Starting phenix.real_space_refine on Sat Jan 18 19:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvv_38720/01_2025/8xvv_38720.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvv_38720/01_2025/8xvv_38720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xvv_38720/01_2025/8xvv_38720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvv_38720/01_2025/8xvv_38720.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvv_38720/01_2025/8xvv_38720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvv_38720/01_2025/8xvv_38720.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.008 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 P 6 5.49 5 S 199 5.16 5 C 18790 2.51 5 N 5084 2.21 5 O 5292 1.98 5 H 29886 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 59257 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2684 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 16, 'TRANS': 149} Chain breaks: 3 Chain: "L" Number of atoms: 56537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3485, 56519 Classifications: {'peptide': 3485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 155, 'TRANS': 3329} Chain breaks: 16 Conformer: "B" Number of residues, atoms: 3485, 56519 Classifications: {'peptide': 3485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 155, 'TRANS': 3329} Chain breaks: 16 bond proxies already assigned to first conformer: 57091 Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS L 982 " occ=0.50 ... (32 atoms not shown) pdb=" HE2BHIS L 982 " occ=0.50 Time building chain proxies: 38.56, per 1000 atoms: 0.65 Number of scatterers: 59257 At special positions: 0 Unit cell: (185.426, 165.416, 138.736, 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) S 199 16.00 P 6 15.00 O 5292 8.00 N 5084 7.00 C 18790 6.00 H 29886 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.05 Conformation dependent library (CDL) restraints added in 6.4 seconds 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7066 Finding SS restraints... Secondary structure from input PDB file: 219 helices and 4 sheets defined 76.1% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'H' and resid 2333 through 2346 Processing helix chain 'H' and resid 2364 through 2373 Processing helix chain 'H' and resid 2382 through 2398 removed outlier: 4.137A pdb=" N ASN H2387 " --> pdb=" O LYS H2383 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU H2390 " --> pdb=" O ARG H2386 " (cutoff:3.500A) Proline residue: H2395 - end of helix Processing helix chain 'H' and resid 2408 through 2415 Processing helix chain 'H' and resid 2419 through 2440 removed outlier: 3.532A pdb=" N SER H2440 " --> pdb=" O ALA H2436 " (cutoff:3.500A) Processing helix chain 'H' and resid 2456 through 2466 removed outlier: 3.733A pdb=" N LEU H2462 " --> pdb=" O HIS H2458 " (cutoff:3.500A) Processing helix chain 'H' and resid 2474 through 2491 Processing helix chain 'L' and resid 20 through 27 Processing helix chain 'L' and resid 36 through 51 Processing helix chain 'L' and resid 54 through 57 Processing helix chain 'L' and resid 58 through 75 removed outlier: 3.998A pdb=" N LEU L 62 " --> pdb=" O TYR L 58 " (cutoff:3.500A) Proline residue: L 67 - end of helix removed outlier: 4.127A pdb=" N ASP L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 100 removed outlier: 4.044A pdb=" N GLN L 88 " --> pdb=" O LYS L 84 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE L 100 " --> pdb=" O ILE L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 119 removed outlier: 3.927A pdb=" N PHE L 118 " --> pdb=" O LEU L 114 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG L 119 " --> pdb=" O SER L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 140 Processing helix chain 'L' and resid 141 through 143 No H-bonds generated for 'chain 'L' and resid 141 through 143' Processing helix chain 'L' and resid 144 through 146 No H-bonds generated for 'chain 'L' and resid 144 through 146' Processing helix chain 'L' and resid 147 through 172 Proline residue: L 166 - end of helix Processing helix chain 'L' and resid 213 through 228 removed outlier: 3.826A pdb=" N ARG L 217 " --> pdb=" O SER L 213 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU L 228 " --> pdb=" O VAL L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 244 removed outlier: 3.627A pdb=" N GLN L 237 " --> pdb=" O VAL L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 294 Processing helix chain 'L' and resid 295 through 299 Processing helix chain 'L' and resid 306 through 320 Processing helix chain 'L' and resid 324 through 339 Processing helix chain 'L' and resid 341 through 346 removed outlier: 3.726A pdb=" N GLN L 346 " --> pdb=" O GLU L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 355 Processing helix chain 'L' and resid 371 through 386 removed outlier: 3.544A pdb=" N ALA L 375 " --> pdb=" O LEU L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 390 removed outlier: 3.712A pdb=" N LEU L 390 " --> pdb=" O ARG L 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 387 through 390' Processing helix chain 'L' and resid 391 through 407 removed outlier: 3.795A pdb=" N LYS L 404 " --> pdb=" O GLN L 400 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN L 405 " --> pdb=" O LEU L 401 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP L 407 " --> pdb=" O ALA L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 434 removed outlier: 3.591A pdb=" N GLN L 416 " --> pdb=" O PRO L 412 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP L 428 " --> pdb=" O LEU L 424 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS L 429 " --> pdb=" O ASN L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 469 removed outlier: 4.226A pdb=" N VAL L 444 " --> pdb=" O ASN L 440 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU L 464 " --> pdb=" O ALA L 460 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER L 465 " --> pdb=" O ARG L 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 535 through 565 removed outlier: 3.616A pdb=" N LYS L 551 " --> pdb=" O ARG L 547 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR L 565 " --> pdb=" O THR L 561 " (cutoff:3.500A) Processing helix chain 'L' and resid 582 through 600 removed outlier: 4.145A pdb=" N GLN L 598 " --> pdb=" O LYS L 594 " (cutoff:3.500A) Processing helix chain 'L' and resid 601 through 603 No H-bonds generated for 'chain 'L' and resid 601 through 603' Processing helix chain 'L' and resid 623 through 627 Processing helix chain 'L' and resid 628 through 641 removed outlier: 3.928A pdb=" N PHE L 639 " --> pdb=" O PHE L 635 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET L 641 " --> pdb=" O GLY L 637 " (cutoff:3.500A) Processing helix chain 'L' and resid 643 through 665 removed outlier: 3.648A pdb=" N GLU L 649 " --> pdb=" O LEU L 645 " (cutoff:3.500A) Proline residue: L 656 - end of helix Processing helix chain 'L' and resid 668 through 678 removed outlier: 3.918A pdb=" N ALA L 672 " --> pdb=" O LEU L 668 " (cutoff:3.500A) Processing helix chain 'L' and resid 681 through 694 Processing helix chain 'L' and resid 696 through 701 Processing helix chain 'L' and resid 704 through 724 Processing helix chain 'L' and resid 724 through 747 removed outlier: 5.105A pdb=" N GLN L 730 " --> pdb=" O ALA L 726 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N MET L 731 " --> pdb=" O GLU L 727 " (cutoff:3.500A) Proline residue: L 734 - end of helix removed outlier: 4.524A pdb=" N HIS L 737 " --> pdb=" O LYS L 733 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS L 738 " --> pdb=" O PRO L 734 " (cutoff:3.500A) Processing helix chain 'L' and resid 748 through 750 No H-bonds generated for 'chain 'L' and resid 748 through 750' Processing helix chain 'L' and resid 754 through 769 Processing helix chain 'L' and resid 774 through 780 removed outlier: 4.222A pdb=" N GLU L 778 " --> pdb=" O LEU L 774 " (cutoff:3.500A) Processing helix chain 'L' and resid 782 through 796 removed outlier: 3.949A pdb=" N GLN L 788 " --> pdb=" O PRO L 784 " (cutoff:3.500A) Processing helix chain 'L' and resid 799 through 812 Processing helix chain 'L' and resid 820 through 826 Proline residue: L 825 - end of helix Processing helix chain 'L' and resid 827 through 836 removed outlier: 3.517A pdb=" N SER L 833 " --> pdb=" O ASP L 829 " (cutoff:3.500A) Processing helix chain 'L' and resid 838 through 855 Processing helix chain 'L' and resid 857 through 866 Processing helix chain 'L' and resid 869 through 880 Processing helix chain 'L' and resid 884 through 899 removed outlier: 3.629A pdb=" N GLY L 899 " --> pdb=" O LEU L 895 " (cutoff:3.500A) Processing helix chain 'L' and resid 900 through 904 removed outlier: 3.573A pdb=" N LYS L 904 " --> pdb=" O SER L 901 " (cutoff:3.500A) Processing helix chain 'L' and resid 939 through 952 Processing helix chain 'L' and resid 956 through 974 Processing helix chain 'L' and resid 980 through 989 Processing helix chain 'L' and resid 990 through 996 removed outlier: 4.217A pdb=" N THR L 994 " --> pdb=" O HIS L 990 " (cutoff:3.500A) Processing helix chain 'L' and resid 1012 through 1029 Processing helix chain 'L' and resid 1034 through 1058 Proline residue: L1040 - end of helix Processing helix chain 'L' and resid 1073 through 1077 removed outlier: 3.542A pdb=" N MET L1076 " --> pdb=" O SER L1073 " (cutoff:3.500A) Processing helix chain 'L' and resid 1090 through 1101 removed outlier: 3.747A pdb=" N ASP L1094 " --> pdb=" O LEU L1090 " (cutoff:3.500A) Processing helix chain 'L' and resid 1106 through 1127 removed outlier: 4.446A pdb=" N ILE L1110 " --> pdb=" O GLU L1106 " (cutoff:3.500A) Processing helix chain 'L' and resid 1128 through 1133 removed outlier: 3.631A pdb=" N ALA L1132 " --> pdb=" O SER L1128 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS L1133 " --> pdb=" O LYS L1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1128 through 1133' Processing helix chain 'L' and resid 1135 through 1148 removed outlier: 3.578A pdb=" N SER L1139 " --> pdb=" O LEU L1135 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS L1148 " --> pdb=" O ARG L1144 " (cutoff:3.500A) Processing helix chain 'L' and resid 1149 through 1151 No H-bonds generated for 'chain 'L' and resid 1149 through 1151' Processing helix chain 'L' and resid 1153 through 1171 removed outlier: 3.602A pdb=" N LYS L1157 " --> pdb=" O ALA L1153 " (cutoff:3.500A) Processing helix chain 'L' and resid 1172 through 1195 removed outlier: 4.390A pdb=" N GLN L1178 " --> pdb=" O THR L1174 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN L1179 " --> pdb=" O TRP L1175 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN L1181 " --> pdb=" O LEU L1177 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR L1182 " --> pdb=" O GLN L1178 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET L1191 " --> pdb=" O LEU L1187 " (cutoff:3.500A) Processing helix chain 'L' and resid 1201 through 1218 Processing helix chain 'L' and resid 1227 through 1250 removed outlier: 4.324A pdb=" N THR L1250 " --> pdb=" O VAL L1246 " (cutoff:3.500A) Processing helix chain 'L' and resid 1253 through 1271 Processing helix chain 'L' and resid 1274 through 1280 Processing helix chain 'L' and resid 1281 through 1287 removed outlier: 4.182A pdb=" N GLU L1284 " --> pdb=" O PRO L1281 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN L1287 " --> pdb=" O GLU L1284 " (cutoff:3.500A) Processing helix chain 'L' and resid 1296 through 1300 Processing helix chain 'L' and resid 1301 through 1316 Processing helix chain 'L' and resid 1329 through 1345 Processing helix chain 'L' and resid 1346 through 1351 Processing helix chain 'L' and resid 1353 through 1358 removed outlier: 4.199A pdb=" N SER L1358 " --> pdb=" O PRO L1354 " (cutoff:3.500A) Processing helix chain 'L' and resid 1362 through 1375 removed outlier: 3.591A pdb=" N ARG L1366 " --> pdb=" O LEU L1362 " (cutoff:3.500A) Processing helix chain 'L' and resid 1379 through 1382 Processing helix chain 'L' and resid 1383 through 1395 Processing helix chain 'L' and resid 1398 through 1413 Processing helix chain 'L' and resid 1419 through 1428 Processing helix chain 'L' and resid 1436 through 1440 Processing helix chain 'L' and resid 1441 through 1455 Processing helix chain 'L' and resid 1456 through 1459 removed outlier: 4.049A pdb=" N PHE L1459 " --> pdb=" O PRO L1456 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1456 through 1459' Processing helix chain 'L' and resid 1460 through 1485 Processing helix chain 'L' and resid 1493 through 1506 removed outlier: 3.921A pdb=" N PHE L1503 " --> pdb=" O ILE L1499 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS L1504 " --> pdb=" O ILE L1500 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU L1505 " --> pdb=" O ASN L1501 " (cutoff:3.500A) Processing helix chain 'L' and resid 1510 through 1512 No H-bonds generated for 'chain 'L' and resid 1510 through 1512' Processing helix chain 'L' and resid 1513 through 1529 Processing helix chain 'L' and resid 1536 through 1545 Processing helix chain 'L' and resid 1547 through 1557 removed outlier: 3.625A pdb=" N MET L1557 " --> pdb=" O GLU L1553 " (cutoff:3.500A) Processing helix chain 'L' and resid 1557 through 1563 removed outlier: 3.820A pdb=" N ASP L1563 " --> pdb=" O ALA L1559 " (cutoff:3.500A) Processing helix chain 'L' and resid 1563 through 1576 Processing helix chain 'L' and resid 1579 through 1588 removed outlier: 3.810A pdb=" N LEU L1586 " --> pdb=" O LEU L1582 " (cutoff:3.500A) Processing helix chain 'L' and resid 1590 through 1595 removed outlier: 3.931A pdb=" N ILE L1594 " --> pdb=" O PRO L1590 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR L1595 " --> pdb=" O ASN L1591 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1590 through 1595' Processing helix chain 'L' and resid 1618 through 1636 removed outlier: 4.137A pdb=" N PHE L1622 " --> pdb=" O LEU L1618 " (cutoff:3.500A) Processing helix chain 'L' and resid 1642 through 1655 removed outlier: 3.767A pdb=" N GLN L1648 " --> pdb=" O SER L1644 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG L1651 " --> pdb=" O SER L1647 " (cutoff:3.500A) Processing helix chain 'L' and resid 1655 through 1665 removed outlier: 4.389A pdb=" N GLU L1665 " --> pdb=" O ARG L1661 " (cutoff:3.500A) Processing helix chain 'L' and resid 1673 through 1687 Processing helix chain 'L' and resid 1691 through 1698 Processing helix chain 'L' and resid 1699 through 1701 No H-bonds generated for 'chain 'L' and resid 1699 through 1701' Processing helix chain 'L' and resid 1709 through 1721 removed outlier: 4.735A pdb=" N PHE L1713 " --> pdb=" O CYS L1709 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU L1714 " --> pdb=" O ASN L1710 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR L1717 " --> pdb=" O PHE L1713 " (cutoff:3.500A) Processing helix chain 'L' and resid 1721 through 1726 removed outlier: 3.711A pdb=" N ASN L1725 " --> pdb=" O GLU L1721 " (cutoff:3.500A) Processing helix chain 'L' and resid 1730 through 1741 Processing helix chain 'L' and resid 1741 through 1749 removed outlier: 3.843A pdb=" N ASP L1748 " --> pdb=" O PRO L1744 " (cutoff:3.500A) Processing helix chain 'L' and resid 1751 through 1756 Processing helix chain 'L' and resid 1758 through 1769 removed outlier: 3.886A pdb=" N ALA L1762 " --> pdb=" O ILE L1758 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR L1765 " --> pdb=" O PRO L1761 " (cutoff:3.500A) Processing helix chain 'L' and resid 1785 through 1796 removed outlier: 3.867A pdb=" N ILE L1789 " --> pdb=" O ASN L1785 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE L1793 " --> pdb=" O ILE L1789 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE L1794 " --> pdb=" O THR L1790 " (cutoff:3.500A) Processing helix chain 'L' and resid 1799 through 1803 Processing helix chain 'L' and resid 1809 through 1824 Processing helix chain 'L' and resid 1827 through 1836 removed outlier: 4.680A pdb=" N ASN L1833 " --> pdb=" O ILE L1829 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS L1834 " --> pdb=" O HIS L1830 " (cutoff:3.500A) Processing helix chain 'L' and resid 1842 through 1853 Proline residue: L1849 - end of helix Processing helix chain 'L' and resid 1858 through 1876 removed outlier: 3.531A pdb=" N LYS L1875 " --> pdb=" O HIS L1871 " (cutoff:3.500A) Processing helix chain 'L' and resid 1881 through 1894 removed outlier: 3.810A pdb=" N GLN L1885 " --> pdb=" O LYS L1881 " (cutoff:3.500A) Processing helix chain 'L' and resid 1898 through 1910 Processing helix chain 'L' and resid 1911 through 1916 removed outlier: 3.942A pdb=" N ALA L1915 " --> pdb=" O PRO L1911 " (cutoff:3.500A) Processing helix chain 'L' and resid 1917 through 1919 No H-bonds generated for 'chain 'L' and resid 1917 through 1919' Processing helix chain 'L' and resid 1920 through 1934 Processing helix chain 'L' and resid 1939 through 1953 Processing helix chain 'L' and resid 1954 through 1957 removed outlier: 3.634A pdb=" N TYR L1957 " --> pdb=" O LYS L1954 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1954 through 1957' Processing helix chain 'L' and resid 1960 through 1962 No H-bonds generated for 'chain 'L' and resid 1960 through 1962' Processing helix chain 'L' and resid 1963 through 1977 removed outlier: 4.050A pdb=" N MET L1967 " --> pdb=" O LEU L1963 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE L1976 " --> pdb=" O GLN L1972 " (cutoff:3.500A) Processing helix chain 'L' and resid 1982 through 2004 removed outlier: 3.815A pdb=" N ARG L1986 " --> pdb=" O ILE L1982 " (cutoff:3.500A) Processing helix chain 'L' and resid 2072 through 2088 Processing helix chain 'L' and resid 2089 through 2094 removed outlier: 3.666A pdb=" N ASN L2093 " --> pdb=" O GLN L2089 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR L2094 " --> pdb=" O VAL L2090 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2089 through 2094' Processing helix chain 'L' and resid 2101 through 2116 removed outlier: 3.716A pdb=" N SER L2105 " --> pdb=" O GLY L2101 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU L2116 " --> pdb=" O LEU L2112 " (cutoff:3.500A) Processing helix chain 'L' and resid 2120 through 2124 removed outlier: 3.992A pdb=" N LYS L2123 " --> pdb=" O MET L2120 " (cutoff:3.500A) Processing helix chain 'L' and resid 2127 through 2137 Processing helix chain 'L' and resid 2138 through 2140 No H-bonds generated for 'chain 'L' and resid 2138 through 2140' Processing helix chain 'L' and resid 2146 through 2165 Processing helix chain 'L' and resid 2166 through 2171 Processing helix chain 'L' and resid 2172 through 2183 removed outlier: 4.081A pdb=" N ARG L2177 " --> pdb=" O LYS L2173 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY L2178 " --> pdb=" O PRO L2174 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA L2180 " --> pdb=" O GLN L2176 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA L2181 " --> pdb=" O ARG L2177 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N CYS L2182 " --> pdb=" O GLY L2178 " (cutoff:3.500A) Processing helix chain 'L' and resid 2190 through 2195 Processing helix chain 'L' and resid 2197 through 2202 Processing helix chain 'L' and resid 2211 through 2215 removed outlier: 3.623A pdb=" N VAL L2214 " --> pdb=" O THR L2211 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA L2215 " --> pdb=" O SER L2212 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2211 through 2215' Processing helix chain 'L' and resid 2223 through 2232 removed outlier: 3.610A pdb=" N VAL L2228 " --> pdb=" O LEU L2224 " (cutoff:3.500A) Processing helix chain 'L' and resid 2232 through 2239 removed outlier: 4.040A pdb=" N LEU L2236 " --> pdb=" O ILE L2232 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR L2239 " --> pdb=" O GLY L2235 " (cutoff:3.500A) Processing helix chain 'L' and resid 2247 through 2261 Processing helix chain 'L' and resid 2268 through 2285 removed outlier: 3.842A pdb=" N ILE L2272 " --> pdb=" O ILE L2268 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L2274 " --> pdb=" O ARG L2270 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG L2277 " --> pdb=" O SER L2273 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER L2278 " --> pdb=" O VAL L2274 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU L2279 " --> pdb=" O PHE L2275 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN L2280 " --> pdb=" O MET L2276 " (cutoff:3.500A) Processing helix chain 'L' and resid 2302 through 2315 Processing helix chain 'L' and resid 2324 through 2336 Processing helix chain 'L' and resid 2342 through 2359 removed outlier: 4.013A pdb=" N LEU L2346 " --> pdb=" O ASP L2342 " (cutoff:3.500A) Processing helix chain 'L' and resid 2370 through 2389 removed outlier: 4.756A pdb=" N GLU L2386 " --> pdb=" O MET L2382 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS L2387 " --> pdb=" O THR L2383 " (cutoff:3.500A) Processing helix chain 'L' and resid 2392 through 2409 removed outlier: 3.686A pdb=" N ASN L2396 " --> pdb=" O ASP L2392 " (cutoff:3.500A) Processing helix chain 'L' and resid 2416 through 2421 removed outlier: 4.386A pdb=" N LYS L2420 " --> pdb=" O GLU L2416 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU L2421 " --> pdb=" O LEU L2417 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2416 through 2421' Processing helix chain 'L' and resid 2421 through 2431 Processing helix chain 'L' and resid 2433 through 2447 removed outlier: 3.821A pdb=" N VAL L2443 " --> pdb=" O LYS L2439 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN L2446 " --> pdb=" O GLU L2442 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER L2447 " --> pdb=" O VAL L2443 " (cutoff:3.500A) Processing helix chain 'L' and resid 2451 through 2462 Processing helix chain 'L' and resid 2473 through 2484 removed outlier: 3.679A pdb=" N VAL L2484 " --> pdb=" O LEU L2480 " (cutoff:3.500A) Processing helix chain 'L' and resid 2495 through 2499 Processing helix chain 'L' and resid 2502 through 2508 removed outlier: 4.207A pdb=" N VAL L2506 " --> pdb=" O ILE L2503 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN L2508 " --> pdb=" O ASN L2505 " (cutoff:3.500A) Processing helix chain 'L' and resid 2511 through 2519 removed outlier: 4.243A pdb=" N ARG L2515 " --> pdb=" O ASP L2511 " (cutoff:3.500A) Processing helix chain 'L' and resid 2568 through 2585 removed outlier: 3.654A pdb=" N LEU L2573 " --> pdb=" O GLN L2569 " (cutoff:3.500A) Processing helix chain 'L' and resid 2586 through 2588 No H-bonds generated for 'chain 'L' and resid 2586 through 2588' Processing helix chain 'L' and resid 2589 through 2603 removed outlier: 3.513A pdb=" N SER L2594 " --> pdb=" O GLY L2590 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA L2595 " --> pdb=" O ALA L2591 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE L2602 " --> pdb=" O GLN L2598 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER L2603 " --> pdb=" O LEU L2599 " (cutoff:3.500A) Processing helix chain 'L' and resid 2607 through 2622 Proline residue: L2616 - end of helix removed outlier: 3.565A pdb=" N ILE L2621 " --> pdb=" O ARG L2617 " (cutoff:3.500A) Processing helix chain 'L' and resid 2623 through 2640 removed outlier: 3.600A pdb=" N ALA L2629 " --> pdb=" O ARG L2625 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER L2635 " --> pdb=" O ALA L2631 " (cutoff:3.500A) Proline residue: L2636 - end of helix Processing helix chain 'L' and resid 2644 through 2649 removed outlier: 3.751A pdb=" N ASP L2648 " --> pdb=" O VAL L2645 " (cutoff:3.500A) Processing helix chain 'L' and resid 2652 through 2663 Processing helix chain 'L' and resid 2671 through 2682 Processing helix chain 'L' and resid 2684 through 2697 Processing helix chain 'L' and resid 2723 through 2737 removed outlier: 4.252A pdb=" N LEU L2727 " --> pdb=" O GLN L2723 " (cutoff:3.500A) Processing helix chain 'L' and resid 2739 through 2751 Processing helix chain 'L' and resid 2753 through 2765 removed outlier: 3.999A pdb=" N ALA L2757 " --> pdb=" O TYR L2753 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR L2758 " --> pdb=" O SER L2754 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS L2765 " --> pdb=" O ALA L2761 " (cutoff:3.500A) Processing helix chain 'L' and resid 2767 through 2789 Processing helix chain 'L' and resid 2792 through 2794 No H-bonds generated for 'chain 'L' and resid 2792 through 2794' Processing helix chain 'L' and resid 2795 through 2813 Processing helix chain 'L' and resid 2815 through 2824 Processing helix chain 'L' and resid 2830 through 2839 removed outlier: 4.651A pdb=" N TRP L2839 " --> pdb=" O LEU L2835 " (cutoff:3.500A) Processing helix chain 'L' and resid 2840 through 2842 No H-bonds generated for 'chain 'L' and resid 2840 through 2842' Processing helix chain 'L' and resid 2843 through 2855 Processing helix chain 'L' and resid 2859 through 2861 No H-bonds generated for 'chain 'L' and resid 2859 through 2861' Processing helix chain 'L' and resid 2862 through 2877 Processing helix chain 'L' and resid 2886 through 2903 Processing helix chain 'L' and resid 2909 through 2911 No H-bonds generated for 'chain 'L' and resid 2909 through 2911' Processing helix chain 'L' and resid 2912 through 2936 removed outlier: 4.077A pdb=" N GLN L2920 " --> pdb=" O LEU L2916 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN L2921 " --> pdb=" O GLN L2917 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN L2930 " --> pdb=" O GLN L2926 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN L2936 " --> pdb=" O ASN L2932 " (cutoff:3.500A) Processing helix chain 'L' and resid 2942 through 2959 removed outlier: 3.573A pdb=" N ASP L2948 " --> pdb=" O ASN L2944 " (cutoff:3.500A) Processing helix chain 'L' and resid 2966 through 2988 removed outlier: 3.708A pdb=" N TRP L2976 " --> pdb=" O SER L2972 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS L2980 " --> pdb=" O TRP L2976 " (cutoff:3.500A) Processing helix chain 'L' and resid 2999 through 3022 Processing helix chain 'L' and resid 3025 through 3036 Processing helix chain 'L' and resid 3042 through 3060 removed outlier: 3.527A pdb=" N CYS L3046 " --> pdb=" O PRO L3042 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN L3048 " --> pdb=" O VAL L3044 " (cutoff:3.500A) Processing helix chain 'L' and resid 3065 through 3079 removed outlier: 3.684A pdb=" N THR L3079 " --> pdb=" O VAL L3075 " (cutoff:3.500A) Processing helix chain 'L' and resid 3086 through 3103 removed outlier: 3.796A pdb=" N ILE L3103 " --> pdb=" O PHE L3099 " (cutoff:3.500A) Processing helix chain 'L' and resid 3107 through 3120 Processing helix chain 'L' and resid 3123 through 3142 removed outlier: 3.563A pdb=" N TRP L3127 " --> pdb=" O LEU L3123 " (cutoff:3.500A) Processing helix chain 'L' and resid 3143 through 3160 removed outlier: 3.726A pdb=" N GLY L3147 " --> pdb=" O GLN L3143 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL L3148 " --> pdb=" O LEU L3144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER L3149 " --> pdb=" O HIS L3145 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS L3160 " --> pdb=" O HIS L3156 " (cutoff:3.500A) Processing helix chain 'L' and resid 3162 through 3177 removed outlier: 4.991A pdb=" N LYS L3168 " --> pdb=" O SER L3164 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR L3169 " --> pdb=" O LYS L3165 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L3177 " --> pdb=" O VAL L3173 " (cutoff:3.500A) Processing helix chain 'L' and resid 3178 through 3180 No H-bonds generated for 'chain 'L' and resid 3178 through 3180' Processing helix chain 'L' and resid 3184 through 3193 Processing helix chain 'L' and resid 3198 through 3204 removed outlier: 3.591A pdb=" N GLN L3201 " --> pdb=" O PRO L3198 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA L3204 " --> pdb=" O GLN L3201 " (cutoff:3.500A) Processing helix chain 'L' and resid 3205 through 3213 removed outlier: 3.689A pdb=" N CYS L3212 " --> pdb=" O GLN L3208 " (cutoff:3.500A) Processing helix chain 'L' and resid 3217 through 3230 removed outlier: 3.680A pdb=" N LEU L3221 " --> pdb=" O GLU L3217 " (cutoff:3.500A) Processing helix chain 'L' and resid 3232 through 3255 removed outlier: 3.512A pdb=" N VAL L3236 " --> pdb=" O TYR L3232 " (cutoff:3.500A) Proline residue: L3239 - end of helix Processing helix chain 'L' and resid 3265 through 3282 removed outlier: 3.716A pdb=" N ILE L3274 " --> pdb=" O ARG L3270 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET L3275 " --> pdb=" O CYS L3271 " (cutoff:3.500A) Processing helix chain 'L' and resid 3282 through 3296 Processing helix chain 'L' and resid 3297 through 3300 Processing helix chain 'L' and resid 3302 through 3327 removed outlier: 3.682A pdb=" N GLU L3306 " --> pdb=" O ASN L3302 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU L3324 " --> pdb=" O SER L3320 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY L3327 " --> pdb=" O PHE L3323 " (cutoff:3.500A) Processing helix chain 'L' and resid 3335 through 3349 Processing helix chain 'L' and resid 3366 through 3379 Processing helix chain 'L' and resid 3381 through 3393 removed outlier: 3.766A pdb=" N GLN L3385 " --> pdb=" O ASP L3381 " (cutoff:3.500A) Processing helix chain 'L' and resid 3404 through 3423 Processing helix chain 'L' and resid 3433 through 3435 No H-bonds generated for 'chain 'L' and resid 3433 through 3435' Processing helix chain 'L' and resid 3436 through 3441 Processing helix chain 'L' and resid 3506 through 3528 removed outlier: 3.720A pdb=" N ARG L3511 " --> pdb=" O LEU L3507 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG L3515 " --> pdb=" O ARG L3511 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL L3516 " --> pdb=" O ARG L3512 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU L3517 " --> pdb=" O GLU L3513 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN L3518 " --> pdb=" O GLU L3514 " (cutoff:3.500A) Proline residue: L3525 - end of helix removed outlier: 3.607A pdb=" N GLU L3528 " --> pdb=" O ASN L3524 " (cutoff:3.500A) Processing helix chain 'L' and resid 3564 through 3576 Processing helix chain 'L' and resid 3580 through 3595 Processing helix chain 'L' and resid 3601 through 3616 Processing helix chain 'L' and resid 3620 through 3630 Processing helix chain 'L' and resid 3632 through 3657 Processing helix chain 'L' and resid 3703 through 3710 Processing helix chain 'L' and resid 3717 through 3732 removed outlier: 3.619A pdb=" N GLN L3732 " --> pdb=" O ARG L3728 " (cutoff:3.500A) Processing helix chain 'L' and resid 3733 through 3735 No H-bonds generated for 'chain 'L' and resid 3733 through 3735' Processing helix chain 'L' and resid 3736 through 3759 removed outlier: 3.882A pdb=" N ILE L3740 " --> pdb=" O LYS L3736 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP L3747 " --> pdb=" O THR L3743 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP L3752 " --> pdb=" O GLU L3748 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP L3759 " --> pdb=" O LYS L3755 " (cutoff:3.500A) Processing helix chain 'L' and resid 3776 through 3798 removed outlier: 3.550A pdb=" N ALA L3788 " --> pdb=" O LYS L3784 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE L3789 " --> pdb=" O ALA L3785 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG L3792 " --> pdb=" O ALA L3788 " (cutoff:3.500A) Processing helix chain 'L' and resid 3799 through 3803 removed outlier: 3.831A pdb=" N GLY L3802 " --> pdb=" O PHE L3799 " (cutoff:3.500A) Processing helix chain 'L' and resid 3804 through 3814 removed outlier: 4.434A pdb=" N THR L3808 " --> pdb=" O SER L3804 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN L3814 " --> pdb=" O VAL L3810 " (cutoff:3.500A) Processing helix chain 'L' and resid 3815 through 3820 Processing helix chain 'L' and resid 3821 through 3822 No H-bonds generated for 'chain 'L' and resid 3821 through 3822' Processing helix chain 'L' and resid 3823 through 3827 Processing sheet with id=AA1, first strand: chain 'L' and resid 605 through 607 Processing sheet with id=AA2, first strand: chain 'L' and resid 923 through 928 Processing sheet with id=AA3, first strand: chain 'L' and resid 3429 through 3431 removed outlier: 6.794A pdb=" N MET L3471 " --> pdb=" O ARG L3490 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ARG L3490 " --> pdb=" O MET L3471 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG L3473 " --> pdb=" O TYR L3488 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR L3488 " --> pdb=" O ARG L3473 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ALA L3483 " --> pdb=" O ASN L3503 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN L3503 " --> pdb=" O ALA L3483 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG L3485 " --> pdb=" O VAL L3501 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 3561 through 3563 1757 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.32 Time building geometry restraints manager: 15.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 29809 1.01 - 1.21: 77 1.21 - 1.41: 11969 1.41 - 1.61: 17704 1.61 - 1.81: 322 Bond restraints: 59881 Sorted by residual: bond pdb=" SG CYS L3526 " pdb=" HG CYS L3526 " ideal model delta sigma weight residual 1.200 1.332 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" NE ARG L3530 " pdb=" HE ARG L3530 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" O15 IHP L3901 " pdb=" P5 IHP L3901 " ideal model delta sigma weight residual 1.675 1.589 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" NZ LYS L3055 " pdb=" HZ3 LYS L3055 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" NZ LYS L3529 " pdb=" HZ2 LYS L3529 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 59876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 107662 1.73 - 3.47: 778 3.47 - 5.20: 114 5.20 - 6.93: 5 6.93 - 8.67: 5 Bond angle restraints: 108564 Sorted by residual: angle pdb=" N ILE L 361 " pdb=" CA ILE L 361 " pdb=" C ILE L 361 " ideal model delta sigma weight residual 111.62 108.12 3.50 7.90e-01 1.60e+00 1.96e+01 angle pdb=" C LYS L3165 " pdb=" CA LYS L3165 " pdb=" CB LYS L3165 " ideal model delta sigma weight residual 110.85 103.89 6.96 1.70e+00 3.46e-01 1.68e+01 angle pdb=" O GLU L3163 " pdb=" C GLU L3163 " pdb=" N SER L3164 " ideal model delta sigma weight residual 122.27 117.68 4.59 1.23e+00 6.61e-01 1.39e+01 angle pdb=" N VAL L1290 " pdb=" CA VAL L1290 " pdb=" C VAL L1290 " ideal model delta sigma weight residual 112.35 108.09 4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CA GLU L3163 " pdb=" C GLU L3163 " pdb=" N SER L3164 " ideal model delta sigma weight residual 117.72 122.31 -4.59 1.31e+00 5.83e-01 1.23e+01 ... (remaining 108559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 27048 29.86 - 59.71: 942 59.71 - 89.57: 86 89.57 - 119.43: 9 119.43 - 149.28: 5 Dihedral angle restraints: 28090 sinusoidal: 15460 harmonic: 12630 Sorted by residual: dihedral pdb=" C6 IHP L3901 " pdb=" C1 IHP L3901 " pdb=" C2 IHP L3901 " pdb=" O12 IHP L3901 " ideal model delta sinusoidal sigma weight residual 61.05 -88.23 149.28 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" CA LEU H2354 " pdb=" C LEU H2354 " pdb=" N THR H2355 " pdb=" CA THR H2355 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA GLN L1319 " pdb=" C GLN L1319 " pdb=" N PRO L1320 " pdb=" CA PRO L1320 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 28087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.977: 4635 0.977 - 1.954: 0 1.954 - 2.931: 0 2.931 - 3.908: 0 3.908 - 4.885: 4 Chirality restraints: 4639 Sorted by residual: chirality pdb=" C2 IHP L3901 " pdb=" C1 IHP L3901 " pdb=" C3 IHP L3901 " pdb=" O12 IHP L3901 " both_signs ideal model delta sigma weight residual False -2.52 2.37 -4.89 2.00e-01 2.50e+01 5.97e+02 chirality pdb=" C1 IHP L3901 " pdb=" C2 IHP L3901 " pdb=" C6 IHP L3901 " pdb=" O11 IHP L3901 " both_signs ideal model delta sigma weight residual False 2.32 -2.40 4.72 2.00e-01 2.50e+01 5.56e+02 chirality pdb=" C3 IHP L3901 " pdb=" C2 IHP L3901 " pdb=" C4 IHP L3901 " pdb=" O13 IHP L3901 " both_signs ideal model delta sigma weight residual False -2.34 2.29 -4.63 2.00e-01 2.50e+01 5.35e+02 ... (remaining 4636 not shown) Planarity restraints: 8599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L3530 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" N LYS L3531 " 0.038 2.00e-02 2.50e+03 pdb=" CA LYS L3531 " -0.010 2.00e-02 2.50e+03 pdb=" H LYS L3531 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L1957 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO L1958 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO L1958 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L1958 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 357 " 0.010 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" N SER L 358 " -0.030 2.00e-02 2.50e+03 pdb=" CA SER L 358 " 0.007 2.00e-02 2.50e+03 pdb=" H SER L 358 " 0.013 2.00e-02 2.50e+03 ... (remaining 8596 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 1366 2.12 - 2.74: 107537 2.74 - 3.36: 175368 3.36 - 3.98: 210028 3.98 - 4.60: 336770 Nonbonded interactions: 831069 Sorted by model distance: nonbonded pdb=" HB3 SER L 663 " pdb="HD11 LEU L 709 " model vdw 1.499 2.440 nonbonded pdb=" O ALA L2607 " pdb=" HG1 THR L2610 " model vdw 1.583 2.450 nonbonded pdb=" HA GLU L1719 " pdb="HD12 LEU L1764 " model vdw 1.586 2.440 nonbonded pdb=" O SER L1128 " pdb=" H ARG L1131 " model vdw 1.590 2.450 nonbonded pdb=" O ASN L2187 " pdb=" H VAL L2190 " model vdw 1.601 2.450 ... (remaining 831064 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.950 Extract box with map and model: 1.980 Check model and map are aligned: 0.360 Set scattering table: 0.460 Process input model: 128.280 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5391 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 : 0.002 0.086 29995 Z= 0.158 Angle : 0.516 8.667 40616 Z= 0.299 Chirality : 0.142 4.885 4639 Planarity : 0.003 0.050 5136 Dihedral : 13.989 149.282 11303 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.25 % Allowed : 9.16 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.13), residues: 3612 helix: -0.62 (0.10), residues: 2421 sheet: -1.31 (0.63), residues: 66 loop : -2.19 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L1848 HIS 0.004 0.000 HIS L2513 PHE 0.015 0.001 PHE L 651 TYR 0.008 0.001 TYR H2389 ARG 0.002 0.000 ARG L3241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 759 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 433 LYS cc_start: 0.6945 (ttpt) cc_final: 0.6686 (ttmt) REVERT: L 447 ARG cc_start: 0.7631 (mmm160) cc_final: 0.7267 (tpp-160) REVERT: L 806 PHE cc_start: 0.7066 (m-10) cc_final: 0.6790 (m-10) REVERT: L 854 ASP cc_start: 0.8278 (m-30) cc_final: 0.7929 (m-30) REVERT: L 855 ASN cc_start: 0.8391 (m-40) cc_final: 0.8093 (m110) REVERT: L 968 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7696 (tttp) REVERT: L 974 MET cc_start: 0.8295 (tpt) cc_final: 0.7616 (mmt) REVERT: L 1468 MET cc_start: 0.8733 (mmm) cc_final: 0.8445 (tpp) REVERT: L 1598 LEU cc_start: 0.6133 (tt) cc_final: 0.5882 (mt) REVERT: L 2306 VAL cc_start: 0.6552 (t) cc_final: 0.6339 (t) REVERT: L 2312 LEU cc_start: 0.8227 (tp) cc_final: 0.7900 (tp) REVERT: L 2324 MET cc_start: 0.6274 (tmm) cc_final: 0.5807 (ttp) REVERT: L 2899 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7358 (ttp-110) REVERT: L 3050 ILE cc_start: 0.8693 (mm) cc_final: 0.8457 (mt) REVERT: L 3106 SER cc_start: 0.7048 (p) cc_final: 0.6642 (m) REVERT: L 3255 TYR cc_start: 0.6518 (m-80) cc_final: 0.6316 (m-80) REVERT: L 3294 ASP cc_start: 0.7304 (m-30) cc_final: 0.7029 (m-30) REVERT: L 3298 TRP cc_start: 0.8182 (m100) cc_final: 0.7879 (m100) REVERT: L 3580 ASP cc_start: 0.7041 (t0) cc_final: 0.6563 (t0) outliers start: 8 outliers final: 4 residues processed: 765 average time/residue: 0.9382 time to fit residues: 1093.6667 Evaluate side-chains 455 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 451 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 368 ARG Chi-restraints excluded: chain L residue 1707 PHE Chi-restraints excluded: chain L residue 3166 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 2.9990 chunk 275 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 285 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 330 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H2384 GLN H2387 ASN H2428 HIS L 51 ASN L 598 GLN L 619 ASN L 621 GLN L 864 HIS L1056 GLN L1057 GLN L1259 GLN L1269 GLN L1371 ASN L1671 ASN L1710 ASN L1835 ASN L2164 GLN L2650 GLN L2800 GLN L2912 HIS L3295 GLN L3406 HIS L3492 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.166754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133076 restraints weight = 141334.295| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.67 r_work: 0.3409 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29995 Z= 0.289 Angle : 0.627 13.122 40616 Z= 0.320 Chirality : 0.041 0.668 4639 Planarity : 0.005 0.056 5136 Dihedral : 5.511 78.373 3974 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.53 % Allowed : 12.47 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3612 helix: 0.21 (0.10), residues: 2461 sheet: -0.93 (0.69), residues: 56 loop : -1.87 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L2747 HIS 0.009 0.001 HIS L 385 PHE 0.025 0.002 PHE L1735 TYR 0.018 0.002 TYR L3193 ARG 0.007 0.001 ARG L 344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 471 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 368 ARG cc_start: 0.4473 (OUTLIER) cc_final: 0.2565 (tpm-80) REVERT: L 447 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7806 (tpp-160) REVERT: L 968 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8698 (tttp) REVERT: L 1267 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8186 (mp) REVERT: L 1468 MET cc_start: 0.8854 (mmm) cc_final: 0.8646 (tpp) REVERT: L 1493 MET cc_start: 0.7349 (mmt) cc_final: 0.6962 (mmm) REVERT: L 1688 ARG cc_start: 0.7038 (tpp-160) cc_final: 0.6807 (tpp80) REVERT: L 1714 LEU cc_start: 0.8535 (tt) cc_final: 0.8136 (tp) REVERT: L 1764 LEU cc_start: 0.7305 (mt) cc_final: 0.7064 (mt) REVERT: L 1835 ASN cc_start: 0.3749 (OUTLIER) cc_final: 0.3118 (m110) REVERT: L 1845 THR cc_start: 0.7015 (p) cc_final: 0.6755 (p) REVERT: L 1876 PHE cc_start: 0.5398 (p90) cc_final: 0.5007 (p90) REVERT: L 2255 MET cc_start: 0.6645 (mmm) cc_final: 0.6204 (mmm) REVERT: L 3064 MET cc_start: 0.5346 (pmm) cc_final: 0.4989 (pmm) REVERT: L 3092 PHE cc_start: 0.7955 (t80) cc_final: 0.7572 (t80) REVERT: L 3096 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7520 (ttmt) REVERT: L 3155 LEU cc_start: 0.7967 (mp) cc_final: 0.7641 (mt) REVERT: L 3298 TRP cc_start: 0.8693 (m100) cc_final: 0.8379 (m100) outliers start: 50 outliers final: 36 residues processed: 509 average time/residue: 0.8488 time to fit residues: 679.2338 Evaluate side-chains 439 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 399 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2370 ASP Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain L residue 320 CYS Chi-restraints excluded: chain L residue 368 ARG Chi-restraints excluded: chain L residue 614 TYR Chi-restraints excluded: chain L residue 681 THR Chi-restraints excluded: chain L residue 737 HIS Chi-restraints excluded: chain L residue 745 GLU Chi-restraints excluded: chain L residue 864 HIS Chi-restraints excluded: chain L residue 1099 CYS Chi-restraints excluded: chain L residue 1120 ASP Chi-restraints excluded: chain L residue 1146 CYS Chi-restraints excluded: chain L residue 1197 GLU Chi-restraints excluded: chain L residue 1267 LEU Chi-restraints excluded: chain L residue 1278 ILE Chi-restraints excluded: chain L residue 1297 LEU Chi-restraints excluded: chain L residue 1343 CYS Chi-restraints excluded: chain L residue 1639 LEU Chi-restraints excluded: chain L residue 1707 PHE Chi-restraints excluded: chain L residue 1785 ASN Chi-restraints excluded: chain L residue 1835 ASN Chi-restraints excluded: chain L residue 1995 VAL Chi-restraints excluded: chain L residue 2340 SER Chi-restraints excluded: chain L residue 2346 LEU Chi-restraints excluded: chain L residue 2459 VAL Chi-restraints excluded: chain L residue 2460 THR Chi-restraints excluded: chain L residue 2574 THR Chi-restraints excluded: chain L residue 2634 ILE Chi-restraints excluded: chain L residue 2661 MET Chi-restraints excluded: chain L residue 2751 CYS Chi-restraints excluded: chain L residue 2886 ILE Chi-restraints excluded: chain L residue 2931 ILE Chi-restraints excluded: chain L residue 3096 LYS Chi-restraints excluded: chain L residue 3127 TRP Chi-restraints excluded: chain L residue 3194 CYS Chi-restraints excluded: chain L residue 3220 LEU Chi-restraints excluded: chain L residue 3276 HIS Chi-restraints excluded: chain L residue 3297 VAL Chi-restraints excluded: chain L residue 3713 ILE Chi-restraints excluded: chain L residue 3716 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 43 optimal weight: 8.9990 chunk 340 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 286 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 619 ASN L 864 HIS L1057 GLN L1180 GLN L1835 ASN L1921 HIS L2091 ASN L2398 GLN L2471 HIS L2571 HIS ** L2932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3014 GLN L3036 HIS L3278 GLN ** L3492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L3818 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124294 restraints weight = 136632.056| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.67 r_work: 0.3286 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 29995 Z= 0.337 Angle : 0.622 9.359 40616 Z= 0.325 Chirality : 0.041 0.586 4639 Planarity : 0.005 0.060 5136 Dihedral : 5.207 59.676 3972 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.96 % Allowed : 13.27 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3612 helix: 0.45 (0.10), residues: 2454 sheet: -0.83 (0.61), residues: 65 loop : -1.90 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L3269 HIS 0.010 0.001 HIS L2601 PHE 0.026 0.002 PHE L1793 TYR 0.013 0.002 TYR L 754 ARG 0.009 0.001 ARG L1836 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 405 time to evaluate : 3.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2348 LEU cc_start: 0.7869 (mm) cc_final: 0.7522 (mp) REVERT: H 2370 ASP cc_start: 0.8425 (t70) cc_final: 0.8180 (t70) REVERT: L 317 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5641 (tt) REVERT: L 469 LYS cc_start: 0.7043 (mmpt) cc_final: 0.6597 (ptmm) REVERT: L 597 MET cc_start: 0.9369 (tpp) cc_final: 0.9068 (mmm) REVERT: L 649 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7636 (pt0) REVERT: L 727 GLU cc_start: 0.7819 (tp30) cc_final: 0.7605 (tp30) REVERT: L 968 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8762 (tttp) REVERT: L 974 MET cc_start: 0.8997 (mmt) cc_final: 0.8531 (mmt) REVERT: L 975 MET cc_start: 0.8283 (ptp) cc_final: 0.8011 (ptp) REVERT: L 1267 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8685 (mp) REVERT: L 1409 MET cc_start: 0.9356 (tpp) cc_final: 0.9019 (tpp) REVERT: L 1468 MET cc_start: 0.9000 (mmm) cc_final: 0.8704 (tpp) REVERT: L 1504 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8309 (p90) REVERT: L 1688 ARG cc_start: 0.7255 (tpp-160) cc_final: 0.6939 (tpp80) REVERT: L 1714 LEU cc_start: 0.8657 (tt) cc_final: 0.8386 (tp) REVERT: L 1876 PHE cc_start: 0.5552 (p90) cc_final: 0.5249 (p90) REVERT: L 2255 MET cc_start: 0.6840 (mmm) cc_final: 0.6260 (mmm) REVERT: L 2442 GLU cc_start: 0.7257 (pp20) cc_final: 0.7021 (pt0) REVERT: L 2468 MET cc_start: 0.8660 (mmt) cc_final: 0.8003 (mmt) REVERT: L 3057 TYR cc_start: 0.6804 (m-10) cc_final: 0.6297 (m-10) REVERT: L 3092 PHE cc_start: 0.8243 (t80) cc_final: 0.7858 (t80) REVERT: L 3425 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7397 (pt0) outliers start: 64 outliers final: 43 residues processed: 452 average time/residue: 0.8330 time to fit residues: 591.9830 Evaluate side-chains 414 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 367 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2369 SER Chi-restraints excluded: chain H residue 2381 SER Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain L residue 320 CYS Chi-restraints excluded: chain L residue 368 ARG Chi-restraints excluded: chain L residue 370 THR Chi-restraints excluded: chain L residue 614 TYR Chi-restraints excluded: chain L residue 649 GLU Chi-restraints excluded: chain L residue 737 HIS Chi-restraints excluded: chain L residue 912 LEU Chi-restraints excluded: chain L residue 1120 ASP Chi-restraints excluded: chain L residue 1197 GLU Chi-restraints excluded: chain L residue 1267 LEU Chi-restraints excluded: chain L residue 1271 THR Chi-restraints excluded: chain L residue 1278 ILE Chi-restraints excluded: chain L residue 1343 CYS Chi-restraints excluded: chain L residue 1504 HIS Chi-restraints excluded: chain L residue 1639 LEU Chi-restraints excluded: chain L residue 1707 PHE Chi-restraints excluded: chain L residue 1734 LEU Chi-restraints excluded: chain L residue 1785 ASN Chi-restraints excluded: chain L residue 1879 HIS Chi-restraints excluded: chain L residue 1913 VAL Chi-restraints excluded: chain L residue 1921 HIS Chi-restraints excluded: chain L residue 1995 VAL Chi-restraints excluded: chain L residue 2142 ASN Chi-restraints excluded: chain L residue 2276 MET Chi-restraints excluded: chain L residue 2346 LEU Chi-restraints excluded: chain L residue 2393 LEU Chi-restraints excluded: chain L residue 2459 VAL Chi-restraints excluded: chain L residue 2460 THR Chi-restraints excluded: chain L residue 2574 THR Chi-restraints excluded: chain L residue 2634 ILE Chi-restraints excluded: chain L residue 2643 HIS Chi-restraints excluded: chain L residue 2661 MET Chi-restraints excluded: chain L residue 2886 ILE Chi-restraints excluded: chain L residue 2931 ILE Chi-restraints excluded: chain L residue 3010 SER Chi-restraints excluded: chain L residue 3032 LEU Chi-restraints excluded: chain L residue 3041 VAL Chi-restraints excluded: chain L residue 3127 TRP Chi-restraints excluded: chain L residue 3194 CYS Chi-restraints excluded: chain L residue 3220 LEU Chi-restraints excluded: chain L residue 3297 VAL Chi-restraints excluded: chain L residue 3337 HIS Chi-restraints excluded: chain L residue 3716 SER Chi-restraints excluded: chain L residue 3747 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 54 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 323 optimal weight: 0.7980 chunk 198 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 320 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 864 HIS L1239 HIS L1710 ASN L1835 ASN L2932 ASN ** L3161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3492 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.160423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125701 restraints weight = 135668.707| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.62 r_work: 0.3296 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29995 Z= 0.190 Angle : 0.551 8.246 40616 Z= 0.284 Chirality : 0.037 0.371 4639 Planarity : 0.004 0.063 5136 Dihedral : 5.095 59.662 3972 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.29 % Allowed : 14.37 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3612 helix: 0.76 (0.11), residues: 2448 sheet: -0.84 (0.60), residues: 65 loop : -1.74 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L3829 HIS 0.011 0.001 HIS L1921 PHE 0.015 0.001 PHE L1763 TYR 0.012 0.001 TYR H2389 ARG 0.006 0.000 ARG L 696 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 383 time to evaluate : 3.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2291 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5555 (mmmt) REVERT: H 2348 LEU cc_start: 0.7782 (mm) cc_final: 0.7422 (mp) REVERT: H 2370 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8126 (t70) REVERT: L 317 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.6018 (tt) REVERT: L 368 ARG cc_start: 0.4517 (OUTLIER) cc_final: 0.2448 (ttm-80) REVERT: L 469 LYS cc_start: 0.7151 (mmpt) cc_final: 0.6617 (ptmm) REVERT: L 597 MET cc_start: 0.9379 (tpp) cc_final: 0.9157 (mmm) REVERT: L 649 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: L 727 GLU cc_start: 0.7715 (tp30) cc_final: 0.7472 (tp30) REVERT: L 968 LYS cc_start: 0.9122 (ttpt) cc_final: 0.8768 (tttp) REVERT: L 974 MET cc_start: 0.9012 (mmt) cc_final: 0.8586 (mmt) REVERT: L 1267 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8696 (mp) REVERT: L 1409 MET cc_start: 0.9375 (tpp) cc_final: 0.9043 (tpp) REVERT: L 1468 MET cc_start: 0.8966 (mmm) cc_final: 0.8659 (tpp) REVERT: L 1493 MET cc_start: 0.7277 (mmt) cc_final: 0.6898 (mmm) REVERT: L 1688 ARG cc_start: 0.7303 (tpp-160) cc_final: 0.6990 (tpp80) REVERT: L 1769 LYS cc_start: 0.6747 (tppp) cc_final: 0.6373 (tptt) REVERT: L 1876 PHE cc_start: 0.5572 (p90) cc_final: 0.5286 (p90) REVERT: L 1906 MET cc_start: 0.8307 (mmm) cc_final: 0.7813 (mmm) REVERT: L 2255 MET cc_start: 0.6767 (mmm) cc_final: 0.6314 (mmm) REVERT: L 2468 MET cc_start: 0.8570 (mmt) cc_final: 0.7928 (mmt) REVERT: L 3057 TYR cc_start: 0.7023 (m-10) cc_final: 0.6583 (m-10) REVERT: L 3092 PHE cc_start: 0.8013 (t80) cc_final: 0.7636 (t80) REVERT: L 3425 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7355 (pt0) outliers start: 42 outliers final: 30 residues processed: 414 average time/residue: 0.8370 time to fit residues: 547.8070 Evaluate side-chains 392 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 356 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2291 LYS Chi-restraints excluded: chain H residue 2370 ASP Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain L residue 320 CYS Chi-restraints excluded: chain L residue 368 ARG Chi-restraints excluded: chain L residue 614 TYR Chi-restraints excluded: chain L residue 649 GLU Chi-restraints excluded: chain L residue 737 HIS Chi-restraints excluded: chain L residue 745 GLU Chi-restraints excluded: chain L residue 864 HIS Chi-restraints excluded: chain L residue 912 LEU Chi-restraints excluded: chain L residue 918 GLU Chi-restraints excluded: chain L residue 1120 ASP Chi-restraints excluded: chain L residue 1197 GLU Chi-restraints excluded: chain L residue 1267 LEU Chi-restraints excluded: chain L residue 1278 ILE Chi-restraints excluded: chain L residue 1343 CYS Chi-restraints excluded: chain L residue 1639 LEU Chi-restraints excluded: chain L residue 1707 PHE Chi-restraints excluded: chain L residue 1785 ASN Chi-restraints excluded: chain L residue 1835 ASN Chi-restraints excluded: chain L residue 1913 VAL Chi-restraints excluded: chain L residue 1995 VAL Chi-restraints excluded: chain L residue 2191 LEU Chi-restraints excluded: chain L residue 2346 LEU Chi-restraints excluded: chain L residue 2393 LEU Chi-restraints excluded: chain L residue 2634 ILE Chi-restraints excluded: chain L residue 2661 MET Chi-restraints excluded: chain L residue 2931 ILE Chi-restraints excluded: chain L residue 3127 TRP Chi-restraints excluded: chain L residue 3194 CYS Chi-restraints excluded: chain L residue 3220 LEU Chi-restraints excluded: chain L residue 3337 HIS Chi-restraints excluded: chain L residue 3548 VAL Chi-restraints excluded: chain L residue 3713 ILE Chi-restraints excluded: chain L residue 3716 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 112 optimal weight: 4.9990 chunk 330 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 268 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 864 HIS L1835 ASN ** L1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2601 HIS ** L3161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.158201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123088 restraints weight = 141087.876| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.85 r_work: 0.3251 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29995 Z= 0.240 Angle : 0.557 8.484 40616 Z= 0.288 Chirality : 0.038 0.350 4639 Planarity : 0.004 0.060 5136 Dihedral : 5.080 58.866 3972 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.44 % Allowed : 14.43 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3612 helix: 0.85 (0.11), residues: 2454 sheet: -0.83 (0.60), residues: 65 loop : -1.70 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L3127 HIS 0.007 0.001 HIS L2601 PHE 0.018 0.001 PHE L 860 TYR 0.013 0.001 TYR L1765 ARG 0.007 0.000 ARG L 761 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 370 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2348 LEU cc_start: 0.7783 (mm) cc_final: 0.7418 (mp) REVERT: H 2370 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7820 (t70) REVERT: L 317 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5920 (tt) REVERT: L 368 ARG cc_start: 0.4522 (OUTLIER) cc_final: 0.2452 (ttm-80) REVERT: L 469 LYS cc_start: 0.7114 (mmpt) cc_final: 0.6752 (ptmt) REVERT: L 540 THR cc_start: 0.6554 (m) cc_final: 0.6164 (p) REVERT: L 727 GLU cc_start: 0.7604 (tp30) cc_final: 0.7346 (tp30) REVERT: L 864 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.8253 (t70) REVERT: L 968 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8707 (tttp) REVERT: L 974 MET cc_start: 0.8969 (mmt) cc_final: 0.8570 (mmt) REVERT: L 1267 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8688 (mp) REVERT: L 1409 MET cc_start: 0.9322 (tpp) cc_final: 0.8984 (tpp) REVERT: L 1493 MET cc_start: 0.7164 (mmt) cc_final: 0.6790 (mmm) REVERT: L 1504 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.8252 (p90) REVERT: L 1688 ARG cc_start: 0.7196 (tpp-160) cc_final: 0.6900 (tpp80) REVERT: L 1769 LYS cc_start: 0.6702 (tppp) cc_final: 0.6260 (tptt) REVERT: L 1971 MET cc_start: 0.7825 (ptt) cc_final: 0.7588 (ptm) REVERT: L 2158 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.5930 (m-80) REVERT: L 2183 MET cc_start: 0.6014 (mtp) cc_final: 0.5785 (mtp) REVERT: L 2255 MET cc_start: 0.6715 (mmm) cc_final: 0.6163 (mmm) REVERT: L 2468 MET cc_start: 0.8504 (mmt) cc_final: 0.7905 (mmt) REVERT: L 3057 TYR cc_start: 0.7123 (m-10) cc_final: 0.6884 (m-10) REVERT: L 3092 PHE cc_start: 0.7896 (t80) cc_final: 0.7523 (t80) REVERT: L 3425 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7388 (pt0) outliers start: 47 outliers final: 37 residues processed: 403 average time/residue: 0.8163 time to fit residues: 521.2253 Evaluate side-chains 402 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 358 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2370 ASP Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain L residue 320 CYS Chi-restraints excluded: chain L residue 368 ARG Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain L residue 614 TYR Chi-restraints excluded: chain L residue 737 HIS Chi-restraints excluded: chain L residue 745 GLU Chi-restraints excluded: chain L residue 864 HIS Chi-restraints excluded: chain L residue 912 LEU Chi-restraints excluded: chain L residue 918 GLU Chi-restraints excluded: chain L residue 1120 ASP Chi-restraints excluded: chain L residue 1267 LEU Chi-restraints excluded: chain L residue 1278 ILE Chi-restraints excluded: chain L residue 1343 CYS Chi-restraints excluded: chain L residue 1504 HIS Chi-restraints excluded: chain L residue 1639 LEU Chi-restraints excluded: chain L residue 1707 PHE Chi-restraints excluded: chain L residue 1785 ASN Chi-restraints excluded: chain L residue 1835 ASN Chi-restraints excluded: chain L residue 1879 HIS Chi-restraints excluded: chain L residue 1995 VAL Chi-restraints excluded: chain L residue 2142 ASN Chi-restraints excluded: chain L residue 2158 PHE Chi-restraints excluded: chain L residue 2191 LEU Chi-restraints excluded: chain L residue 2346 LEU Chi-restraints excluded: chain L residue 2393 LEU Chi-restraints excluded: chain L residue 2634 ILE Chi-restraints excluded: chain L residue 2643 HIS Chi-restraints excluded: chain L residue 2661 MET Chi-restraints excluded: chain L residue 2931 ILE Chi-restraints excluded: chain L residue 3010 SER Chi-restraints excluded: chain L residue 3032 LEU Chi-restraints excluded: chain L residue 3127 TRP Chi-restraints excluded: chain L residue 3194 CYS Chi-restraints excluded: chain L residue 3220 LEU Chi-restraints excluded: chain L residue 3286 LEU Chi-restraints excluded: chain L residue 3297 VAL Chi-restraints excluded: chain L residue 3337 HIS Chi-restraints excluded: chain L residue 3456 LEU Chi-restraints excluded: chain L residue 3570 GLN Chi-restraints excluded: chain L residue 3616 MET Chi-restraints excluded: chain L residue 3713 ILE Chi-restraints excluded: chain L residue 3716 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 619 ASN L 669 GLN L1398 ASN L1835 ASN ** L1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2936 GLN ** L3161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121894 restraints weight = 135652.133| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.68 r_work: 0.3249 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29995 Z= 0.227 Angle : 0.552 8.130 40616 Z= 0.285 Chirality : 0.038 0.326 4639 Planarity : 0.004 0.062 5136 Dihedral : 5.032 58.139 3972 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.65 % Allowed : 14.19 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3612 helix: 0.94 (0.11), residues: 2460 sheet: -0.83 (0.60), residues: 65 loop : -1.55 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L3127 HIS 0.010 0.001 HIS L 864 PHE 0.018 0.001 PHE L1876 TYR 0.012 0.001 TYR H2389 ARG 0.007 0.000 ARG L 696 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 375 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2348 LEU cc_start: 0.7834 (mm) cc_final: 0.7478 (mp) REVERT: L 368 ARG cc_start: 0.4682 (OUTLIER) cc_final: 0.2539 (ttm-80) REVERT: L 469 LYS cc_start: 0.7194 (mmpt) cc_final: 0.6785 (ptmt) REVERT: L 540 THR cc_start: 0.6354 (m) cc_final: 0.6000 (p) REVERT: L 727 GLU cc_start: 0.7845 (tp30) cc_final: 0.7557 (tp30) REVERT: L 968 LYS cc_start: 0.9172 (ttpt) cc_final: 0.8787 (tttp) REVERT: L 974 MET cc_start: 0.9157 (mmt) cc_final: 0.8755 (mmt) REVERT: L 1279 MET cc_start: 0.8002 (mtp) cc_final: 0.7731 (mtp) REVERT: L 1409 MET cc_start: 0.9377 (tpp) cc_final: 0.9059 (tpp) REVERT: L 1493 MET cc_start: 0.7261 (mmt) cc_final: 0.6848 (mmm) REVERT: L 1504 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8315 (p90) REVERT: L 1688 ARG cc_start: 0.7451 (tpp-160) cc_final: 0.7229 (tpp80) REVERT: L 1769 LYS cc_start: 0.6792 (tppp) cc_final: 0.6346 (tptt) REVERT: L 1824 HIS cc_start: 0.3698 (t70) cc_final: 0.3476 (t-170) REVERT: L 2158 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.5994 (m-80) REVERT: L 2183 MET cc_start: 0.6137 (mtp) cc_final: 0.5917 (mtp) REVERT: L 2255 MET cc_start: 0.6815 (mmm) cc_final: 0.6133 (mmm) REVERT: L 2372 ARG cc_start: 0.7832 (tpt-90) cc_final: 0.7600 (tpt90) REVERT: L 3057 TYR cc_start: 0.7589 (m-10) cc_final: 0.7216 (m-10) REVERT: L 3092 PHE cc_start: 0.8021 (t80) cc_final: 0.7632 (t80) REVERT: L 3391 PHE cc_start: 0.6004 (m-10) cc_final: 0.5774 (m-10) REVERT: L 3425 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7437 (pt0) outliers start: 54 outliers final: 38 residues processed: 412 average time/residue: 0.8236 time to fit residues: 536.7359 Evaluate side-chains 397 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 356 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2369 SER Chi-restraints excluded: chain L residue 320 CYS Chi-restraints excluded: chain L residue 368 ARG Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain L residue 614 TYR Chi-restraints excluded: chain L residue 737 HIS Chi-restraints excluded: chain L residue 745 GLU Chi-restraints excluded: chain L residue 912 LEU Chi-restraints excluded: chain L residue 918 GLU Chi-restraints excluded: chain L residue 1120 ASP Chi-restraints excluded: chain L residue 1197 GLU Chi-restraints excluded: chain L residue 1278 ILE Chi-restraints excluded: chain L residue 1343 CYS Chi-restraints excluded: chain L residue 1504 HIS Chi-restraints excluded: chain L residue 1639 LEU Chi-restraints excluded: chain L residue 1697 PHE Chi-restraints excluded: chain L residue 1707 PHE Chi-restraints excluded: chain L residue 1785 ASN Chi-restraints excluded: chain L residue 1879 HIS Chi-restraints excluded: chain L residue 1913 VAL Chi-restraints excluded: chain L residue 1995 VAL Chi-restraints excluded: chain L residue 2142 ASN Chi-restraints excluded: chain L residue 2158 PHE Chi-restraints excluded: chain L residue 2191 LEU Chi-restraints excluded: chain L residue 2346 LEU Chi-restraints excluded: chain L residue 2393 LEU Chi-restraints excluded: chain L residue 2634 ILE Chi-restraints excluded: chain L residue 2643 HIS Chi-restraints excluded: chain L residue 2661 MET Chi-restraints excluded: chain L residue 2931 ILE Chi-restraints excluded: chain L residue 3010 SER Chi-restraints excluded: chain L residue 3032 LEU Chi-restraints excluded: chain L residue 3127 TRP Chi-restraints excluded: chain L residue 3194 CYS Chi-restraints excluded: chain L residue 3220 LEU Chi-restraints excluded: chain L residue 3286 LEU Chi-restraints excluded: chain L residue 3297 VAL Chi-restraints excluded: chain L residue 3337 HIS Chi-restraints excluded: chain L residue 3570 GLN Chi-restraints excluded: chain L residue 3616 MET Chi-restraints excluded: chain L residue 3716 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 100 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 619 ASN L1424 HIS L1835 ASN ** L3161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.156159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120636 restraints weight = 137770.492| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.77 r_work: 0.3251 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29995 Z= 0.214 Angle : 0.546 7.854 40616 Z= 0.281 Chirality : 0.037 0.308 4639 Planarity : 0.004 0.064 5136 Dihedral : 4.968 57.617 3972 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.47 % Allowed : 14.47 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3612 helix: 0.99 (0.11), residues: 2466 sheet: -0.82 (0.58), residues: 70 loop : -1.49 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L3127 HIS 0.007 0.001 HIS L1947 PHE 0.016 0.001 PHE L1763 TYR 0.013 0.001 TYR H2389 ARG 0.007 0.000 ARG L 696 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 370 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2348 LEU cc_start: 0.7826 (mm) cc_final: 0.7482 (mp) REVERT: H 2439 ARG cc_start: 0.7694 (ptp-170) cc_final: 0.7470 (ptp-170) REVERT: L 41 MET cc_start: 0.3664 (mmt) cc_final: 0.3247 (tpp) REVERT: L 368 ARG cc_start: 0.4691 (OUTLIER) cc_final: 0.2557 (ttm-80) REVERT: L 469 LYS cc_start: 0.7186 (mmpt) cc_final: 0.6812 (ptmt) REVERT: L 727 GLU cc_start: 0.7853 (tp30) cc_final: 0.7573 (tp30) REVERT: L 974 MET cc_start: 0.9113 (mmt) cc_final: 0.8719 (mmt) REVERT: L 1279 MET cc_start: 0.8108 (mtp) cc_final: 0.7845 (mtp) REVERT: L 1409 MET cc_start: 0.9356 (tpp) cc_final: 0.9036 (tpp) REVERT: L 1504 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.8304 (p90) REVERT: L 1688 ARG cc_start: 0.7453 (tpp-160) cc_final: 0.7222 (tpp80) REVERT: L 1735 PHE cc_start: 0.6427 (t80) cc_final: 0.6097 (t80) REVERT: L 1769 LYS cc_start: 0.6779 (tppp) cc_final: 0.6287 (tptt) REVERT: L 1824 HIS cc_start: 0.3893 (t70) cc_final: 0.3658 (t-170) REVERT: L 2158 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6031 (m-80) REVERT: L 2183 MET cc_start: 0.6212 (mtp) cc_final: 0.5945 (mtp) REVERT: L 2255 MET cc_start: 0.6799 (mmm) cc_final: 0.6128 (mmm) REVERT: L 2372 ARG cc_start: 0.7823 (tpt-90) cc_final: 0.7592 (tpt90) REVERT: L 2786 HIS cc_start: 0.6334 (OUTLIER) cc_final: 0.5937 (t-90) REVERT: L 3057 TYR cc_start: 0.7830 (m-10) cc_final: 0.7485 (m-10) REVERT: L 3092 PHE cc_start: 0.8046 (t80) cc_final: 0.7697 (t80) REVERT: L 3425 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7422 (pt0) outliers start: 48 outliers final: 39 residues processed: 403 average time/residue: 0.8243 time to fit residues: 526.1094 Evaluate side-chains 402 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 359 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2369 SER Chi-restraints excluded: chain L residue 317 LEU Chi-restraints excluded: chain L residue 320 CYS Chi-restraints excluded: chain L residue 368 ARG Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain L residue 614 TYR Chi-restraints excluded: chain L residue 737 HIS Chi-restraints excluded: chain L residue 745 GLU Chi-restraints excluded: chain L residue 809 LEU Chi-restraints excluded: chain L residue 912 LEU Chi-restraints excluded: chain L residue 918 GLU Chi-restraints excluded: chain L residue 1120 ASP Chi-restraints excluded: chain L residue 1278 ILE Chi-restraints excluded: chain L residue 1343 CYS Chi-restraints excluded: chain L residue 1504 HIS Chi-restraints excluded: chain L residue 1639 LEU Chi-restraints excluded: chain L residue 1697 PHE Chi-restraints excluded: chain L residue 1707 PHE Chi-restraints excluded: chain L residue 1756 GLN Chi-restraints excluded: chain L residue 1785 ASN Chi-restraints excluded: chain L residue 1879 HIS Chi-restraints excluded: chain L residue 1913 VAL Chi-restraints excluded: chain L residue 1995 VAL Chi-restraints excluded: chain L residue 2142 ASN Chi-restraints excluded: chain L residue 2158 PHE Chi-restraints excluded: chain L residue 2191 LEU Chi-restraints excluded: chain L residue 2346 LEU Chi-restraints excluded: chain L residue 2393 LEU Chi-restraints excluded: chain L residue 2634 ILE Chi-restraints excluded: chain L residue 2643 HIS Chi-restraints excluded: chain L residue 2661 MET Chi-restraints excluded: chain L residue 2786 HIS Chi-restraints excluded: chain L residue 3010 SER Chi-restraints excluded: chain L residue 3127 TRP Chi-restraints excluded: chain L residue 3194 CYS Chi-restraints excluded: chain L residue 3220 LEU Chi-restraints excluded: chain L residue 3286 LEU Chi-restraints excluded: chain L residue 3297 VAL Chi-restraints excluded: chain L residue 3337 HIS Chi-restraints excluded: chain L residue 3384 PHE Chi-restraints excluded: chain L residue 3570 GLN Chi-restraints excluded: chain L residue 3616 MET Chi-restraints excluded: chain L residue 3716 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 261 optimal weight: 5.9990 chunk 225 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 319 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 346 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 619 ASN ** L3161 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 = 0.4056 r_free = 0.4056 target = 0.160050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124237 restraints weight = 131502.839| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.39 r_work: 0.3310 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29995 Z= 0.175 Angle : 0.530 7.485 40616 Z= 0.270 Chirality : 0.037 0.266 4639 Planarity : 0.004 0.065 5136 Dihedral : 4.862 57.084 3972 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.32 % Allowed : 14.80 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3612 helix: 1.12 (0.11), residues: 2468 sheet: -0.69 (0.60), residues: 70 loop : -1.37 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H2365 HIS 0.007 0.001 HIS L1894 PHE 0.031 0.001 PHE L3455 TYR 0.014 0.001 TYR H2389 ARG 0.005 0.000 ARG L1960 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 367 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 41 MET cc_start: 0.3722 (mmt) cc_final: 0.3263 (tpp) REVERT: L 368 ARG cc_start: 0.4615 (OUTLIER) cc_final: 0.2342 (ttm-80) REVERT: L 448 MET cc_start: 0.8461 (ttp) cc_final: 0.8225 (ttp) REVERT: L 469 LYS cc_start: 0.7104 (mmpt) cc_final: 0.6887 (ptmt) REVERT: L 727 GLU cc_start: 0.7871 (tp30) cc_final: 0.7574 (tp30) REVERT: L 974 MET cc_start: 0.9154 (mmt) cc_final: 0.8796 (mmt) REVERT: L 1279 MET cc_start: 0.8222 (mtp) cc_final: 0.7988 (mtp) REVERT: L 1409 MET cc_start: 0.9357 (tpp) cc_final: 0.9037 (tpp) REVERT: L 1504 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8334 (p90) REVERT: L 1667 MET cc_start: 0.3927 (mtt) cc_final: 0.3567 (mtm) REVERT: L 1769 LYS cc_start: 0.7038 (tppp) cc_final: 0.6373 (tptt) REVERT: L 1971 MET cc_start: 0.7851 (ptt) cc_final: 0.7515 (ptm) REVERT: L 2158 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: L 2255 MET cc_start: 0.6721 (mmm) cc_final: 0.6224 (mmm) REVERT: L 2372 ARG cc_start: 0.7794 (tpt-90) cc_final: 0.7557 (tpt90) REVERT: L 2474 ILE cc_start: 0.8711 (pt) cc_final: 0.8265 (mt) REVERT: L 2786 HIS cc_start: 0.6369 (OUTLIER) cc_final: 0.5946 (t-90) REVERT: L 3057 TYR cc_start: 0.7971 (m-10) cc_final: 0.7657 (m-10) REVERT: L 3092 PHE cc_start: 0.8012 (t80) cc_final: 0.7681 (t80) REVERT: L 3425 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7455 (pt0) REVERT: L 3455 PHE cc_start: 0.8671 (m-80) cc_final: 0.8373 (m-80) outliers start: 43 outliers final: 35 residues processed: 393 average time/residue: 0.8317 time to fit residues: 517.9699 Evaluate side-chains 396 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 357 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 320 CYS Chi-restraints excluded: chain L residue 368 ARG Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain L residue 614 TYR Chi-restraints excluded: chain L residue 737 HIS Chi-restraints excluded: chain L residue 912 LEU Chi-restraints excluded: chain L residue 918 GLU Chi-restraints excluded: chain L residue 1120 ASP Chi-restraints excluded: chain L residue 1197 GLU Chi-restraints excluded: chain L residue 1278 ILE Chi-restraints excluded: chain L residue 1343 CYS Chi-restraints excluded: chain L residue 1504 HIS Chi-restraints excluded: chain L residue 1639 LEU Chi-restraints excluded: chain L residue 1697 PHE Chi-restraints excluded: chain L residue 1701 ARG Chi-restraints excluded: chain L residue 1707 PHE Chi-restraints excluded: chain L residue 1785 ASN Chi-restraints excluded: chain L residue 1879 HIS Chi-restraints excluded: chain L residue 1913 VAL Chi-restraints excluded: chain L residue 1995 VAL Chi-restraints excluded: chain L residue 2142 ASN Chi-restraints excluded: chain L residue 2158 PHE Chi-restraints excluded: chain L residue 2191 LEU Chi-restraints excluded: chain L residue 2346 LEU Chi-restraints excluded: chain L residue 2393 LEU Chi-restraints excluded: chain L residue 2634 ILE Chi-restraints excluded: chain L residue 2661 MET Chi-restraints excluded: chain L residue 2786 HIS Chi-restraints excluded: chain L residue 3010 SER Chi-restraints excluded: chain L residue 3032 LEU Chi-restraints excluded: chain L residue 3127 TRP Chi-restraints excluded: chain L residue 3194 CYS Chi-restraints excluded: chain L residue 3220 LEU Chi-restraints excluded: chain L residue 3286 LEU Chi-restraints excluded: chain L residue 3297 VAL Chi-restraints excluded: chain L residue 3337 HIS Chi-restraints excluded: chain L residue 3384 PHE Chi-restraints excluded: chain L residue 3616 MET Chi-restraints excluded: chain L residue 3716 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 116 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 308 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 353 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 619 ASN ** L1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L3053 GLN ** L3161 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 = 0.3973 r_free = 0.3973 target = 0.154523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119311 restraints weight = 138545.620| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.80 r_work: 0.3202 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29995 Z= 0.257 Angle : 0.563 6.699 40616 Z= 0.292 Chirality : 0.038 0.275 4639 Planarity : 0.004 0.067 5136 Dihedral : 4.966 56.038 3972 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.38 % Allowed : 14.96 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3612 helix: 1.04 (0.11), residues: 2471 sheet: -0.84 (0.59), residues: 72 loop : -1.41 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L3127 HIS 0.008 0.001 HIS L1947 PHE 0.019 0.001 PHE L1763 TYR 0.013 0.001 TYR H2389 ARG 0.005 0.000 ARG L 696 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 359 time to evaluate : 3.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2348 LEU cc_start: 0.7911 (mm) cc_final: 0.7556 (mp) REVERT: L 41 MET cc_start: 0.3735 (mmt) cc_final: 0.3291 (tpp) REVERT: L 368 ARG cc_start: 0.4939 (OUTLIER) cc_final: 0.2607 (ttm-80) REVERT: L 448 MET cc_start: 0.8573 (ttp) cc_final: 0.8325 (ttp) REVERT: L 469 LYS cc_start: 0.7164 (mmpt) cc_final: 0.6926 (ptmt) REVERT: L 700 MET cc_start: 0.8265 (mtp) cc_final: 0.7925 (mtp) REVERT: L 727 GLU cc_start: 0.7993 (tp30) cc_final: 0.7666 (tp30) REVERT: L 974 MET cc_start: 0.9233 (mmt) cc_final: 0.8875 (mmt) REVERT: L 1279 MET cc_start: 0.8274 (mtp) cc_final: 0.8056 (mtp) REVERT: L 1409 MET cc_start: 0.9347 (tpp) cc_final: 0.9061 (tpp) REVERT: L 1504 HIS cc_start: 0.8803 (OUTLIER) cc_final: 0.8348 (p90) REVERT: L 1769 LYS cc_start: 0.7084 (tppp) cc_final: 0.6576 (tptt) REVERT: L 1971 MET cc_start: 0.7950 (ptt) cc_final: 0.7554 (ptm) REVERT: L 2158 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: L 2255 MET cc_start: 0.6605 (mmm) cc_final: 0.6067 (mmm) REVERT: L 2372 ARG cc_start: 0.7847 (tpt-90) cc_final: 0.7612 (tpt90) REVERT: L 2474 ILE cc_start: 0.8837 (pt) cc_final: 0.8422 (mt) REVERT: L 2786 HIS cc_start: 0.6367 (OUTLIER) cc_final: 0.5992 (t-90) REVERT: L 3092 PHE cc_start: 0.8110 (t80) cc_final: 0.7760 (t80) REVERT: L 3425 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7485 (pt0) REVERT: L 3457 MET cc_start: 0.7996 (mmm) cc_final: 0.7782 (mmt) outliers start: 45 outliers final: 37 residues processed: 389 average time/residue: 0.8459 time to fit residues: 521.2062 Evaluate side-chains 389 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 348 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2369 SER Chi-restraints excluded: chain L residue 320 CYS Chi-restraints excluded: chain L residue 368 ARG Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain L residue 614 TYR Chi-restraints excluded: chain L residue 737 HIS Chi-restraints excluded: chain L residue 809 LEU Chi-restraints excluded: chain L residue 912 LEU Chi-restraints excluded: chain L residue 918 GLU Chi-restraints excluded: chain L residue 1120 ASP Chi-restraints excluded: chain L residue 1278 ILE Chi-restraints excluded: chain L residue 1343 CYS Chi-restraints excluded: chain L residue 1504 HIS Chi-restraints excluded: chain L residue 1639 LEU Chi-restraints excluded: chain L residue 1697 PHE Chi-restraints excluded: chain L residue 1707 PHE Chi-restraints excluded: chain L residue 1756 GLN Chi-restraints excluded: chain L residue 1785 ASN Chi-restraints excluded: chain L residue 1879 HIS Chi-restraints excluded: chain L residue 1913 VAL Chi-restraints excluded: chain L residue 1995 VAL Chi-restraints excluded: chain L residue 2142 ASN Chi-restraints excluded: chain L residue 2158 PHE Chi-restraints excluded: chain L residue 2191 LEU Chi-restraints excluded: chain L residue 2346 LEU Chi-restraints excluded: chain L residue 2393 LEU Chi-restraints excluded: chain L residue 2634 ILE Chi-restraints excluded: chain L residue 2786 HIS Chi-restraints excluded: chain L residue 2881 GLN Chi-restraints excluded: chain L residue 3010 SER Chi-restraints excluded: chain L residue 3032 LEU Chi-restraints excluded: chain L residue 3127 TRP Chi-restraints excluded: chain L residue 3194 CYS Chi-restraints excluded: chain L residue 3220 LEU Chi-restraints excluded: chain L residue 3286 LEU Chi-restraints excluded: chain L residue 3297 VAL Chi-restraints excluded: chain L residue 3337 HIS Chi-restraints excluded: chain L residue 3384 PHE Chi-restraints excluded: chain L residue 3570 GLN Chi-restraints excluded: chain L residue 3616 MET Chi-restraints excluded: chain L residue 3716 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 224 optimal weight: 2.9990 chunk 175 optimal weight: 0.0010 chunk 348 optimal weight: 0.1980 chunk 297 optimal weight: 0.0980 chunk 298 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 302 optimal weight: 0.0570 chunk 296 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 755 ASN L 844 GLN L2867 ASN ** L3161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.122848 restraints weight = 142909.051| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.89 r_work: 0.3261 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29995 Z= 0.149 Angle : 0.524 7.166 40616 Z= 0.266 Chirality : 0.036 0.201 4639 Planarity : 0.004 0.067 5136 Dihedral : 4.805 56.706 3972 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.98 % Allowed : 15.45 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3612 helix: 1.26 (0.11), residues: 2470 sheet: -0.60 (0.60), residues: 71 loop : -1.26 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H2365 HIS 0.010 0.001 HIS L1947 PHE 0.016 0.001 PHE L 651 TYR 0.013 0.001 TYR L1765 ARG 0.005 0.000 ARG L 696 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 358 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 368 ARG cc_start: 0.4782 (OUTLIER) cc_final: 0.2376 (ttm-80) REVERT: L 469 LYS cc_start: 0.7150 (mmpt) cc_final: 0.6906 (ptmt) REVERT: L 727 GLU cc_start: 0.7885 (tp30) cc_final: 0.7576 (tp30) REVERT: L 744 MET cc_start: 0.8988 (tpt) cc_final: 0.8781 (tpt) REVERT: L 974 MET cc_start: 0.9171 (mmt) cc_final: 0.8831 (mmt) REVERT: L 1409 MET cc_start: 0.9346 (tpp) cc_final: 0.9071 (tpp) REVERT: L 1504 HIS cc_start: 0.8732 (OUTLIER) cc_final: 0.8263 (p90) REVERT: L 1769 LYS cc_start: 0.6959 (tppp) cc_final: 0.6622 (tptt) REVERT: L 1971 MET cc_start: 0.7903 (ptt) cc_final: 0.7490 (ptm) REVERT: L 2158 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: L 2255 MET cc_start: 0.6492 (mmm) cc_final: 0.5980 (mmm) REVERT: L 2372 ARG cc_start: 0.7813 (tpt-90) cc_final: 0.7580 (tpt90) REVERT: L 2474 ILE cc_start: 0.8776 (pt) cc_final: 0.8327 (mt) REVERT: L 2786 HIS cc_start: 0.6295 (OUTLIER) cc_final: 0.5912 (t-90) REVERT: L 3092 PHE cc_start: 0.8031 (t80) cc_final: 0.7699 (t80) REVERT: L 3425 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7372 (pt0) REVERT: L 3455 PHE cc_start: 0.8965 (m-80) cc_final: 0.8442 (m-80) outliers start: 32 outliers final: 25 residues processed: 376 average time/residue: 0.8508 time to fit residues: 508.0684 Evaluate side-chains 379 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 350 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 368 ARG Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain L residue 614 TYR Chi-restraints excluded: chain L residue 737 HIS Chi-restraints excluded: chain L residue 809 LEU Chi-restraints excluded: chain L residue 918 GLU Chi-restraints excluded: chain L residue 1278 ILE Chi-restraints excluded: chain L residue 1343 CYS Chi-restraints excluded: chain L residue 1504 HIS Chi-restraints excluded: chain L residue 1697 PHE Chi-restraints excluded: chain L residue 1701 ARG Chi-restraints excluded: chain L residue 1707 PHE Chi-restraints excluded: chain L residue 1756 GLN Chi-restraints excluded: chain L residue 1879 HIS Chi-restraints excluded: chain L residue 1913 VAL Chi-restraints excluded: chain L residue 1995 VAL Chi-restraints excluded: chain L residue 2158 PHE Chi-restraints excluded: chain L residue 2191 LEU Chi-restraints excluded: chain L residue 2346 LEU Chi-restraints excluded: chain L residue 2393 LEU Chi-restraints excluded: chain L residue 2634 ILE Chi-restraints excluded: chain L residue 2661 MET Chi-restraints excluded: chain L residue 2786 HIS Chi-restraints excluded: chain L residue 3127 TRP Chi-restraints excluded: chain L residue 3220 LEU Chi-restraints excluded: chain L residue 3286 LEU Chi-restraints excluded: chain L residue 3337 HIS Chi-restraints excluded: chain L residue 3384 PHE Chi-restraints excluded: chain L residue 3616 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 93 optimal weight: 0.0570 chunk 355 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1830 HIS ** L1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3161 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 = 0.3993 r_free = 0.3993 target = 0.156148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120912 restraints weight = 144409.701| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.82 r_work: 0.3242 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29995 Z= 0.184 Angle : 0.530 7.632 40616 Z= 0.271 Chirality : 0.037 0.217 4639 Planarity : 0.004 0.068 5136 Dihedral : 4.813 55.601 3972 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.98 % Allowed : 15.38 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3612 helix: 1.27 (0.11), residues: 2470 sheet: -0.73 (0.60), residues: 73 loop : -1.25 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H2365 HIS 0.008 0.001 HIS L1947 PHE 0.018 0.001 PHE L 651 TYR 0.015 0.001 TYR L2405 ARG 0.004 0.000 ARG L 696 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29128.18 seconds wall clock time: 497 minutes 25.18 seconds (29845.18 seconds total)