Starting phenix.real_space_refine on Sun Aug 24 10:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z8k_11118/08_2025/6z8k_11118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z8k_11118/08_2025/6z8k_11118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6z8k_11118/08_2025/6z8k_11118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z8k_11118/08_2025/6z8k_11118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z8k_11118/08_2025/6z8k_11118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z8k_11118/08_2025/6z8k_11118.map" } resolution = 3.02 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= 0.002 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 44 5.49 5 Mg 1 5.21 5 S 114 5.16 5 C 11707 2.51 5 N 3120 2.21 5 O 3600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18587 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "X" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "T" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 216 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "P" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 17631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2158, 17631 Classifications: {'peptide': 2158} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 2087} Chain breaks: 10 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 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 17114 SG CYS A2064 86.345 101.656 90.538 1.00 77.50 S Time building chain proxies: 4.25, per 1000 atoms: 0.23 Number of scatterers: 18587 At special positions: 0 Unit cell: (120.596, 133.812, 148.68, 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 114 16.00 P 44 15.00 Mg 1 11.99 O 3600 8.00 N 3120 7.00 C 11707 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: 1.84 Conformation dependent library (CDL) restraints added in 955.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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 " 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4162 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 19 sheets defined 54.8% alpha, 9.2% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 21 through 46 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 99 through 118 removed outlier: 3.847A pdb=" N ILE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.660A pdb=" N TRP A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.627A pdb=" N MET A 214 " --> pdb=" O PHE A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.818A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 261 removed outlier: 5.325A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.521A pdb=" N GLN A 301 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.642A pdb=" N MET A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 475 through 489 removed outlier: 5.939A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 removed outlier: 3.511A pdb=" N TYR A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 522 removed outlier: 3.669A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.756A pdb=" N ARG A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 620 removed outlier: 3.559A pdb=" N LEU A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 638 removed outlier: 4.152A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 661 removed outlier: 4.059A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.212A 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: 3.652A pdb=" N PHE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 758 through 780 removed outlier: 4.262A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 779 " --> pdb=" O CYS A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 814 removed outlier: 3.756A 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 850 through 870 removed outlier: 3.951A pdb=" N LYS A 870 " --> pdb=" O VAL A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 899 removed outlier: 3.929A pdb=" N ALA A 899 " --> pdb=" O MET A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.776A pdb=" N GLN A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 983 removed outlier: 3.774A pdb=" N ARG A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1020 removed outlier: 3.598A pdb=" N GLU A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 removed outlier: 4.416A pdb=" N GLU A1028 " --> pdb=" O ASP A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1047 Processing helix chain 'A' and resid 1071 through 1079 removed outlier: 3.979A 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 Processing helix chain 'A' and resid 1123 through 1129 Processing helix chain 'A' and resid 1148 through 1173 Processing helix chain 'A' and resid 1201 through 1219 removed outlier: 3.703A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1258 Processing helix chain 'A' and resid 1259 through 1261 No H-bonds generated for 'chain 'A' and resid 1259 through 1261' Processing helix chain 'A' and resid 1269 through 1285 removed outlier: 3.700A pdb=" N ALA A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A1281 " --> pdb=" O SER A1277 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A1282 " --> pdb=" O SER A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1307 removed outlier: 3.556A pdb=" N TYR A1307 " --> pdb=" O THR A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1320 removed outlier: 4.333A pdb=" N ASP A1319 " --> pdb=" O ASP A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1329 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 1373 through 1379 Processing helix chain 'A' and resid 1380 through 1384 Processing helix chain 'A' and resid 1390 through 1403 Processing helix chain 'A' and resid 1441 through 1452 removed outlier: 3.600A pdb=" N SER A1445 " --> pdb=" O LEU A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1467 removed outlier: 3.728A pdb=" N LEU A1460 " --> pdb=" O GLY A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1472 Processing helix chain 'A' and resid 1477 through 1488 Processing helix chain 'A' and resid 1491 through 1499 removed outlier: 3.748A pdb=" N LYS A1495 " --> pdb=" O SER A1491 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A1499 " --> pdb=" O LYS A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1513 removed outlier: 3.548A 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 Processing helix chain 'A' and resid 1566 through 1578 Processing helix chain 'A' and resid 1581 through 1593 Processing helix chain 'A' and resid 1622 through 1631 Processing helix chain 'A' and resid 1645 through 1659 removed outlier: 3.641A pdb=" N LEU A1649 " --> pdb=" O MET A1645 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A1650 " --> pdb=" O ALA A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1677 Processing helix chain 'A' and resid 1681 through 1700 Processing helix chain 'A' and resid 1717 through 1729 removed outlier: 3.619A pdb=" N PHE A1721 " --> pdb=" O THR A1717 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A1729 " --> pdb=" O MET A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1760 through 1778 removed outlier: 3.924A pdb=" N ALA A1764 " --> pdb=" O GLU A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1784 through 1793 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 1823 Processing helix chain 'A' and resid 1829 through 1840 removed outlier: 3.602A pdb=" N LEU A1833 " --> pdb=" O ARG A1829 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A1839 " --> pdb=" O LYS A1835 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A1840 " --> pdb=" O TYR A1836 " (cutoff:3.500A) 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 1983 through 1991 removed outlier: 3.797A pdb=" N ASP A1988 " --> pdb=" O ILE A1984 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A1989 " --> pdb=" O ARG A1985 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1990 " --> pdb=" O SER A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2021 removed outlier: 3.576A pdb=" N LYS A2017 " --> pdb=" O HIS A2014 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A2020 " --> pdb=" O LYS A2017 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A2021 " --> pdb=" O MET A2018 " (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 removed outlier: 3.500A pdb=" N PHE A2058 " --> pdb=" O ASN A2054 " (cutoff:3.500A) 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 2154 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: 3.986A 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: 6.242A pdb=" N LEU A 88 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 127 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE A 90 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE A 129 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP A 92 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE A 131 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS A 94 " --> pdb=" O ILE A 131 " (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 388 removed outlier: 5.280A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.983A 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 388 removed outlier: 5.280A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 709 through 710 removed outlier: 3.732A pdb=" N GLU A2088 " --> pdb=" O ILE A2098 " (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 842 through 846 Processing sheet with id=AA9, first strand: chain 'A' and resid 959 through 963 removed outlier: 6.219A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A1101 " --> pdb=" O ILE A1139 " (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 Processing sheet with id=AB3, first strand: chain 'A' and resid 1519 through 1520 Processing sheet with id=AB4, first strand: chain 'A' and resid 1594 through 1595 Processing sheet with id=AB5, first strand: chain 'A' and resid 1606 through 1609 Processing sheet with id=AB6, first strand: chain 'A' and resid 1796 through 1797 Processing sheet with id=AB7, 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: 6.548A 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: 7.771A pdb=" N TYR A1925 " --> pdb=" O VAL A1970 " (cutoff:3.500A) Processing sheet with id=AB8, 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=AB9, first strand: chain 'A' and resid 2027 through 2028 Processing sheet with id=AC1, first strand: chain 'A' and resid 2083 through 2085 875 hydrogen bonds defined for protein. 2502 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 6.03 Time building geometry restraints manager: 2.43 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: 4739 1.33 - 1.45: 3851 1.45 - 1.57: 10186 1.57 - 1.69: 84 1.69 - 1.81: 189 Bond restraints: 19049 Sorted by residual: bond pdb=" C LEU A 747 " pdb=" N PRO A 748 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.08e-02 8.57e+03 1.84e+01 bond pdb=" C LYS A 270 " pdb=" N GLN A 271 " ideal model delta sigma weight residual 1.331 1.260 0.071 2.83e-02 1.25e+03 6.24e+00 bond pdb=" CA PHE A2015 " pdb=" C PHE A2015 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.34e-02 5.57e+03 3.94e+00 bond pdb=" CG1 ILE A 128 " pdb=" CD1 ILE A 128 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.74e+00 bond pdb=" CB ILE A1298 " pdb=" CG2 ILE A1298 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.74e+00 ... (remaining 19044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 25370 2.84 - 5.69: 469 5.69 - 8.53: 44 8.53 - 11.38: 5 11.38 - 14.22: 1 Bond angle restraints: 25889 Sorted by residual: angle pdb=" N PHE A2015 " pdb=" CA PHE A2015 " pdb=" C PHE A2015 " ideal model delta sigma weight residual 110.80 125.02 -14.22 2.13e+00 2.20e-01 4.46e+01 angle pdb=" N ARG A1958 " pdb=" CA ARG A1958 " pdb=" C ARG A1958 " ideal model delta sigma weight residual 108.19 115.22 -7.03 1.29e+00 6.01e-01 2.97e+01 angle pdb=" C LEU A1144 " pdb=" CA LEU A1144 " pdb=" CB LEU A1144 " ideal model delta sigma weight residual 116.54 110.50 6.04 1.15e+00 7.56e-01 2.76e+01 angle pdb=" C ASN A 51 " pdb=" N ASP A 52 " pdb=" CA ASP A 52 " ideal model delta sigma weight residual 122.46 129.75 -7.29 1.41e+00 5.03e-01 2.67e+01 angle pdb=" N CYS A1969 " pdb=" CA CYS A1969 " pdb=" C CYS A1969 " ideal model delta sigma weight residual 110.80 120.95 -10.15 2.13e+00 2.20e-01 2.27e+01 ... (remaining 25884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 10905 17.73 - 35.46: 534 35.46 - 53.19: 149 53.19 - 70.92: 57 70.92 - 88.65: 18 Dihedral angle restraints: 11663 sinusoidal: 5257 harmonic: 6406 Sorted by residual: dihedral pdb=" CA THR A1846 " pdb=" C THR A1846 " pdb=" N TRP A1847 " pdb=" CA TRP A1847 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA LYS A1917 " pdb=" C LYS A1917 " pdb=" N ILE A1918 " pdb=" CA ILE A1918 " ideal model delta harmonic sigma weight residual 180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP A1793 " pdb=" C ASP A1793 " pdb=" N GLU A1794 " pdb=" CA GLU A1794 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 11660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2732 0.106 - 0.212: 176 0.212 - 0.319: 9 0.319 - 0.425: 1 0.425 - 0.531: 1 Chirality restraints: 2919 Sorted by residual: chirality pdb=" CA PHE A2015 " pdb=" N PHE A2015 " pdb=" C PHE A2015 " pdb=" CB PHE A2015 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.05e+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 2.61e+00 chirality pdb=" CG LEU A1805 " pdb=" CB LEU A1805 " pdb=" CD1 LEU A1805 " pdb=" CD2 LEU A1805 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2916 not shown) Planarity restraints: 3112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 511 " 0.024 2.00e-02 2.50e+03 2.33e-02 9.50e+00 pdb=" CG PHE A 511 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 511 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 511 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 511 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 511 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 511 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A2007 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C PHE A2007 " -0.052 2.00e-02 2.50e+03 pdb=" O PHE A2007 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A2008 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1795 " -0.015 2.00e-02 2.50e+03 1.92e-02 6.44e+00 pdb=" CG PHE A1795 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A1795 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A1795 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A1795 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A1795 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A1795 " 0.004 2.00e-02 2.50e+03 ... (remaining 3109 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 3 2.18 - 2.86: 6400 2.86 - 3.54: 25504 3.54 - 4.22: 45725 4.22 - 4.90: 77758 Nonbonded interactions: 155390 Sorted by model distance: nonbonded pdb=" CD1 LEU A2151 " pdb=" CE2 PHE A2204 " model vdw 1.496 3.760 nonbonded pdb=" CD1 LEU A2151 " pdb=" CZ PHE A2204 " model vdw 1.811 3.760 nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2301 " model vdw 2.097 2.230 nonbonded pdb=" O VAL A2148 " pdb=" CD1 ILE A2152 " model vdw 2.186 3.460 nonbonded pdb=" OD2 ASP A1776 " pdb=" OG SER A1998 " model vdw 2.255 3.040 ... (remaining 155385 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 Found NCS groups: ncs_group { reference = (chain 'C' and ((resid 1 and (name P or name OP1 or name OP2 or name O5' or name \ C5' or name C4' or name O4' or name C3' or name O3' or name C2' or name O2' or \ name C1' or name N9 or name C8 or name N7 or name C5 or name C6 or name N6 or na \ me N1 or name C2 or name N3 or name C4 )) or resid 2 through 10)) selection = chain 'T' } ncs_group { reference = (chain 'H' and resid 7 through 16) selection = chain 'P' } 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: 2.780 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: 0.030 Set scattering table: 0.030 Process input model: 26.040 Find NCS groups from input model: 0.200 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.010 0.566 19052 Z= 0.418 Angle : 0.962 14.223 25889 Z= 0.545 Chirality : 0.058 0.531 2919 Planarity : 0.007 0.054 3112 Dihedral : 12.851 88.654 7501 Min Nonbonded Distance : 1.496 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.66 % Favored : 94.01 % Rotamer: Outliers : 1.76 % Allowed : 3.82 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (0.14), residues: 2136 helix: -1.91 (0.12), residues: 1098 sheet: -2.12 (0.36), residues: 160 loop : -2.83 (0.17), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 531 TYR 0.040 0.003 TYR A1740 PHE 0.053 0.004 PHE A 511 TRP 0.023 0.003 TRP A 395 HIS 0.021 0.002 HIS A1773 Details of bonding type rmsd covalent geometry : bond 0.00905 (19049) covalent geometry : angle 0.96208 (25889) hydrogen bonds : bond 0.16917 ( 891) hydrogen bonds : angle 7.01684 ( 2558) metal coordination : bond 0.37930 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 313 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6195 (ptm) cc_final: 0.5344 (ptp) REVERT: A 165 LYS cc_start: 0.8461 (tmmt) cc_final: 0.8255 (ttmm) REVERT: A 284 MET cc_start: 0.8914 (tmm) cc_final: 0.8702 (tmm) REVERT: A 416 LYS cc_start: 0.8684 (tptt) cc_final: 0.8321 (mptt) REVERT: A 696 ASP cc_start: 0.7903 (m-30) cc_final: 0.7668 (m-30) REVERT: A 765 ASP cc_start: 0.8141 (t70) cc_final: 0.7836 (t0) REVERT: A 895 MET cc_start: 0.6844 (ppp) cc_final: 0.6486 (tmm) REVERT: A 897 ARG cc_start: 0.8436 (tpt-90) cc_final: 0.8117 (tpt-90) REVERT: A 1269 TYR cc_start: 0.8794 (t80) cc_final: 0.8229 (t80) REVERT: A 1350 GLU cc_start: 0.7481 (tp30) cc_final: 0.7238 (tp30) REVERT: A 1492 LYS cc_start: 0.8328 (mptt) cc_final: 0.8085 (mptt) REVERT: A 1720 ASP cc_start: 0.8540 (m-30) cc_final: 0.8249 (m-30) REVERT: A 1794 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 1918 ILE cc_start: 0.4007 (OUTLIER) cc_final: 0.3430 (pt) REVERT: A 2070 ILE cc_start: 0.7636 (pt) cc_final: 0.7369 (mt) REVERT: A 2177 MET cc_start: 0.6147 (mmm) cc_final: 0.5494 (mmm) outliers start: 35 outliers final: 12 residues processed: 340 average time/residue: 0.1810 time to fit residues: 87.1581 Evaluate side-chains 202 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1746 SER Chi-restraints excluded: chain A residue 1840 LYS Chi-restraints excluded: chain A residue 1906 SER Chi-restraints excluded: chain A residue 1918 ILE Chi-restraints excluded: chain A residue 1958 ARG Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 2085 THR Chi-restraints excluded: chain A residue 2152 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 0.1980 chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 332 GLN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 ASN A 489 ASN A 523 GLN A 565 HIS A 602 GLN A 665 ASN A 795 ASN A 826 ASN A 892 ASN A 902 ASN A1058 ASN A1145 GLN A1181 ASN A1233 ASN A1243 ASN A1369 GLN A1392 ASN ** A1580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 HIS A1678 GLN A1704 HIS A1762 ASN A1924 ASN A2071 ASN A2141 ASN A2175 ASN A2209 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.116826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083160 restraints weight = 35779.449| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.40 r_work: 0.2993 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19052 Z= 0.126 Angle : 0.585 7.736 25889 Z= 0.311 Chirality : 0.041 0.182 2919 Planarity : 0.005 0.053 3112 Dihedral : 12.358 89.750 3045 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 1.61 % Allowed : 6.98 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 aren not related in a simple way. whole: -1.62 (0.17), residues: 2136 helix: -0.11 (0.15), residues: 1106 sheet: -1.31 (0.34), residues: 190 loop : -2.31 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 119 TYR 0.024 0.001 TYR A1576 PHE 0.032 0.001 PHE A2204 TRP 0.017 0.001 TRP A2219 HIS 0.005 0.001 HIS A1651 Details of bonding type rmsd covalent geometry : bond 0.00251 (19049) covalent geometry : angle 0.58487 (25889) hydrogen bonds : bond 0.04398 ( 891) hydrogen bonds : angle 4.70878 ( 2558) metal coordination : bond 0.00557 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8496 (m-30) cc_final: 0.8224 (m-30) REVERT: A 416 LYS cc_start: 0.8618 (tptt) cc_final: 0.8196 (mptt) REVERT: A 765 ASP cc_start: 0.8413 (t70) cc_final: 0.8136 (t0) REVERT: A 895 MET cc_start: 0.6826 (ppp) cc_final: 0.6587 (tmm) REVERT: A 954 THR cc_start: 0.8188 (m) cc_final: 0.7932 (p) REVERT: A 991 SER cc_start: 0.8536 (p) cc_final: 0.8326 (p) REVERT: A 1014 GLU cc_start: 0.8964 (tp30) cc_final: 0.8712 (mm-30) REVERT: A 1424 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7327 (ttm-80) REVERT: A 1492 LYS cc_start: 0.8323 (mptt) cc_final: 0.8017 (pttt) REVERT: A 1697 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: A 1720 ASP cc_start: 0.8987 (m-30) cc_final: 0.8641 (m-30) REVERT: A 1805 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8588 (mt) REVERT: A 1870 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7287 (mtm180) REVERT: A 1918 ILE cc_start: 0.5244 (OUTLIER) cc_final: 0.4631 (pt) REVERT: A 2070 ILE cc_start: 0.7898 (pt) cc_final: 0.7343 (mt) REVERT: A 2160 TRP cc_start: 0.7259 (m-90) cc_final: 0.6839 (p90) REVERT: A 2191 MET cc_start: 0.6648 (mmt) cc_final: 0.6417 (mmt) REVERT: A 2219 TRP cc_start: 0.8011 (m100) cc_final: 0.7513 (m100) outliers start: 32 outliers final: 12 residues processed: 256 average time/residue: 0.1528 time to fit residues: 57.9500 Evaluate side-chains 203 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1465 LEU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1697 GLU Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1840 LYS Chi-restraints excluded: chain A residue 1918 ILE Chi-restraints excluded: chain A residue 1958 ARG Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 2062 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 193 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 752 ASN A 801 HIS A 902 ASN A1530 ASN A1567 ASN A1621 HIS A2107 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.078554 restraints weight = 36156.020| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.38 r_work: 0.2899 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19052 Z= 0.247 Angle : 0.620 7.818 25889 Z= 0.327 Chirality : 0.044 0.190 2919 Planarity : 0.004 0.053 3112 Dihedral : 12.246 89.670 3038 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 1.86 % Allowed : 8.48 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 aren not related in a simple way. whole: -0.82 (0.18), residues: 2136 helix: 0.61 (0.15), residues: 1105 sheet: -0.96 (0.35), residues: 198 loop : -2.03 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 119 TYR 0.023 0.002 TYR A1576 PHE 0.028 0.002 PHE A2190 TRP 0.019 0.002 TRP A 395 HIS 0.009 0.002 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00572 (19049) covalent geometry : angle 0.62011 (25889) hydrogen bonds : bond 0.04714 ( 891) hydrogen bonds : angle 4.52110 ( 2558) metal coordination : bond 0.00332 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8443 (m-30) cc_final: 0.8162 (m-30) REVERT: A 416 LYS cc_start: 0.8727 (tptt) cc_final: 0.8253 (mptt) REVERT: A 765 ASP cc_start: 0.8460 (t70) cc_final: 0.8175 (t0) REVERT: A 895 MET cc_start: 0.6877 (ppp) cc_final: 0.6586 (tmm) REVERT: A 954 THR cc_start: 0.8249 (m) cc_final: 0.7956 (p) REVERT: A 1014 GLU cc_start: 0.9009 (tp30) cc_final: 0.8778 (mm-30) REVERT: A 1324 GLU cc_start: 0.7933 (pp20) cc_final: 0.7554 (pp20) REVERT: A 1492 LYS cc_start: 0.8617 (mptt) cc_final: 0.7980 (pttt) REVERT: A 1697 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: A 1720 ASP cc_start: 0.9124 (m-30) cc_final: 0.8757 (m-30) REVERT: A 1805 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8632 (mt) REVERT: A 1817 ASP cc_start: 0.8850 (t0) cc_final: 0.8639 (t0) REVERT: A 1839 MET cc_start: 0.8097 (mmt) cc_final: 0.7529 (mmm) REVERT: A 2070 ILE cc_start: 0.7985 (pt) cc_final: 0.7496 (mt) REVERT: A 2095 ILE cc_start: 0.8857 (tp) cc_final: 0.8637 (pt) REVERT: A 2191 MET cc_start: 0.6729 (mmt) cc_final: 0.6427 (mmt) REVERT: A 2219 TRP cc_start: 0.8036 (m100) cc_final: 0.7454 (m100) outliers start: 37 outliers final: 16 residues processed: 230 average time/residue: 0.1343 time to fit residues: 46.9130 Evaluate side-chains 200 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1697 GLU Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 2062 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 138 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 902 ASN A1369 GLN A1678 GLN A2235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.114134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.080389 restraints weight = 36193.672| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.38 r_work: 0.2937 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19052 Z= 0.151 Angle : 0.540 7.456 25889 Z= 0.285 Chirality : 0.041 0.158 2919 Planarity : 0.004 0.047 3112 Dihedral : 12.047 90.177 3028 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 1.81 % Allowed : 8.99 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 aren not related in a simple way. whole: -0.33 (0.18), residues: 2136 helix: 1.05 (0.16), residues: 1106 sheet: -0.76 (0.35), residues: 198 loop : -1.84 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 603 TYR 0.015 0.001 TYR A 677 PHE 0.014 0.001 PHE A2226 TRP 0.011 0.001 TRP A1143 HIS 0.005 0.001 HIS A1773 Details of bonding type rmsd covalent geometry : bond 0.00346 (19049) covalent geometry : angle 0.54049 (25889) hydrogen bonds : bond 0.03961 ( 891) hydrogen bonds : angle 4.26848 ( 2558) metal coordination : bond 0.00306 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8406 (m-30) cc_final: 0.8126 (m-30) REVERT: A 416 LYS cc_start: 0.8725 (tptt) cc_final: 0.8281 (mptt) REVERT: A 765 ASP cc_start: 0.8417 (t70) cc_final: 0.8135 (t0) REVERT: A 895 MET cc_start: 0.6858 (ppp) cc_final: 0.6558 (tmm) REVERT: A 954 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7945 (p) REVERT: A 1014 GLU cc_start: 0.8991 (tp30) cc_final: 0.8755 (mm-30) REVERT: A 1424 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.7185 (ttm-80) REVERT: A 1432 PHE cc_start: 0.8864 (t80) cc_final: 0.8660 (t80) REVERT: A 1492 LYS cc_start: 0.8583 (mptt) cc_final: 0.7980 (pttt) REVERT: A 1697 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: A 1720 ASP cc_start: 0.9071 (m-30) cc_final: 0.8780 (m-30) REVERT: A 1768 PHE cc_start: 0.8723 (m-80) cc_final: 0.8475 (m-80) REVERT: A 1805 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 1817 ASP cc_start: 0.8878 (t0) cc_final: 0.8663 (t0) REVERT: A 1829 ARG cc_start: 0.8238 (mpp80) cc_final: 0.7994 (mmt-90) REVERT: A 2070 ILE cc_start: 0.7977 (pt) cc_final: 0.7500 (mt) REVERT: A 2095 ILE cc_start: 0.8823 (tp) cc_final: 0.8599 (pt) REVERT: A 2106 ARG cc_start: 0.8445 (tpp-160) cc_final: 0.8045 (tpp-160) REVERT: A 2191 MET cc_start: 0.6724 (mmt) cc_final: 0.6360 (mmt) REVERT: A 2203 MET cc_start: 0.6519 (ptt) cc_final: 0.6270 (tmm) REVERT: A 2219 TRP cc_start: 0.8064 (m100) cc_final: 0.7539 (m100) REVERT: A 2222 MET cc_start: 0.8258 (ttt) cc_final: 0.7473 (tpp) outliers start: 36 outliers final: 16 residues processed: 219 average time/residue: 0.1526 time to fit residues: 50.2972 Evaluate side-chains 199 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1697 GLU Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 2062 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 87 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 16 optimal weight: 0.2980 chunk 217 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 902 ASN A1678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.116108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.082576 restraints weight = 35686.835| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.38 r_work: 0.2979 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19052 Z= 0.106 Angle : 0.496 7.682 25889 Z= 0.262 Chirality : 0.040 0.176 2919 Planarity : 0.003 0.044 3112 Dihedral : 11.926 88.257 3028 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.41 % Allowed : 10.09 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.18), residues: 2136 helix: 1.35 (0.16), residues: 1116 sheet: -0.31 (0.37), residues: 192 loop : -1.66 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 17 TYR 0.019 0.001 TYR A1696 PHE 0.010 0.001 PHE A 948 TRP 0.012 0.001 TRP A1143 HIS 0.005 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00233 (19049) covalent geometry : angle 0.49647 (25889) hydrogen bonds : bond 0.03467 ( 891) hydrogen bonds : angle 4.03105 ( 2558) metal coordination : bond 0.00156 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8386 (m-30) cc_final: 0.8105 (m-30) REVERT: A 416 LYS cc_start: 0.8662 (tptt) cc_final: 0.8281 (mptt) REVERT: A 696 ASP cc_start: 0.8602 (m-30) cc_final: 0.8375 (m-30) REVERT: A 765 ASP cc_start: 0.8438 (t70) cc_final: 0.8171 (t0) REVERT: A 895 MET cc_start: 0.6839 (ppp) cc_final: 0.6499 (tmm) REVERT: A 936 MET cc_start: 0.9183 (tpp) cc_final: 0.8980 (tpp) REVERT: A 954 THR cc_start: 0.8202 (m) cc_final: 0.7964 (p) REVERT: A 1409 MET cc_start: 0.8283 (mtt) cc_final: 0.7985 (mtt) REVERT: A 1492 LYS cc_start: 0.8556 (mptt) cc_final: 0.8046 (pttt) REVERT: A 1697 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: A 1720 ASP cc_start: 0.9060 (m-30) cc_final: 0.8860 (m-30) REVERT: A 1805 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8617 (mt) REVERT: A 1817 ASP cc_start: 0.8858 (t0) cc_final: 0.8642 (t0) REVERT: A 1829 ARG cc_start: 0.8216 (mpp80) cc_final: 0.7965 (mmt-90) REVERT: A 1839 MET cc_start: 0.7691 (mmm) cc_final: 0.7166 (mmm) REVERT: A 2070 ILE cc_start: 0.7968 (pt) cc_final: 0.7504 (mt) REVERT: A 2095 ILE cc_start: 0.8805 (tp) cc_final: 0.8581 (pt) REVERT: A 2106 ARG cc_start: 0.8407 (tpp-160) cc_final: 0.7962 (tpp-160) REVERT: A 2121 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 2191 MET cc_start: 0.6587 (mmt) cc_final: 0.6220 (mmt) REVERT: A 2219 TRP cc_start: 0.8034 (m100) cc_final: 0.7556 (m100) REVERT: A 2222 MET cc_start: 0.8279 (ttt) cc_final: 0.7549 (tpp) outliers start: 28 outliers final: 18 residues processed: 230 average time/residue: 0.1490 time to fit residues: 51.7101 Evaluate side-chains 211 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1697 GLU Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1805 LEU Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 1979 ASP Chi-restraints excluded: chain A residue 2062 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 120 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 166 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN A1190 GLN A1678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.114921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081261 restraints weight = 35560.349| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.36 r_work: 0.2953 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19052 Z= 0.143 Angle : 0.511 7.318 25889 Z= 0.269 Chirality : 0.041 0.156 2919 Planarity : 0.003 0.042 3112 Dihedral : 11.906 88.562 3028 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 1.41 % Allowed : 10.64 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.18), residues: 2136 helix: 1.45 (0.16), residues: 1115 sheet: -0.31 (0.37), residues: 197 loop : -1.58 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 17 TYR 0.015 0.001 TYR A1576 PHE 0.021 0.001 PHE A2058 TRP 0.010 0.001 TRP A 395 HIS 0.005 0.001 HIS A1773 Details of bonding type rmsd covalent geometry : bond 0.00327 (19049) covalent geometry : angle 0.51087 (25889) hydrogen bonds : bond 0.03671 ( 891) hydrogen bonds : angle 4.03541 ( 2558) metal coordination : bond 0.00299 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8413 (m-30) cc_final: 0.8135 (m-30) REVERT: A 416 LYS cc_start: 0.8721 (tptt) cc_final: 0.8311 (mptt) REVERT: A 696 ASP cc_start: 0.8623 (m-30) cc_final: 0.8397 (m-30) REVERT: A 765 ASP cc_start: 0.8422 (t70) cc_final: 0.8151 (t0) REVERT: A 954 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7967 (p) REVERT: A 1424 ARG cc_start: 0.7348 (ttm-80) cc_final: 0.6937 (ttm-80) REVERT: A 1470 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9017 (pp) REVERT: A 1492 LYS cc_start: 0.8560 (mptt) cc_final: 0.7982 (pttt) REVERT: A 1697 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: A 1817 ASP cc_start: 0.8862 (t0) cc_final: 0.8574 (t0) REVERT: A 1829 ARG cc_start: 0.8291 (mpp80) cc_final: 0.7988 (mmt-90) REVERT: A 1839 MET cc_start: 0.7660 (mmm) cc_final: 0.7174 (mmm) REVERT: A 2070 ILE cc_start: 0.7983 (pt) cc_final: 0.7534 (mt) REVERT: A 2095 ILE cc_start: 0.8840 (tp) cc_final: 0.8585 (pt) REVERT: A 2106 ARG cc_start: 0.8393 (tpp-160) cc_final: 0.7947 (tpp-160) REVERT: A 2121 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8098 (mm-30) REVERT: A 2191 MET cc_start: 0.6584 (mmt) cc_final: 0.6292 (mmt) REVERT: A 2219 TRP cc_start: 0.8008 (m100) cc_final: 0.7556 (m100) outliers start: 28 outliers final: 18 residues processed: 213 average time/residue: 0.1449 time to fit residues: 46.5783 Evaluate side-chains 204 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1697 GLU Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 2045 LEU Chi-restraints excluded: chain A residue 2062 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 55 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 195 optimal weight: 4.9990 chunk 10 optimal weight: 0.0040 chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN A1678 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.081416 restraints weight = 35892.320| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.39 r_work: 0.2952 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19052 Z= 0.133 Angle : 0.502 7.171 25889 Z= 0.265 Chirality : 0.041 0.155 2919 Planarity : 0.003 0.041 3112 Dihedral : 11.876 89.295 3028 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 1.56 % Allowed : 10.79 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.19), residues: 2136 helix: 1.54 (0.16), residues: 1116 sheet: -0.23 (0.38), residues: 189 loop : -1.48 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 17 TYR 0.021 0.001 TYR A1696 PHE 0.009 0.001 PHE A 210 TRP 0.009 0.001 TRP A 395 HIS 0.005 0.001 HIS A1739 Details of bonding type rmsd covalent geometry : bond 0.00303 (19049) covalent geometry : angle 0.50187 (25889) hydrogen bonds : bond 0.03608 ( 891) hydrogen bonds : angle 3.99888 ( 2558) metal coordination : bond 0.00301 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8378 (m-30) cc_final: 0.8096 (m-30) REVERT: A 416 LYS cc_start: 0.8728 (tptt) cc_final: 0.8308 (mptt) REVERT: A 696 ASP cc_start: 0.8614 (m-30) cc_final: 0.8386 (m-30) REVERT: A 765 ASP cc_start: 0.8421 (t70) cc_final: 0.8146 (t0) REVERT: A 954 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7972 (p) REVERT: A 1424 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.7005 (ttm-80) REVERT: A 1470 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9015 (pp) REVERT: A 1492 LYS cc_start: 0.8551 (mptt) cc_final: 0.7980 (pttt) REVERT: A 1697 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 1768 PHE cc_start: 0.8646 (m-80) cc_final: 0.8417 (m-80) REVERT: A 1829 ARG cc_start: 0.8355 (mpp80) cc_final: 0.7993 (mmt-90) REVERT: A 1839 MET cc_start: 0.7676 (mmm) cc_final: 0.7188 (mmm) REVERT: A 1983 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7249 (mm) REVERT: A 2070 ILE cc_start: 0.8006 (pt) cc_final: 0.7589 (mm) REVERT: A 2106 ARG cc_start: 0.8409 (tpp-160) cc_final: 0.7959 (tpp-160) REVERT: A 2108 MET cc_start: 0.7853 (mtp) cc_final: 0.7541 (mtm) REVERT: A 2219 TRP cc_start: 0.7965 (m100) cc_final: 0.7567 (m100) outliers start: 31 outliers final: 19 residues processed: 215 average time/residue: 0.1465 time to fit residues: 47.8115 Evaluate side-chains 210 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1697 GLU Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2045 LEU Chi-restraints excluded: chain A residue 2062 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 187 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 173 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN A1678 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.116307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082773 restraints weight = 35586.839| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.39 r_work: 0.2979 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19052 Z= 0.106 Angle : 0.487 7.929 25889 Z= 0.256 Chirality : 0.040 0.144 2919 Planarity : 0.003 0.040 3112 Dihedral : 11.825 88.696 3028 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 1.56 % Allowed : 10.69 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.19), residues: 2136 helix: 1.64 (0.16), residues: 1118 sheet: -0.12 (0.38), residues: 189 loop : -1.42 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 17 TYR 0.019 0.001 TYR A1696 PHE 0.010 0.001 PHE A 948 TRP 0.011 0.001 TRP A1143 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00234 (19049) covalent geometry : angle 0.48653 (25889) hydrogen bonds : bond 0.03393 ( 891) hydrogen bonds : angle 3.91607 ( 2558) metal coordination : bond 0.00155 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8330 (m-30) cc_final: 0.8051 (m-30) REVERT: A 355 ASP cc_start: 0.8820 (p0) cc_final: 0.8430 (p0) REVERT: A 416 LYS cc_start: 0.8710 (tptt) cc_final: 0.8306 (mptt) REVERT: A 672 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8627 (mp0) REVERT: A 762 VAL cc_start: 0.8813 (m) cc_final: 0.8588 (p) REVERT: A 765 ASP cc_start: 0.8377 (t70) cc_final: 0.8113 (t0) REVERT: A 936 MET cc_start: 0.9228 (tpp) cc_final: 0.8946 (tpp) REVERT: A 954 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7995 (p) REVERT: A 1017 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8585 (mmm-85) REVERT: A 1492 LYS cc_start: 0.8539 (mptt) cc_final: 0.7970 (pttt) REVERT: A 1697 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 1720 ASP cc_start: 0.8973 (m-30) cc_final: 0.8735 (m-30) REVERT: A 1768 PHE cc_start: 0.8561 (m-80) cc_final: 0.8361 (m-80) REVERT: A 1829 ARG cc_start: 0.8273 (mpp80) cc_final: 0.7960 (mmt-90) REVERT: A 1839 MET cc_start: 0.7604 (mmm) cc_final: 0.7125 (mmm) REVERT: A 1915 MET cc_start: 0.6815 (tpt) cc_final: 0.6613 (mmt) REVERT: A 1983 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.6922 (mm) REVERT: A 2022 GLU cc_start: 0.8346 (tp30) cc_final: 0.7734 (tm-30) REVERT: A 2070 ILE cc_start: 0.7953 (pt) cc_final: 0.7524 (mt) REVERT: A 2106 ARG cc_start: 0.8396 (tpp-160) cc_final: 0.7892 (tpp-160) REVERT: A 2108 MET cc_start: 0.7902 (mtp) cc_final: 0.7672 (mtp) REVERT: A 2191 MET cc_start: 0.6503 (mmm) cc_final: 0.6234 (mmm) REVERT: A 2219 TRP cc_start: 0.7933 (m100) cc_final: 0.7566 (m100) outliers start: 31 outliers final: 20 residues processed: 229 average time/residue: 0.1556 time to fit residues: 54.1937 Evaluate side-chains 214 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1697 GLU Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2032 ASP Chi-restraints excluded: chain A residue 2062 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 86 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN A1678 GLN A2107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.115445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081663 restraints weight = 35687.404| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.40 r_work: 0.2958 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19052 Z= 0.139 Angle : 0.510 8.831 25889 Z= 0.267 Chirality : 0.041 0.154 2919 Planarity : 0.003 0.040 3112 Dihedral : 11.821 88.818 3028 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.78 % Favored : 95.18 % Rotamer: Outliers : 1.56 % Allowed : 11.14 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.19), residues: 2136 helix: 1.69 (0.16), residues: 1111 sheet: -0.07 (0.38), residues: 189 loop : -1.41 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 17 TYR 0.018 0.001 TYR A1696 PHE 0.009 0.001 PHE A1768 TRP 0.010 0.001 TRP A 395 HIS 0.005 0.001 HIS A1739 Details of bonding type rmsd covalent geometry : bond 0.00320 (19049) covalent geometry : angle 0.51032 (25889) hydrogen bonds : bond 0.03594 ( 891) hydrogen bonds : angle 3.96881 ( 2558) metal coordination : bond 0.00276 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8305 (m-30) cc_final: 0.8035 (m-30) REVERT: A 355 ASP cc_start: 0.8815 (p0) cc_final: 0.8433 (p0) REVERT: A 416 LYS cc_start: 0.8736 (tptt) cc_final: 0.8314 (mptt) REVERT: A 672 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8604 (mp0) REVERT: A 762 VAL cc_start: 0.8828 (m) cc_final: 0.8602 (p) REVERT: A 765 ASP cc_start: 0.8371 (t70) cc_final: 0.8108 (t0) REVERT: A 936 MET cc_start: 0.9268 (tpp) cc_final: 0.8967 (tpp) REVERT: A 954 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7995 (p) REVERT: A 1409 MET cc_start: 0.8267 (mtt) cc_final: 0.7935 (mtt) REVERT: A 1492 LYS cc_start: 0.8549 (mptt) cc_final: 0.7986 (pttt) REVERT: A 1697 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: A 1720 ASP cc_start: 0.8993 (m-30) cc_final: 0.8754 (m-30) REVERT: A 1768 PHE cc_start: 0.8634 (m-80) cc_final: 0.8408 (m-80) REVERT: A 1829 ARG cc_start: 0.8320 (mpp80) cc_final: 0.7984 (mmt-90) REVERT: A 1839 MET cc_start: 0.7647 (mmm) cc_final: 0.7169 (mmm) REVERT: A 1983 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7446 (mm) REVERT: A 2022 GLU cc_start: 0.8388 (tp30) cc_final: 0.7804 (tm-30) REVERT: A 2070 ILE cc_start: 0.7969 (pt) cc_final: 0.7555 (mm) REVERT: A 2106 ARG cc_start: 0.8428 (tpp-160) cc_final: 0.7904 (tpp-160) REVERT: A 2191 MET cc_start: 0.6514 (mmm) cc_final: 0.6227 (mmm) REVERT: A 2219 TRP cc_start: 0.7946 (m100) cc_final: 0.7551 (m100) outliers start: 31 outliers final: 22 residues processed: 215 average time/residue: 0.1692 time to fit residues: 55.0015 Evaluate side-chains 214 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1697 GLU Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2032 ASP Chi-restraints excluded: chain A residue 2045 LEU Chi-restraints excluded: chain A residue 2062 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 172 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 196 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN A1678 GLN A2107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.117543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.083137 restraints weight = 35379.995| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.42 r_work: 0.2985 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19052 Z= 0.106 Angle : 0.497 9.071 25889 Z= 0.261 Chirality : 0.040 0.152 2919 Planarity : 0.003 0.040 3112 Dihedral : 11.789 88.804 3028 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 1.51 % Allowed : 11.30 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.19), residues: 2136 helix: 1.77 (0.16), residues: 1107 sheet: -0.02 (0.38), residues: 189 loop : -1.36 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 17 TYR 0.018 0.001 TYR A1696 PHE 0.012 0.001 PHE A 948 TRP 0.011 0.001 TRP A2160 HIS 0.004 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00237 (19049) covalent geometry : angle 0.49721 (25889) hydrogen bonds : bond 0.03365 ( 891) hydrogen bonds : angle 3.89741 ( 2558) metal coordination : bond 0.00187 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.8318 (m-30) cc_final: 0.8068 (m-30) REVERT: A 355 ASP cc_start: 0.8850 (p0) cc_final: 0.8457 (p0) REVERT: A 416 LYS cc_start: 0.8646 (tptt) cc_final: 0.8214 (mptt) REVERT: A 602 GLN cc_start: 0.9049 (tp40) cc_final: 0.8816 (tt0) REVERT: A 672 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8583 (mp0) REVERT: A 762 VAL cc_start: 0.8720 (m) cc_final: 0.8499 (p) REVERT: A 765 ASP cc_start: 0.8365 (t70) cc_final: 0.8099 (t0) REVERT: A 936 MET cc_start: 0.9270 (tpp) cc_final: 0.8964 (tpp) REVERT: A 954 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7943 (p) REVERT: A 1017 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.8531 (mmm-85) REVERT: A 1409 MET cc_start: 0.8198 (mtt) cc_final: 0.7866 (mtt) REVERT: A 1424 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6823 (ttm-80) REVERT: A 1492 LYS cc_start: 0.8482 (mptt) cc_final: 0.7894 (pttt) REVERT: A 1697 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: A 1720 ASP cc_start: 0.8998 (m-30) cc_final: 0.8735 (m-30) REVERT: A 1829 ARG cc_start: 0.8380 (mpp80) cc_final: 0.7956 (mmt-90) REVERT: A 1835 LYS cc_start: 0.9156 (tppt) cc_final: 0.8922 (tppt) REVERT: A 1839 MET cc_start: 0.7574 (mmm) cc_final: 0.7073 (mmm) REVERT: A 1983 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7336 (mm) REVERT: A 2022 GLU cc_start: 0.8313 (tp30) cc_final: 0.7708 (tm-30) REVERT: A 2070 ILE cc_start: 0.7932 (pt) cc_final: 0.7510 (mt) REVERT: A 2106 ARG cc_start: 0.8360 (tpp-160) cc_final: 0.7904 (tpp-160) REVERT: A 2108 MET cc_start: 0.8017 (mtp) cc_final: 0.7575 (mtm) REVERT: A 2191 MET cc_start: 0.6651 (mmm) cc_final: 0.6230 (mmm) REVERT: A 2219 TRP cc_start: 0.7867 (m100) cc_final: 0.7498 (m100) outliers start: 30 outliers final: 22 residues processed: 223 average time/residue: 0.1612 time to fit residues: 54.3495 Evaluate side-chains 218 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1470 LEU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1697 GLU Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1771 ILE Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1960 ARG Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2016 SER Chi-restraints excluded: chain A residue 2045 LEU Chi-restraints excluded: chain A residue 2062 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 79 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN A1678 GLN A1954 HIS A2107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.082141 restraints weight = 35536.374| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.37 r_work: 0.2973 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19052 Z= 0.126 Angle : 0.504 8.771 25889 Z= 0.264 Chirality : 0.040 0.158 2919 Planarity : 0.003 0.040 3112 Dihedral : 11.786 88.826 3028 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.41 % Rotamer: Outliers : 1.51 % Allowed : 11.60 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.19), residues: 2136 helix: 1.81 (0.16), residues: 1107 sheet: -0.01 (0.39), residues: 189 loop : -1.36 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 17 TYR 0.018 0.001 TYR A1696 PHE 0.025 0.001 PHE A2058 TRP 0.010 0.001 TRP A2160 HIS 0.005 0.001 HIS A1739 Details of bonding type rmsd covalent geometry : bond 0.00287 (19049) covalent geometry : angle 0.50398 (25889) hydrogen bonds : bond 0.03484 ( 891) hydrogen bonds : angle 3.93199 ( 2558) metal coordination : bond 0.00249 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5901.09 seconds wall clock time: 101 minutes 57.81 seconds (6117.81 seconds total)