Starting phenix.real_space_refine on Sat Jul 4 05:39:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7orj_13039/07_2026/7orj_13039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7orj_13039/07_2026/7orj_13039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7orj_13039/07_2026/7orj_13039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7orj_13039/07_2026/7orj_13039.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7orj_13039/07_2026/7orj_13039.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7orj_13039/07_2026/7orj_13039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7orj_13039/07_2026/7orj_13039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7orj_13039/07_2026/7orj_13039.map" } resolution = 3.9 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= 0.001 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 41 5.49 5 S 110 5.16 5 C 11475 2.51 5 N 3043 2.21 5 O 3527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18197 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2129, 17369 Classifications: {'peptide': 2129} Link IDs: {'PTRANS': 71, 'TRANS': 2057} Chain breaks: 8 Chain: "H" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 365 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "T" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 357 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 11} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GTG': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p_pur': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16054 SG CYS A2064 60.445 21.986 41.983 1.00 82.98 S Time building chain proxies: 2.99, per 1000 atoms: 0.16 Number of scatterers: 18197 At special positions: 0 Unit cell: (114.5, 130.53, 151.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 110 16.00 P 41 15.00 O 3527 8.00 N 3043 7.00 C 11475 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 654.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2064 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2169 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2182 " 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 16 sheets defined 56.7% alpha, 10.5% beta 8 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 18 through 46 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 98 through 121 removed outlier: 4.421A pdb=" N SER A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.621A pdb=" N LEU A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.584A pdb=" N TRP A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.510A pdb=" N ASP A 300 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 301 " --> pdb=" O LEU A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 301' Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 356 through 371 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: 6.640A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 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 620 Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 626 through 639 Processing helix chain 'A' and resid 642 through 661 removed outlier: 4.095A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.540A 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 701 removed outlier: 4.544A pdb=" N TYR A 698 " --> pdb=" O CYS A 694 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP A 699 " --> pdb=" O PHE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 704 No H-bonds generated for 'chain 'A' and resid 702 through 704' Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 748 through 751 removed outlier: 3.578A pdb=" N PHE A 751 " --> pdb=" O PRO A 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 751' Processing helix chain 'A' and resid 758 through 781 removed outlier: 4.454A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 814 removed outlier: 3.627A pdb=" N SER A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 4.214A 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 838 removed outlier: 5.864A pdb=" N SER A 835 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 836 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 900 removed outlier: 3.792A pdb=" N MET A 900 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 4.039A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 980 removed outlier: 4.046A pdb=" N GLU A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1030 removed outlier: 3.847A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE A1023 " --> pdb=" O LYS A1019 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1048 Processing helix chain 'A' and resid 1070 through 1079 removed outlier: 3.999A pdb=" N PHE A1074 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 3.670A 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 1128 Processing helix chain 'A' and resid 1148 through 1173 Processing helix chain 'A' and resid 1201 through 1220 removed outlier: 3.580A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1262 removed outlier: 3.789A pdb=" N LEU A1256 " --> pdb=" O TYR A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1285 Processing helix chain 'A' and resid 1288 through 1307 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 1364 Processing helix chain 'A' and resid 1366 through 1370 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 1404 Processing helix chain 'A' and resid 1434 through 1440 removed outlier: 3.914A pdb=" N LYS A1440 " --> pdb=" O GLY A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1452 removed outlier: 3.569A pdb=" N SER A1445 " --> pdb=" O LEU A1441 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A1446 " --> pdb=" O TYR A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1467 Processing helix chain 'A' and resid 1468 through 1473 removed outlier: 4.409A pdb=" N VAL A1472 " --> pdb=" O PRO A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1489 Processing helix chain 'A' and resid 1493 through 1498 Processing helix chain 'A' and resid 1502 through 1513 removed outlier: 3.965A pdb=" N GLN A1510 " --> pdb=" O LEU A1506 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A1511 " --> pdb=" O PHE A1507 " (cutoff:3.500A) 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 1633 Processing helix chain 'A' and resid 1641 through 1659 removed outlier: 3.859A pdb=" N ARG A1647 " --> pdb=" O THR A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1677 Processing helix chain 'A' and resid 1680 through 1703 removed outlier: 3.655A pdb=" N THR A1702 " --> pdb=" O TYR A1698 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A1703 " --> pdb=" O VAL A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1728 Processing helix chain 'A' and resid 1760 through 1779 removed outlier: 3.864A pdb=" N HIS A1773 " --> pdb=" O LYS A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1795 removed outlier: 4.681A pdb=" N SER A1785 " --> pdb=" O SER A1781 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA A1786 " --> pdb=" O LEU A1782 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1812 Processing helix chain 'A' and resid 1813 through 1817 removed outlier: 4.484A pdb=" N THR A1816 " --> pdb=" O TYR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1826 Processing helix chain 'A' and resid 1829 through 1839 Processing helix chain 'A' and resid 1892 through 1905 Processing helix chain 'A' and resid 1944 through 1955 Processing helix chain 'A' and resid 1983 through 1991 removed outlier: 3.696A pdb=" N LEU A1987 " --> pdb=" O LEU A1983 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP A1988 " --> pdb=" O ILE A1984 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR A1989 " --> pdb=" O ARG A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2019 removed outlier: 4.192A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2039 Processing helix chain 'A' and resid 2040 through 2043 Processing helix chain 'A' and resid 2046 through 2052 Processing helix chain 'A' and resid 2055 through 2062 Processing helix chain 'A' and resid 2070 through 2075 removed outlier: 3.541A pdb=" N LEU A2074 " --> pdb=" O ILE A2070 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A2075 " --> pdb=" O ASN A2071 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2070 through 2075' Processing helix chain 'A' and resid 2109 through 2129 removed outlier: 4.107A pdb=" N LYS A2123 " --> pdb=" O GLU A2119 " (cutoff:3.500A) Processing helix chain 'A' and resid 2138 through 2155 removed outlier: 3.678A pdb=" N CYS A2144 " --> pdb=" O GLU A2140 " (cutoff:3.500A) Processing helix chain 'A' and resid 2161 through 2175 Processing helix chain 'A' and resid 2177 through 2181 Processing helix chain 'A' and resid 2200 through 2211 removed outlier: 4.261A pdb=" N PHE A2204 " --> pdb=" O ASN A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2218 through 2237 removed outlier: 4.115A pdb=" N MET A2222 " --> pdb=" O PRO A2218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.454A pdb=" N LEU A 88 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL A 127 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE A 90 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 129 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP A 92 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE A 131 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 7.044A 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 387 removed outlier: 3.760A pdb=" N VAL A 393 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 586 " --> pdb=" O CYS A 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 387 removed outlier: 3.760A pdb=" N VAL A 393 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 663 through 664 removed outlier: 3.587A pdb=" N SER A 663 " --> pdb=" O VAL A1231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 716 through 718 removed outlier: 6.190A pdb=" N TYR A 710 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 709 " --> pdb=" O TYR A2099 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N SER A2101 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N LEU A 711 " --> pdb=" O SER A2101 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A2096 " --> pdb=" O ILE A2090 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A2086 " --> pdb=" O TYR A2100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA8, first strand: chain 'A' and resid 842 through 846 removed outlier: 3.600A pdb=" N THR A 909 " --> pdb=" O CYS A 843 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 959 through 963 removed outlier: 6.419A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A1101 " --> pdb=" O ILE A1139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1235 through 1238 Processing sheet with id=AB2, first strand: chain 'A' and resid 1594 through 1600 removed outlier: 4.768A pdb=" N THR A1737 " --> pdb=" O GLY A1597 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP A1735 " --> pdb=" O PRO A1599 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1606 through 1608 Processing sheet with id=AB4, first strand: chain 'A' and resid 1800 through 1801 Processing sheet with id=AB5, first strand: chain 'A' and resid 1844 through 1847 removed outlier: 3.812A pdb=" N ARG A1870 " --> pdb=" O GLY A1867 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A1883 " --> pdb=" O ILE A1875 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU A1877 " --> pdb=" O LEU A1881 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A1881 " --> pdb=" O GLU A1877 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LYS A1880 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N VAL A1970 " --> pdb=" O LYS A1880 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR A1882 " --> pdb=" O VAL A1970 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASN A1972 " --> pdb=" O THR A1882 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA A1884 " --> pdb=" O ASN A1972 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA A1974 " --> pdb=" O ALA A1884 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A1886 " --> pdb=" O ALA A1974 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR A1929 " --> pdb=" O PRO A1967 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS A1969 " --> pdb=" O ILE A1927 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR A1925 " --> pdb=" O VAL A1971 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A1942 " --> pdb=" O TYR A1926 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1999 through 2000 Processing sheet with id=AB7, first strand: chain 'A' and resid 2027 through 2028 915 hydrogen bonds defined for protein. 2622 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4065 1.33 - 1.45: 4058 1.45 - 1.57: 10259 1.57 - 1.69: 78 1.69 - 1.81: 182 Bond restraints: 18642 Sorted by residual: bond pdb=" C5B GTG P 1 " pdb=" C6B GTG P 1 " ideal model delta sigma weight residual 1.424 1.329 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C5A GTG P 1 " pdb=" C6A GTG P 1 " ideal model delta sigma weight residual 1.427 1.335 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O5D GTG P 1 " pdb=" PA GTG P 1 " ideal model delta sigma weight residual 1.653 1.585 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" N ILE A2062 " pdb=" CA ILE A2062 " ideal model delta sigma weight residual 1.458 1.500 -0.043 1.27e-02 6.20e+03 1.13e+01 bond pdb=" C2E GTG P 1 " pdb=" C3E GTG P 1 " ideal model delta sigma weight residual 1.531 1.466 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 18637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 24637 1.98 - 3.96: 607 3.96 - 5.94: 63 5.94 - 7.92: 19 7.92 - 9.90: 6 Bond angle restraints: 25332 Sorted by residual: angle pdb=" PB ATP A2302 " pdb=" O3B ATP A2302 " pdb=" PG ATP A2302 " ideal model delta sigma weight residual 139.87 132.10 7.77 1.00e+00 1.00e+00 6.04e+01 angle pdb=" PA ATP A2302 " pdb=" O3A ATP A2302 " pdb=" PB ATP A2302 " ideal model delta sigma weight residual 136.83 131.06 5.77 1.00e+00 1.00e+00 3.33e+01 angle pdb=" N ILE A2062 " pdb=" CA ILE A2062 " pdb=" C ILE A2062 " ideal model delta sigma weight residual 109.37 117.05 -7.68 1.35e+00 5.49e-01 3.24e+01 angle pdb=" N MET A1226 " pdb=" CA MET A1226 " pdb=" C MET A1226 " ideal model delta sigma weight residual 111.69 106.04 5.65 1.23e+00 6.61e-01 2.11e+01 angle pdb=" CA GLY A 847 " pdb=" C GLY A 847 " pdb=" O GLY A 847 " ideal model delta sigma weight residual 121.04 117.93 3.11 7.90e-01 1.60e+00 1.55e+01 ... (remaining 25327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.24: 10240 18.24 - 36.48: 871 36.48 - 54.73: 143 54.73 - 72.97: 22 72.97 - 91.21: 17 Dihedral angle restraints: 11293 sinusoidal: 4973 harmonic: 6320 Sorted by residual: dihedral pdb=" O4' C T 21 " pdb=" C1' C T 21 " pdb=" N1 C T 21 " pdb=" C2 C T 21 " ideal model delta sinusoidal sigma weight residual -128.00 -56.50 -71.50 1 1.70e+01 3.46e-03 2.27e+01 dihedral pdb=" CA PHE A2084 " pdb=" C PHE A2084 " pdb=" N THR A2085 " pdb=" CA THR A2085 " ideal model delta harmonic sigma weight residual 180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA MET A1128 " pdb=" C MET A1128 " pdb=" N THR A1129 " pdb=" CA THR A1129 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 11290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2384 0.058 - 0.117: 409 0.117 - 0.175: 42 0.175 - 0.233: 8 0.233 - 0.291: 7 Chirality restraints: 2850 Sorted by residual: chirality pdb=" C4D GTG P 1 " pdb=" C3D GTG P 1 " pdb=" C5D GTG P 1 " pdb=" O4D GTG P 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.81 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA MET A1226 " pdb=" N MET A1226 " pdb=" C MET A1226 " pdb=" CB MET A1226 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA CYS A2063 " pdb=" N CYS A2063 " pdb=" C CYS A2063 " pdb=" CB CYS A2063 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2847 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A1877 " -0.013 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C GLU A1877 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU A1877 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A1878 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A2061 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C LEU A2061 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A2061 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A2062 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1967 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C PRO A1967 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO A1967 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A1968 " 0.011 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1672 2.74 - 3.28: 18555 3.28 - 3.82: 31384 3.82 - 4.36: 37582 4.36 - 4.90: 63551 Nonbonded interactions: 152744 Sorted by model distance: nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2301 " model vdw 2.203 2.230 nonbonded pdb=" OG SER A1443 " pdb=" OH TYR A1489 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR A 504 " pdb=" OD1 ASN A 632 " model vdw 2.237 3.040 nonbonded pdb=" O THR A 790 " pdb=" OG1 THR A 793 " model vdw 2.278 3.040 nonbonded pdb=" O ILE A2056 " pdb=" OG SER A2059 " model vdw 2.307 3.040 ... (remaining 152739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.970 Find NCS groups from input model: 0.070 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.005 0.128 18646 Z= 0.266 Angle : 0.713 9.899 25332 Z= 0.437 Chirality : 0.046 0.291 2850 Planarity : 0.004 0.051 3066 Dihedral : 13.729 91.209 7189 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.71 % Allowed : 0.81 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2111 helix: 1.28 (0.16), residues: 1085 sheet: 0.23 (0.40), residues: 176 loop : -1.43 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1668 TYR 0.015 0.001 TYR A1230 PHE 0.019 0.002 PHE A1220 TRP 0.011 0.001 TRP A1143 HIS 0.004 0.001 HIS A1185 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.26 (18642) covalent geometry : angle 0.71336 / 0.44 (25332) hydrogen bonds : bond 0.16165 / 10.65 ( 923) hydrogen bonds : angle 5.97137 / 4.30 ( 2664) metal coordination : bond 0.10464 / 5.33 ( 3) Misc. bond : bond 0.05879 / 3.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 457 MET cc_start: 0.7939 (tmm) cc_final: 0.7608 (ttp) REVERT: A 625 LEU cc_start: 0.8818 (mt) cc_final: 0.8478 (mt) REVERT: A 995 ASP cc_start: 0.7859 (m-30) cc_final: 0.7609 (m-30) REVERT: A 1025 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7759 (tm-30) REVERT: A 1473 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7663 (p) REVERT: A 1649 LEU cc_start: 0.8886 (mt) cc_final: 0.8675 (mt) outliers start: 14 outliers final: 2 residues processed: 249 average time/residue: 0.1138 time to fit residues: 44.9182 Evaluate side-chains 171 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 1473 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0060 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 GLN A1190 GLN A1233 ASN A1567 ASN A1571 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2054 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.105503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087811 restraints weight = 47821.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089498 restraints weight = 27978.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090543 restraints weight = 19289.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091361 restraints weight = 15056.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091817 restraints weight = 12628.973| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18646 Z= 0.205 Angle : 0.592 8.916 25332 Z= 0.314 Chirality : 0.043 0.164 2850 Planarity : 0.004 0.040 3066 Dihedral : 8.146 78.887 2792 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.81 % Allowed : 7.18 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2111 helix: 1.30 (0.15), residues: 1106 sheet: 0.19 (0.41), residues: 179 loop : -1.50 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1930 TYR 0.015 0.002 TYR A 504 PHE 0.033 0.002 PHE A2084 TRP 0.014 0.001 TRP A2201 HIS 0.009 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (18642) covalent geometry : angle 0.59171 / 0.31 (25332) hydrogen bonds : bond 0.04408 / 2.92 ( 923) hydrogen bonds : angle 4.71413 / 3.41 ( 2664) metal coordination : bond 0.00280 / 0.13 ( 3) Misc. bond : bond 0.00148 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 MET cc_start: 0.8659 (tpp) cc_final: 0.8369 (tpp) REVERT: A 1056 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: A 1099 MET cc_start: 0.8030 (mmm) cc_final: 0.7826 (mmm) REVERT: A 1144 LEU cc_start: 0.8274 (mt) cc_final: 0.7995 (mt) REVERT: A 1309 MET cc_start: 0.7792 (mtt) cc_final: 0.7170 (mtt) REVERT: A 1334 ASN cc_start: 0.8048 (m-40) cc_final: 0.7505 (m-40) REVERT: A 1497 SER cc_start: 0.8655 (p) cc_final: 0.8406 (m) REVERT: A 1649 LEU cc_start: 0.8943 (mt) cc_final: 0.8693 (mt) REVERT: A 1654 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6547 (tp30) outliers start: 16 outliers final: 10 residues processed: 196 average time/residue: 0.1080 time to fit residues: 34.6049 Evaluate side-chains 171 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1688 MET Chi-restraints excluded: chain A residue 1767 CYS Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 33 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 177 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 819 ASN A1743 GLN A2054 ASN A2134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089169 restraints weight = 47973.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.090950 restraints weight = 28081.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092127 restraints weight = 19191.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.092884 restraints weight = 14782.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.093298 restraints weight = 12398.199| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18646 Z= 0.116 Angle : 0.497 8.459 25332 Z= 0.264 Chirality : 0.040 0.161 2850 Planarity : 0.003 0.034 3066 Dihedral : 7.865 81.030 2791 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.17 % Allowed : 10.08 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2111 helix: 1.56 (0.16), residues: 1097 sheet: 0.78 (0.42), residues: 161 loop : -1.46 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1930 TYR 0.012 0.001 TYR A 207 PHE 0.027 0.001 PHE A2084 TRP 0.013 0.001 TRP A1143 HIS 0.007 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (18642) covalent geometry : angle 0.49710 / 0.26 (25332) hydrogen bonds : bond 0.03693 / 2.42 ( 923) hydrogen bonds : angle 4.38936 / 3.18 ( 2664) metal coordination : bond 0.00088 / 0.05 ( 3) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7905 (m90) REVERT: A 504 TYR cc_start: 0.8954 (m-80) cc_final: 0.8731 (m-80) REVERT: A 1056 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: A 1334 ASN cc_start: 0.8080 (m-40) cc_final: 0.7587 (m-40) REVERT: A 1497 SER cc_start: 0.8656 (p) cc_final: 0.8411 (m) REVERT: A 1610 MET cc_start: 0.7752 (tmm) cc_final: 0.7308 (tmm) REVERT: A 1649 LEU cc_start: 0.8952 (mt) cc_final: 0.8750 (mt) REVERT: A 1654 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6634 (tp30) REVERT: A 2228 LYS cc_start: 0.8557 (mmtt) cc_final: 0.7400 (ttmt) outliers start: 23 outliers final: 9 residues processed: 198 average time/residue: 0.1067 time to fit residues: 34.5201 Evaluate side-chains 172 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 2114 ILE Chi-restraints excluded: chain A residue 2199 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1739 HIS ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.087471 restraints weight = 48124.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089194 restraints weight = 28021.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090384 restraints weight = 19190.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091086 restraints weight = 14699.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.091639 restraints weight = 12342.184| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18646 Z= 0.177 Angle : 0.540 9.568 25332 Z= 0.286 Chirality : 0.042 0.175 2850 Planarity : 0.004 0.035 3066 Dihedral : 7.794 86.391 2791 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.48 % Allowed : 11.66 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2111 helix: 1.50 (0.16), residues: 1098 sheet: 0.67 (0.42), residues: 161 loop : -1.53 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1930 TYR 0.014 0.001 TYR A 207 PHE 0.023 0.002 PHE A 751 TRP 0.010 0.001 TRP A2201 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (18642) covalent geometry : angle 0.54004 / 0.29 (25332) hydrogen bonds : bond 0.03885 / 2.57 ( 923) hydrogen bonds : angle 4.40539 / 3.20 ( 2664) metal coordination : bond 0.00315 / 0.16 ( 3) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1025 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7632 (tm-30) REVERT: A 1056 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: A 1144 LEU cc_start: 0.8288 (mt) cc_final: 0.7985 (mt) REVERT: A 1334 ASN cc_start: 0.8079 (m-40) cc_final: 0.7727 (m-40) REVERT: A 1610 MET cc_start: 0.7880 (tmm) cc_final: 0.7280 (tmm) REVERT: A 1649 LEU cc_start: 0.8981 (mt) cc_final: 0.8771 (mt) REVERT: A 1654 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6415 (tp30) outliers start: 29 outliers final: 18 residues processed: 189 average time/residue: 0.1015 time to fit residues: 31.5558 Evaluate side-chains 176 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1688 MET Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2058 PHE Chi-restraints excluded: chain A residue 2084 PHE Chi-restraints excluded: chain A residue 2114 ILE Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2199 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 170 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.106618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089666 restraints weight = 47621.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091217 restraints weight = 27709.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.092193 restraints weight = 18786.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092666 restraints weight = 14697.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.092756 restraints weight = 13791.798| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18646 Z= 0.108 Angle : 0.484 10.791 25332 Z= 0.257 Chirality : 0.040 0.162 2850 Planarity : 0.003 0.032 3066 Dihedral : 7.604 89.554 2791 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.27 % Allowed : 12.63 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 2111 helix: 1.66 (0.16), residues: 1097 sheet: 0.71 (0.42), residues: 161 loop : -1.42 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1930 TYR 0.012 0.001 TYR A 207 PHE 0.022 0.001 PHE A 751 TRP 0.013 0.001 TRP A1143 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (18642) covalent geometry : angle 0.48444 / 0.26 (25332) hydrogen bonds : bond 0.03370 / 2.21 ( 923) hydrogen bonds : angle 4.22127 / 3.06 ( 2664) metal coordination : bond 0.00105 / 0.05 ( 3) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1025 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7753 (tm-30) REVERT: A 1053 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8558 (tp) REVERT: A 1056 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: A 1144 LEU cc_start: 0.8316 (mt) cc_final: 0.7934 (mt) REVERT: A 1610 MET cc_start: 0.7781 (tmm) cc_final: 0.7099 (tmm) REVERT: A 1654 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6449 (tp30) REVERT: A 2184 PHE cc_start: 0.4321 (m-10) cc_final: 0.3926 (m-80) outliers start: 25 outliers final: 15 residues processed: 191 average time/residue: 0.1017 time to fit residues: 31.9042 Evaluate side-chains 173 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1645 MET Chi-restraints excluded: chain A residue 1688 MET Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 2114 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 131 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 132 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 718 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.107377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089800 restraints weight = 47491.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091574 restraints weight = 27831.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.092753 restraints weight = 18937.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093514 restraints weight = 14524.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.093919 restraints weight = 12192.906| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18646 Z= 0.099 Angle : 0.476 11.407 25332 Z= 0.250 Chirality : 0.040 0.176 2850 Planarity : 0.003 0.032 3066 Dihedral : 7.480 89.566 2791 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.32 % Allowed : 13.29 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2111 helix: 1.76 (0.16), residues: 1099 sheet: 0.75 (0.41), residues: 161 loop : -1.37 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1930 TYR 0.013 0.001 TYR A1269 PHE 0.021 0.001 PHE A 751 TRP 0.013 0.001 TRP A1143 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (18642) covalent geometry : angle 0.47588 / 0.25 (25332) hydrogen bonds : bond 0.03179 / 2.10 ( 923) hydrogen bonds : angle 4.11206 / 2.98 ( 2664) metal coordination : bond 0.00318 / 0.16 ( 3) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.5375 (ptp) cc_final: 0.4743 (pmm) REVERT: A 969 MET cc_start: 0.7745 (mtm) cc_final: 0.7527 (mtp) REVERT: A 1053 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8477 (tp) REVERT: A 1056 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: A 1099 MET cc_start: 0.8058 (mmm) cc_final: 0.7845 (mmm) REVERT: A 1144 LEU cc_start: 0.8291 (mt) cc_final: 0.7908 (mt) REVERT: A 1334 ASN cc_start: 0.8017 (m-40) cc_final: 0.7662 (m-40) REVERT: A 1610 MET cc_start: 0.7882 (tmm) cc_final: 0.7184 (tmm) REVERT: A 2018 MET cc_start: 0.8309 (mmm) cc_final: 0.8045 (tpp) REVERT: A 2228 LYS cc_start: 0.8554 (mmtt) cc_final: 0.7363 (ttmt) outliers start: 26 outliers final: 14 residues processed: 196 average time/residue: 0.1089 time to fit residues: 35.0339 Evaluate side-chains 176 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1645 MET Chi-restraints excluded: chain A residue 1688 MET Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 84 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 152 optimal weight: 0.0970 chunk 113 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.106133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089293 restraints weight = 48099.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090933 restraints weight = 28045.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.091718 restraints weight = 18829.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.092453 restraints weight = 14758.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.092515 restraints weight = 14279.418| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18646 Z= 0.141 Angle : 0.509 12.297 25332 Z= 0.267 Chirality : 0.041 0.189 2850 Planarity : 0.003 0.032 3066 Dihedral : 7.506 89.432 2791 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.17 % Allowed : 13.70 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 2111 helix: 1.73 (0.16), residues: 1098 sheet: 0.66 (0.41), residues: 161 loop : -1.36 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1930 TYR 0.013 0.001 TYR A 207 PHE 0.023 0.001 PHE A 751 TRP 0.010 0.001 TRP A1143 HIS 0.004 0.001 HIS A1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (18642) covalent geometry : angle 0.50912 / 0.27 (25332) hydrogen bonds : bond 0.03407 / 2.25 ( 923) hydrogen bonds : angle 4.15788 / 3.01 ( 2664) metal coordination : bond 0.00152 / 0.08 ( 3) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.5425 (ptp) cc_final: 0.4682 (pmm) REVERT: A 1025 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 1053 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8528 (tp) REVERT: A 1056 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: A 1144 LEU cc_start: 0.8351 (mt) cc_final: 0.7944 (mt) REVERT: A 1605 MET cc_start: 0.8703 (mmm) cc_final: 0.8329 (mmm) outliers start: 23 outliers final: 15 residues processed: 179 average time/residue: 0.0989 time to fit residues: 29.1166 Evaluate side-chains 172 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1406 ASP Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1688 MET Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 2055 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 206 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 174 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 chunk 92 optimal weight: 0.0060 chunk 147 optimal weight: 0.5980 chunk 200 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 117 optimal weight: 0.0070 chunk 94 optimal weight: 0.7980 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A1334 ASN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.107760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.090365 restraints weight = 47751.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.092138 restraints weight = 27719.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.093328 restraints weight = 18825.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094083 restraints weight = 14400.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.094496 restraints weight = 12023.556| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18646 Z= 0.098 Angle : 0.488 12.676 25332 Z= 0.256 Chirality : 0.040 0.190 2850 Planarity : 0.003 0.037 3066 Dihedral : 7.412 87.267 2791 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.07 % Allowed : 13.75 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2111 helix: 1.83 (0.16), residues: 1098 sheet: 0.74 (0.42), residues: 161 loop : -1.29 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1930 TYR 0.014 0.001 TYR A 504 PHE 0.023 0.001 PHE A 751 TRP 0.014 0.001 TRP A1143 HIS 0.004 0.001 HIS A1591 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (18642) covalent geometry : angle 0.48809 / 0.26 (25332) hydrogen bonds : bond 0.03086 / 2.03 ( 923) hydrogen bonds : angle 4.07379 / 2.95 ( 2664) metal coordination : bond 0.00301 / 0.15 ( 3) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.5266 (ptp) cc_final: 0.4558 (pmm) REVERT: A 1053 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8494 (tp) REVERT: A 1056 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: A 1099 MET cc_start: 0.7842 (mmm) cc_final: 0.7576 (mmm) REVERT: A 1144 LEU cc_start: 0.8304 (mt) cc_final: 0.7890 (mt) REVERT: A 1160 MET cc_start: 0.7966 (ttm) cc_final: 0.7680 (ttm) REVERT: A 2018 MET cc_start: 0.8610 (mmm) cc_final: 0.8332 (tpp) REVERT: A 2228 LYS cc_start: 0.8575 (mmtt) cc_final: 0.7456 (ttmt) outliers start: 21 outliers final: 14 residues processed: 189 average time/residue: 0.1082 time to fit residues: 33.2222 Evaluate side-chains 177 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1334 ASN Chi-restraints excluded: chain A residue 1406 ASP Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 2055 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 101 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 0.0470 chunk 165 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.107411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.090082 restraints weight = 47558.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.091845 restraints weight = 27576.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.093004 restraints weight = 18698.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.093644 restraints weight = 14340.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094219 restraints weight = 12158.894| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18646 Z= 0.106 Angle : 0.495 13.020 25332 Z= 0.258 Chirality : 0.040 0.200 2850 Planarity : 0.003 0.040 3066 Dihedral : 7.372 87.128 2791 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.02 % Allowed : 13.75 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2111 helix: 1.82 (0.16), residues: 1098 sheet: 0.72 (0.41), residues: 161 loop : -1.28 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1930 TYR 0.016 0.001 TYR A 504 PHE 0.029 0.001 PHE A1111 TRP 0.012 0.001 TRP A1143 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (18642) covalent geometry : angle 0.49548 / 0.26 (25332) hydrogen bonds : bond 0.03091 / 2.04 ( 923) hydrogen bonds : angle 4.05377 / 2.94 ( 2664) metal coordination : bond 0.00353 / 0.18 ( 3) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1053 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8445 (tp) REVERT: A 1056 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: A 1144 LEU cc_start: 0.8333 (mt) cc_final: 0.7939 (mt) REVERT: A 1160 MET cc_start: 0.7990 (ttm) cc_final: 0.7659 (ttm) REVERT: A 2018 MET cc_start: 0.8614 (mmm) cc_final: 0.8326 (tpp) REVERT: A 2184 PHE cc_start: 0.4205 (m-10) cc_final: 0.3943 (m-80) outliers start: 20 outliers final: 17 residues processed: 176 average time/residue: 0.1133 time to fit residues: 32.5933 Evaluate side-chains 177 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1406 ASP Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1688 MET Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2058 PHE Chi-restraints excluded: chain A residue 2216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 149 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 117 optimal weight: 0.0670 chunk 59 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 153 optimal weight: 0.4980 chunk 121 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.090926 restraints weight = 47608.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.092691 restraints weight = 27327.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.093867 restraints weight = 18486.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094657 restraints weight = 14076.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095080 restraints weight = 11725.285| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18646 Z= 0.096 Angle : 0.494 13.107 25332 Z= 0.255 Chirality : 0.039 0.198 2850 Planarity : 0.003 0.040 3066 Dihedral : 7.250 85.626 2791 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.02 % Allowed : 14.00 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2111 helix: 1.86 (0.16), residues: 1100 sheet: 0.75 (0.41), residues: 161 loop : -1.21 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1930 TYR 0.017 0.001 TYR A 504 PHE 0.023 0.001 PHE A 751 TRP 0.013 0.001 TRP A1143 HIS 0.004 0.001 HIS A1591 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (18642) covalent geometry : angle 0.49401 / 0.26 (25332) hydrogen bonds : bond 0.02964 / 1.96 ( 923) hydrogen bonds : angle 3.99658 / 2.90 ( 2664) metal coordination : bond 0.00298 / 0.15 ( 3) Misc. bond : bond 0.00036 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.5353 (m-80) cc_final: 0.5098 (m-80) REVERT: A 1053 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8396 (tp) REVERT: A 1056 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8428 (pm20) REVERT: A 1144 LEU cc_start: 0.8313 (mt) cc_final: 0.7902 (mt) REVERT: A 1160 MET cc_start: 0.8016 (ttm) cc_final: 0.7667 (ttm) REVERT: A 1344 ILE cc_start: 0.9195 (mt) cc_final: 0.8898 (tp) REVERT: A 1421 MET cc_start: 0.7813 (ptm) cc_final: 0.7512 (ptm) REVERT: A 2018 MET cc_start: 0.8625 (mmm) cc_final: 0.8326 (tpp) REVERT: A 2184 PHE cc_start: 0.4337 (m-10) cc_final: 0.4053 (m-80) outliers start: 20 outliers final: 16 residues processed: 191 average time/residue: 0.1068 time to fit residues: 33.1527 Evaluate side-chains 186 residues out of total 1964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1406 ASP Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1938 VAL Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2058 PHE Chi-restraints excluded: chain A residue 2216 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 161 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 156 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 0.0170 chunk 201 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 139 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 ASN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.108468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091256 restraints weight = 47551.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093067 restraints weight = 27692.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094252 restraints weight = 18532.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.094997 restraints weight = 14106.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.095421 restraints weight = 11812.668| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18646 Z= 0.095 Angle : 0.488 13.273 25332 Z= 0.254 Chirality : 0.040 0.204 2850 Planarity : 0.003 0.040 3066 Dihedral : 7.176 85.017 2791 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.02 % Allowed : 14.36 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2111 helix: 1.85 (0.16), residues: 1107 sheet: 0.80 (0.41), residues: 161 loop : -1.18 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1815 TYR 0.017 0.001 TYR A 504 PHE 0.024 0.001 PHE A 751 TRP 0.013 0.001 TRP A1143 HIS 0.005 0.001 HIS A1591 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (18642) covalent geometry : angle 0.48849 / 0.25 (25332) hydrogen bonds : bond 0.02932 / 1.94 ( 923) hydrogen bonds : angle 3.99496 / 2.89 ( 2664) metal coordination : bond 0.00315 / 0.16 ( 3) Misc. bond : bond 0.00033 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2356.06 seconds wall clock time: 41 minutes 56.31 seconds (2516.31 seconds total)