8349 (pp) REVERT: A 1571 GLN cc_start: 0.8400 (mt0) cc_final: 0.8161 (mt0) REVERT: A 1633 ASN cc_start: 0.7515 (m-40) cc_final: 0.7157 (m-40) REVERT: A 1645 MET cc_start: 0.5694 (tpt) cc_final: 0.4347 (ttm) REVERT: A 1666 LYS cc_start: 0.8048 (ptpt) cc_final: 0.7603 (tptt) REVERT: A 1688 MET cc_start: 0.8344 (tpp) cc_final: 0.7887 (tpt) REVERT: A 1756 ASN cc_start: 0.8261 (m110) cc_final: 0.8049 (m110) REVERT: A 1835 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7818 (tptp) REVERT: A 1918 ILE cc_start: 0.1908 (OUTLIER) cc_final: 0.1635 (tp) REVERT: A 2012 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7301 (tptt) outliers start: 28 outliers final: 9 residues processed: 237 average time/residue: 0.1401 time to fit residues: 49.7287 Evaluate side-chains 184 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 1834 ASP 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: 0.6980 chunk 134 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 188 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 29 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A1571 GLN A2141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100615 restraints weight = 29675.379| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.20 r_work: 0.2967 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18485 Z= 0.113 Angle : 0.507 8.170 25042 Z= 0.273 Chirality : 0.040 0.162 2812 Planarity : 0.004 0.055 3066 Dihedral : 10.232 91.726 2759 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 1.42 % Allowed : 7.27 % Favored : 91.31 % 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: -0.50 (0.18), residues: 2116 helix: 0.70 (0.16), residues: 1139 sheet: -0.15 (0.40), residues: 171 loop : -1.89 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 144 TYR 0.017 0.001 TYR A1576 PHE 0.019 0.001 PHE A1768 TRP 0.008 0.001 TRP A1847 HIS 0.005 0.001 HIS A1739 Details of bonding type rmsd covalent geometry : bond 0.00240 (18482) covalent geometry : angle 0.50685 (25042) hydrogen bonds : bond 0.03997 ( 897) hydrogen bonds : angle 4.24562 ( 2603) metal coordination : bond 0.00227 ( 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 214 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.8574 (t0) cc_final: 0.8339 (t0) REVERT: A 57 ASP cc_start: 0.7513 (m-30) cc_final: 0.6879 (t0) REVERT: A 61 ASP cc_start: 0.6695 (m-30) cc_final: 0.4977 (m-30) REVERT: A 144 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8081 (mmm-85) REVERT: A 162 PHE cc_start: 0.8533 (m-10) cc_final: 0.7922 (m-80) REVERT: A 190 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8896 (p) REVERT: A 1177 SER cc_start: 0.8965 (m) cc_final: 0.8627 (p) REVERT: A 1371 ARG cc_start: 0.8400 (ptp-110) cc_final: 0.7543 (mmm160) REVERT: A 1385 LYS cc_start: 0.7757 (mppt) cc_final: 0.7442 (mmtm) REVERT: A 1391 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: A 1476 GLU cc_start: 0.7315 (pt0) cc_final: 0.6821 (pm20) REVERT: A 1633 ASN cc_start: 0.7602 (m-40) cc_final: 0.7198 (m-40) REVERT: A 1645 MET cc_start: 0.5833 (tpt) cc_final: 0.4290 (ttm) REVERT: A 1756 ASN cc_start: 0.8239 (m110) cc_final: 0.7981 (m110) REVERT: A 1835 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7609 (tptt) REVERT: A 1918 ILE cc_start: 0.2075 (OUTLIER) cc_final: 0.1706 (tp) REVERT: A 2012 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7380 (tptt) REVERT: A 2177 MET cc_start: 0.7850 (ptm) cc_final: 0.7645 (ptm) REVERT: A 2204 PHE cc_start: 0.5739 (OUTLIER) cc_final: 0.4927 (t80) REVERT: A 2251 MET cc_start: 0.0856 (tpp) cc_final: 0.0579 (mmt) outliers start: 28 outliers final: 11 residues processed: 208 average time/residue: 0.1428 time to fit residues: 45.2988 Evaluate side-chains 190 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 1391 ASP Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1918 ILE 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: 6.9990 chunk 42 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 15 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A 469 ASN A 806 ASN A1190 GLN A1285 HIS A1755 HIS A2112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098310 restraints weight = 29566.517| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.17 r_work: 0.2916 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18485 Z= 0.174 Angle : 0.541 8.134 25042 Z= 0.290 Chirality : 0.042 0.179 2812 Planarity : 0.004 0.055 3066 Dihedral : 10.148 92.240 2754 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 1.52 % Allowed : 8.18 % Favored : 90.29 % 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: -0.25 (0.18), residues: 2116 helix: 0.90 (0.16), residues: 1139 sheet: 0.27 (0.41), residues: 161 loop : -1.82 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 12 TYR 0.022 0.002 TYR A 677 PHE 0.025 0.002 PHE A2204 TRP 0.010 0.001 TRP A 395 HIS 0.006 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00406 (18482) covalent geometry : angle 0.54073 (25042) hydrogen bonds : bond 0.04435 ( 897) hydrogen bonds : angle 4.24882 ( 2603) metal coordination : bond 0.00279 ( 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: 30 poor density : 187 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 46 ASN cc_start: 0.8586 (t0) cc_final: 0.8111 (t0) REVERT: A 57 ASP cc_start: 0.7480 (m-30) cc_final: 0.6873 (t0) REVERT: A 61 ASP cc_start: 0.6586 (m-30) cc_final: 0.4913 (m-30) REVERT: A 144 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: A 162 PHE cc_start: 0.8487 (m-10) cc_final: 0.8022 (m-80) REVERT: A 726 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: A 855 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7204 (mm) REVERT: A 1177 SER cc_start: 0.8984 (m) cc_final: 0.8681 (p) REVERT: A 1371 ARG cc_start: 0.8485 (ptp-110) cc_final: 0.7585 (mmm160) REVERT: A 1385 LYS cc_start: 0.7807 (mppt) cc_final: 0.7430 (mmtm) REVERT: A 1391 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: A 1431 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7504 (mttp) REVERT: A 1470 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8408 (pt) REVERT: A 1633 ASN cc_start: 0.7672 (m-40) cc_final: 0.7254 (m-40) REVERT: A 1645 MET cc_start: 0.5710 (tpt) cc_final: 0.4192 (ttm) REVERT: A 1688 MET cc_start: 0.8431 (tpp) cc_final: 0.8014 (tpt) REVERT: A 1756 ASN cc_start: 0.8358 (m110) cc_final: 0.8101 (m110) REVERT: A 1835 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7792 (tptp) REVERT: A 1918 ILE cc_start: 0.2041 (OUTLIER) cc_final: 0.0955 (pt) REVERT: A 2012 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7448 (tptt) REVERT: A 2204 PHE cc_start: 0.5153 (OUTLIER) cc_final: 0.4851 (t80) outliers start: 30 outliers final: 13 residues processed: 209 average time/residue: 0.1434 time to fit residues: 45.0202 Evaluate side-chains 189 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 855 LEU 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 1464 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 1771 ILE Chi-restraints excluded: chain A residue 1918 ILE Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2108 MET Chi-restraints excluded: chain A residue 2118 ILE 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: 4.9990 chunk 53 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100443 restraints weight = 29469.860| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.11 r_work: 0.2968 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18485 Z= 0.104 Angle : 0.485 7.651 25042 Z= 0.259 Chirality : 0.040 0.169 2812 Planarity : 0.004 0.054 3066 Dihedral : 9.907 79.360 2754 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 1.32 % Allowed : 9.35 % Favored : 89.33 % 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: 0.09 (0.18), residues: 2116 helix: 1.17 (0.16), residues: 1141 sheet: 0.53 (0.41), residues: 160 loop : -1.68 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 12 TYR 0.019 0.001 TYR A1576 PHE 0.025 0.001 PHE A2204 TRP 0.009 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00225 (18482) covalent geometry : angle 0.48469 (25042) hydrogen bonds : bond 0.03691 ( 897) hydrogen bonds : angle 4.06111 ( 2603) metal coordination : bond 0.00126 ( 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 212 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8104 (m-30) cc_final: 0.7648 (m-30) REVERT: A 46 ASN cc_start: 0.8576 (t0) cc_final: 0.8072 (t0) REVERT: A 57 ASP cc_start: 0.7513 (m-30) cc_final: 0.6899 (t0) REVERT: A 61 ASP cc_start: 0.6579 (m-30) cc_final: 0.4838 (m-30) REVERT: A 144 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8005 (mmm-85) REVERT: A 162 PHE cc_start: 0.8464 (m-10) cc_final: 0.8057 (m-80) REVERT: A 726 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: A 855 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7263 (mm) REVERT: A 1177 SER cc_start: 0.8957 (m) cc_final: 0.8648 (p) REVERT: A 1371 ARG cc_start: 0.8464 (ptp-110) cc_final: 0.7568 (mmm160) REVERT: A 1385 LYS cc_start: 0.7722 (mppt) cc_final: 0.7517 (mmtm) REVERT: A 1470 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8402 (pt) REVERT: A 1633 ASN cc_start: 0.7637 (m-40) cc_final: 0.7201 (m-40) REVERT: A 1645 MET cc_start: 0.5759 (tpt) cc_final: 0.4343 (ttp) REVERT: A 1688 MET cc_start: 0.8406 (tpp) cc_final: 0.8043 (tpt) REVERT: A 1835 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7847 (tptp) REVERT: A 2004 LEU cc_start: 0.8117 (tp) cc_final: 0.7715 (mt) REVERT: A 2012 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7381 (tptp) REVERT: A 2204 PHE cc_start: 0.5195 (OUTLIER) cc_final: 0.4774 (t80) outliers start: 26 outliers final: 12 residues processed: 204 average time/residue: 0.1357 time to fit residues: 42.3242 Evaluate side-chains 185 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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 1055 MET 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 1557 MET Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 2204 PHE 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: 0.9990 chunk 115 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 117 optimal weight: 0.2980 chunk 166 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN 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 = 0.3778 r_free = 0.3778 target = 0.134654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.089498 restraints weight = 29286.664| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.13 r_work: 0.2941 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18485 Z= 0.156 Angle : 0.523 8.679 25042 Z= 0.278 Chirality : 0.042 0.185 2812 Planarity : 0.004 0.054 3066 Dihedral : 9.944 77.085 2752 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 1.52 % Allowed : 9.96 % Favored : 88.52 % 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: 0.17 (0.18), residues: 2116 helix: 1.22 (0.16), residues: 1142 sheet: 0.44 (0.41), residues: 162 loop : -1.59 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 12 TYR 0.021 0.001 TYR A1576 PHE 0.026 0.001 PHE A2204 TRP 0.008 0.001 TRP A 395 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00360 (18482) covalent geometry : angle 0.52344 (25042) hydrogen bonds : bond 0.04157 ( 897) hydrogen bonds : angle 4.13493 ( 2603) metal coordination : bond 0.00190 ( 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 204 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8050 (m-30) cc_final: 0.7583 (m-30) REVERT: A 46 ASN cc_start: 0.8558 (t0) cc_final: 0.8022 (t0) REVERT: A 57 ASP cc_start: 0.7612 (m-30) cc_final: 0.6938 (t0) REVERT: A 61 ASP cc_start: 0.6450 (m-30) cc_final: 0.4681 (m-30) REVERT: A 111 GLU cc_start: 0.7418 (mp0) cc_final: 0.6957 (mp0) REVERT: A 115 ASP cc_start: 0.7195 (t0) cc_final: 0.6875 (m-30) REVERT: A 144 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.8001 (mmm-85) REVERT: A 162 PHE cc_start: 0.8452 (m-10) cc_final: 0.8047 (m-80) REVERT: A 726 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: A 855 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7155 (mm) REVERT: A 1056 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: A 1177 SER cc_start: 0.8995 (m) cc_final: 0.8595 (p) REVERT: A 1371 ARG cc_start: 0.8427 (ptp-110) cc_final: 0.7490 (mmm160) REVERT: A 1385 LYS cc_start: 0.7820 (mppt) cc_final: 0.7443 (mmtm) REVERT: A 1391 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: A 1470 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8324 (pt) REVERT: A 1633 ASN cc_start: 0.7841 (m-40) cc_final: 0.7391 (m-40) REVERT: A 1645 MET cc_start: 0.5568 (tpt) cc_final: 0.4031 (ttm) REVERT: A 1688 MET cc_start: 0.8423 (tpp) cc_final: 0.7987 (tpt) REVERT: A 1734 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8810 (pt0) REVERT: A 1835 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7796 (tptp) REVERT: A 2012 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7301 (tptm) REVERT: A 2204 PHE cc_start: 0.5258 (OUTLIER) cc_final: 0.4777 (t80) outliers start: 30 outliers final: 13 residues processed: 195 average time/residue: 0.1373 time to fit residues: 40.8406 Evaluate side-chains 188 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 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 1055 MET Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1238 PHE 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 1557 MET Chi-restraints excluded: chain A residue 1734 GLU Chi-restraints excluded: chain A residue 1771 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: 6.9990 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A 469 ASN A1112 ASN A1133 ASN A1842 HIS A2071 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.088694 restraints weight = 29439.357| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.15 r_work: 0.2926 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18485 Z= 0.180 Angle : 0.539 8.396 25042 Z= 0.287 Chirality : 0.042 0.191 2812 Planarity : 0.004 0.054 3066 Dihedral : 9.993 73.710 2752 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 1.63 % Allowed : 10.16 % Favored : 88.21 % 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: 0.19 (0.18), residues: 2116 helix: 1.20 (0.16), residues: 1141 sheet: 0.44 (0.42), residues: 162 loop : -1.52 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 12 TYR 0.022 0.001 TYR A1576 PHE 0.026 0.001 PHE A2204 TRP 0.008 0.001 TRP A 395 HIS 0.007 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00420 (18482) covalent geometry : angle 0.53890 (25042) hydrogen bonds : bond 0.04326 ( 897) hydrogen bonds : angle 4.19051 ( 2603) metal coordination : bond 0.00293 ( 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 207 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8098 (m-30) cc_final: 0.7613 (m-30) REVERT: A 46 ASN cc_start: 0.8579 (t0) cc_final: 0.8090 (t0) REVERT: A 57 ASP cc_start: 0.7594 (m-30) cc_final: 0.6931 (t0) REVERT: A 61 ASP cc_start: 0.6450 (m-30) cc_final: 0.4719 (m-30) REVERT: A 111 GLU cc_start: 0.7342 (mp0) cc_final: 0.6958 (mp0) REVERT: A 115 ASP cc_start: 0.7106 (t0) cc_final: 0.6882 (m-30) REVERT: A 144 ARG cc_start: 0.8397 (mmm-85) cc_final: 0.7952 (mmm-85) REVERT: A 162 PHE cc_start: 0.8412 (m-10) cc_final: 0.8040 (m-80) REVERT: A 190 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8600 (p) REVERT: A 726 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: A 854 GLU cc_start: 0.8120 (pp20) cc_final: 0.7598 (mm-30) REVERT: A 989 MET cc_start: 0.6186 (mmm) cc_final: 0.5794 (mmm) REVERT: A 1056 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: A 1177 SER cc_start: 0.9000 (m) cc_final: 0.8636 (p) REVERT: A 1371 ARG cc_start: 0.8484 (ptp-110) cc_final: 0.7529 (mmm160) REVERT: A 1385 LYS cc_start: 0.7875 (mppt) cc_final: 0.7509 (mmtm) REVERT: A 1391 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: A 1470 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8401 (pt) REVERT: A 1633 ASN cc_start: 0.7758 (m-40) cc_final: 0.7295 (m-40) REVERT: A 1645 MET cc_start: 0.5595 (tpt) cc_final: 0.4001 (ttm) REVERT: A 1688 MET cc_start: 0.8471 (tpp) cc_final: 0.8038 (tpt) REVERT: A 1734 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8854 (pt0) REVERT: A 2012 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7326 (tptm) REVERT: A 2204 PHE cc_start: 0.4936 (OUTLIER) cc_final: 0.4690 (t80) outliers start: 32 outliers final: 18 residues processed: 198 average time/residue: 0.1363 time to fit residues: 41.6143 Evaluate side-chains 193 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 1055 MET Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1238 PHE 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 1577 ILE Chi-restraints excluded: chain A residue 1734 GLU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1988 ASP 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: 0.9980 chunk 29 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS 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 = 0.3771 r_free = 0.3771 target = 0.134035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.088974 restraints weight = 29393.982| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.18 r_work: 0.2933 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18485 Z= 0.164 Angle : 0.530 9.629 25042 Z= 0.282 Chirality : 0.042 0.196 2812 Planarity : 0.004 0.054 3066 Dihedral : 9.969 73.720 2752 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 1.52 % Allowed : 10.57 % Favored : 87.91 % 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: 0.25 (0.18), residues: 2116 helix: 1.24 (0.16), residues: 1141 sheet: 0.74 (0.44), residues: 143 loop : -1.49 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 595 TYR 0.023 0.001 TYR A1576 PHE 0.026 0.001 PHE A2204 TRP 0.008 0.001 TRP A 395 HIS 0.007 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00380 (18482) covalent geometry : angle 0.52972 (25042) hydrogen bonds : bond 0.04204 ( 897) hydrogen bonds : angle 4.15972 ( 2603) metal coordination : bond 0.00179 ( 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 203 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8144 (m-30) cc_final: 0.7632 (m-30) REVERT: A 46 ASN cc_start: 0.8567 (t0) cc_final: 0.8119 (t0) REVERT: A 57 ASP cc_start: 0.7594 (m-30) cc_final: 0.7189 (t0) REVERT: A 111 GLU cc_start: 0.7372 (mp0) cc_final: 0.6965 (mp0) REVERT: A 115 ASP cc_start: 0.7077 (t0) cc_final: 0.6851 (m-30) REVERT: A 144 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.7941 (mmm-85) REVERT: A 162 PHE cc_start: 0.8423 (m-10) cc_final: 0.7993 (m-80) REVERT: A 190 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8587 (p) REVERT: A 726 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: A 776 GLU cc_start: 0.7962 (tp30) cc_final: 0.7605 (mm-30) REVERT: A 854 GLU cc_start: 0.8088 (pp20) cc_final: 0.7577 (mm-30) REVERT: A 989 MET cc_start: 0.6245 (mmm) cc_final: 0.5919 (mmm) REVERT: A 1056 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: A 1177 SER cc_start: 0.8992 (m) cc_final: 0.8609 (p) REVERT: A 1371 ARG cc_start: 0.8485 (ptp-110) cc_final: 0.7561 (mmm160) REVERT: A 1385 LYS cc_start: 0.7862 (mppt) cc_final: 0.7480 (mmtm) REVERT: A 1391 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: A 1470 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8387 (pt) REVERT: A 1633 ASN cc_start: 0.7799 (m-40) cc_final: 0.7336 (m-40) REVERT: A 1645 MET cc_start: 0.5529 (tpt) cc_final: 0.3874 (ttm) REVERT: A 1688 MET cc_start: 0.8477 (tpp) cc_final: 0.8055 (tpt) REVERT: A 1734 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8854 (pt0) REVERT: A 2004 LEU cc_start: 0.8140 (tp) cc_final: 0.7809 (mt) REVERT: A 2012 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7298 (tptm) REVERT: A 2204 PHE cc_start: 0.4987 (OUTLIER) cc_final: 0.4692 (t80) outliers start: 30 outliers final: 18 residues processed: 195 average time/residue: 0.1304 time to fit residues: 39.1977 Evaluate side-chains 195 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN 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 1055 MET Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1238 PHE 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 1577 ILE Chi-restraints excluded: chain A residue 1734 GLU Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1771 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: 4.9990 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A1133 ASN A1243 ASN A2071 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091308 restraints weight = 29352.921| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.14 r_work: 0.2972 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18485 Z= 0.106 Angle : 0.486 7.392 25042 Z= 0.259 Chirality : 0.040 0.188 2812 Planarity : 0.003 0.053 3066 Dihedral : 9.820 73.694 2752 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 1.27 % Allowed : 10.82 % Favored : 87.91 % 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: 0.47 (0.19), residues: 2116 helix: 1.41 (0.16), residues: 1142 sheet: 0.90 (0.45), residues: 142 loop : -1.39 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 12 TYR 0.022 0.001 TYR A1576 PHE 0.025 0.001 PHE A2204 TRP 0.010 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00230 (18482) covalent geometry : angle 0.48623 (25042) hydrogen bonds : bond 0.03661 ( 897) hydrogen bonds : angle 4.02608 ( 2603) metal coordination : bond 0.00153 ( 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 203 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8132 (m-30) cc_final: 0.7627 (m-30) REVERT: A 46 ASN cc_start: 0.8555 (t0) cc_final: 0.8153 (t0) REVERT: A 57 ASP cc_start: 0.7595 (m-30) cc_final: 0.7192 (t0) REVERT: A 111 GLU cc_start: 0.7450 (mp0) cc_final: 0.7064 (mp0) REVERT: A 144 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.7931 (mmm-85) REVERT: A 162 PHE cc_start: 0.8399 (m-10) cc_final: 0.8075 (m-80) REVERT: A 190 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8602 (p) REVERT: A 212 MET cc_start: 0.8102 (pp-130) cc_final: 0.7733 (mmp) REVERT: A 726 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: A 989 MET cc_start: 0.6284 (mmm) cc_final: 0.5990 (mmm) REVERT: A 1177 SER cc_start: 0.8993 (m) cc_final: 0.8593 (p) REVERT: A 1371 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.7542 (mmm160) REVERT: A 1385 LYS cc_start: 0.7855 (mppt) cc_final: 0.7461 (mmtm) REVERT: A 1391 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: A 1470 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8335 (pt) REVERT: A 1633 ASN cc_start: 0.7813 (m-40) cc_final: 0.7330 (m-40) REVERT: A 1645 MET cc_start: 0.5465 (tpt) cc_final: 0.3830 (ttm) REVERT: A 1688 MET cc_start: 0.8473 (tpp) cc_final: 0.8095 (tpt) REVERT: A 1756 ASN cc_start: 0.8183 (m110) cc_final: 0.7980 (m110) REVERT: A 2004 LEU cc_start: 0.8217 (tp) cc_final: 0.7892 (mt) REVERT: A 2012 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7283 (tptm) REVERT: A 2204 PHE cc_start: 0.4938 (OUTLIER) cc_final: 0.4690 (t80) outliers start: 25 outliers final: 15 residues processed: 194 average time/residue: 0.1389 time to fit residues: 41.2005 Evaluate side-chains 190 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 726 GLU Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL 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 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 1577 ILE Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 131 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 190 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 213 optimal weight: 0.0370 chunk 83 optimal weight: 5.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 299 HIS 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 = 0.3797 r_free = 0.3797 target = 0.135936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.091193 restraints weight = 29350.415| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.09 r_work: 0.2970 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18485 Z= 0.115 Angle : 0.508 12.322 25042 Z= 0.267 Chirality : 0.040 0.208 2812 Planarity : 0.003 0.053 3066 Dihedral : 9.724 73.713 2750 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 1.17 % Allowed : 11.08 % Favored : 87.75 % 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: 0.55 (0.19), residues: 2116 helix: 1.48 (0.16), residues: 1142 sheet: 0.78 (0.43), residues: 152 loop : -1.35 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 12 TYR 0.014 0.001 TYR A 677 PHE 0.025 0.001 PHE A2204 TRP 0.007 0.001 TRP A1143 HIS 0.006 0.001 HIS A2179 Details of bonding type rmsd covalent geometry : bond 0.00256 (18482) covalent geometry : angle 0.50801 (25042) hydrogen bonds : bond 0.03706 ( 897) hydrogen bonds : angle 4.00191 ( 2603) metal coordination : bond 0.00060 ( 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 197 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8122 (m-30) cc_final: 0.7610 (m-30) REVERT: A 46 ASN cc_start: 0.8533 (t0) cc_final: 0.8134 (t0) REVERT: A 57 ASP cc_start: 0.7587 (m-30) cc_final: 0.7243 (t70) REVERT: A 144 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.7924 (mmm-85) REVERT: A 162 PHE cc_start: 0.8409 (m-10) cc_final: 0.8187 (m-80) REVERT: A 190 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8634 (p) REVERT: A 212 MET cc_start: 0.8115 (pp-130) cc_final: 0.7736 (mmp) REVERT: A 726 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: A 989 MET cc_start: 0.6310 (mmm) cc_final: 0.6008 (mmm) REVERT: A 1177 SER cc_start: 0.9000 (m) cc_final: 0.8602 (p) REVERT: A 1371 ARG cc_start: 0.8430 (ptp-110) cc_final: 0.7536 (mmm160) REVERT: A 1385 LYS cc_start: 0.7851 (mppt) cc_final: 0.7476 (mmtm) REVERT: A 1391 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8221 (m-30) REVERT: A 1470 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8365 (pt) REVERT: A 1633 ASN cc_start: 0.7822 (m-40) cc_final: 0.7339 (m-40) REVERT: A 1645 MET cc_start: 0.5458 (tpt) cc_final: 0.3823 (ttm) REVERT: A 1688 MET cc_start: 0.8485 (tpp) cc_final: 0.8104 (tpt) REVERT: A 1756 ASN cc_start: 0.8182 (m110) cc_final: 0.7978 (m110) REVERT: A 2004 LEU cc_start: 0.8218 (tp) cc_final: 0.7908 (mt) REVERT: A 2012 LYS cc_start: 0.8093 (ttmt) cc_final: 0.7288 (tptm) REVERT: A 2204 PHE cc_start: 0.5007 (OUTLIER) cc_final: 0.4743 (t80) outliers start: 23 outliers final: 16 residues processed: 191 average time/residue: 0.1361 time to fit residues: 40.1294 Evaluate side-chains 185 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN 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 900 MET Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1055 MET 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 1577 ILE Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 2204 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 147 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 299 HIS 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 = 0.3795 r_free = 0.3795 target = 0.135878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.091077 restraints weight = 29447.725| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.09 r_work: 0.2967 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 18485 Z= 0.144 Angle : 0.705 59.198 25042 Z= 0.403 Chirality : 0.043 0.825 2812 Planarity : 0.004 0.077 3066 Dihedral : 9.723 73.717 2750 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.08 % Rotamer: Outliers : 1.17 % Allowed : 11.28 % Favored : 87.55 % Cbeta Deviations : 0.05 % 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: 0.54 (0.19), residues: 2116 helix: 1.48 (0.16), residues: 1142 sheet: 0.78 (0.43), residues: 152 loop : -1.36 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1424 TYR 0.014 0.001 TYR A 677 PHE 0.025 0.001 PHE A2204 TRP 0.007 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00304 (18482) covalent geometry : angle 0.70531 (25042) hydrogen bonds : bond 0.03718 ( 897) hydrogen bonds : angle 4.00195 ( 2603) metal coordination : bond 0.00046 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5235.34 seconds wall clock time: 90 minutes 49.97 seconds (5449.97 seconds total)