Starting phenix.real_space_refine on Fri May 16 07:12:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1p_38842/05_2025/8y1p_38842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1p_38842/05_2025/8y1p_38842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y1p_38842/05_2025/8y1p_38842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1p_38842/05_2025/8y1p_38842.map" model { file = "/net/cci-nas-00/data/ceres_data/8y1p_38842/05_2025/8y1p_38842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1p_38842/05_2025/8y1p_38842.cif" } resolution = 3.45 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= -0.002 sd= 0.092 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 65 5.16 5 C 9071 2.51 5 N 2451 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14041 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13933 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1800, 13925 Classifications: {'peptide': 1800} Link IDs: {'PTRANS': 111, 'TRANS': 1688} Chain breaks: 9 Conformer: "B" Number of residues, atoms: 1800, 13925 Classifications: {'peptide': 1800} Link IDs: {'PTRANS': 111, 'TRANS': 1688} Chain breaks: 9 bond proxies already assigned to first conformer: 14257 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'17F': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALEU A1881 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A1881 " occ=0.50 Time building chain proxies: 15.53, per 1000 atoms: 1.11 Number of scatterers: 14041 At special positions: 0 Unit cell: (80.25, 108.07, 214, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 2 15.00 O 2452 8.00 N 2451 7.00 C 9071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.06 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 225 " distance=2.00 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A1347 " distance=2.05 Simple disulfide: pdb=" SG CYS A1345 " - pdb=" SG CYS A1359 " distance=2.03 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 Atom "HETATM13983 O6 17F A2201 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 3.7 seconds 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 10 sheets defined 51.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 4.623A pdb=" N MET A 8 " --> pdb=" O TRP A 4 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.681A pdb=" N VAL A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.517A pdb=" N GLY A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 66 through 75 Processing helix chain 'A' and resid 100 through 114 Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.791A pdb=" N HIS A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 removed outlier: 4.043A pdb=" N GLN A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 219 through 224 removed outlier: 4.072A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 removed outlier: 4.030A pdb=" N GLU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 4.596A pdb=" N ARG A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 301 through 317 removed outlier: 4.328A pdb=" N GLN A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.885A pdb=" N LEU A 321 " --> pdb=" O LEU A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.741A pdb=" N GLU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.818A pdb=" N GLY A 383 " --> pdb=" O PRO A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.873A pdb=" N THR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.825A pdb=" N SER A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.565A pdb=" N TRP A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 520 removed outlier: 3.812A pdb=" N ASP A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 removed outlier: 3.590A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'A' and resid 558 through 575 removed outlier: 3.583A pdb=" N THR A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 575 " --> pdb=" O ARG A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 588 through 600 removed outlier: 3.618A pdb=" N TRP A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 598 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 624 through 633 removed outlier: 3.569A pdb=" N VAL A 628 " --> pdb=" O HIS A 624 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 645 through 648 Processing helix chain 'A' and resid 656 through 666 removed outlier: 3.893A pdb=" N GLY A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 676 removed outlier: 3.501A pdb=" N VAL A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 676 " --> pdb=" O VAL A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 697 through 705 removed outlier: 4.073A pdb=" N SER A 703 " --> pdb=" O PHE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 743 removed outlier: 3.785A pdb=" N VAL A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 755 removed outlier: 5.658A pdb=" N ALA A 753 " --> pdb=" O TRP A 749 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 754 " --> pdb=" O TYR A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.731A pdb=" N THR A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 851 " --> pdb=" O LYS A 847 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 880 removed outlier: 4.221A pdb=" N ILE A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.609A pdb=" N VAL A 902 " --> pdb=" O VAL A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 927 removed outlier: 3.696A pdb=" N GLN A 920 " --> pdb=" O VAL A 916 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 949 Processing helix chain 'A' and resid 950 through 954 removed outlier: 3.859A pdb=" N ALA A 953 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 985 Processing helix chain 'A' and resid 997 through 1004 removed outlier: 4.093A pdb=" N ALA A1001 " --> pdb=" O HIS A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1030 Processing helix chain 'A' and resid 1074 through 1083 removed outlier: 4.033A pdb=" N LEU A1078 " --> pdb=" O GLY A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 removed outlier: 3.856A pdb=" N ASP A1110 " --> pdb=" O GLY A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1122 removed outlier: 3.542A pdb=" N THR A1122 " --> pdb=" O ARG A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 3.679A pdb=" N ILE A1142 " --> pdb=" O SER A1138 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A1149 " --> pdb=" O LYS A1145 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS A1150 " --> pdb=" O VAL A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1235 removed outlier: 4.059A pdb=" N LEU A1224 " --> pdb=" O GLN A1220 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A1227 " --> pdb=" O ALA A1223 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1257 removed outlier: 4.070A pdb=" N ALA A1247 " --> pdb=" O ILE A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1305 removed outlier: 3.539A pdb=" N LEU A1296 " --> pdb=" O GLY A1292 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A1297 " --> pdb=" O ARG A1293 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A1298 " --> pdb=" O ALA A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1332 Processing helix chain 'A' and resid 1386 through 1394 removed outlier: 3.743A pdb=" N LEU A1391 " --> pdb=" O LEU A1387 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL A1392 " --> pdb=" O SER A1388 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A1393 " --> pdb=" O ASP A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 removed outlier: 3.511A pdb=" N LEU A1398 " --> pdb=" O THR A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1404 removed outlier: 3.839A pdb=" N LYS A1404 " --> pdb=" O GLN A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1440 Processing helix chain 'A' and resid 1451 through 1464 removed outlier: 3.951A pdb=" N LEU A1455 " --> pdb=" O LEU A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1480 removed outlier: 3.594A pdb=" N TRP A1480 " --> pdb=" O ASN A1477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1477 through 1480' Processing helix chain 'A' and resid 1481 through 1496 Processing helix chain 'A' and resid 1520 through 1532 removed outlier: 3.758A pdb=" N GLU A1526 " --> pdb=" O GLU A1522 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A1527 " --> pdb=" O GLN A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1549 removed outlier: 4.203A pdb=" N VAL A1549 " --> pdb=" O ALA A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1559 removed outlier: 3.960A pdb=" N LEU A1555 " --> pdb=" O ALA A1551 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A1556 " --> pdb=" O SER A1552 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A1557 " --> pdb=" O PHE A1553 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A1559 " --> pdb=" O LEU A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1605 removed outlier: 4.536A pdb=" N TYR A1579 " --> pdb=" O SER A1575 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A1581 " --> pdb=" O THR A1577 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE A1584 " --> pdb=" O TRP A1580 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL A1593 " --> pdb=" O CYS A1589 " (cutoff:3.500A) Proline residue: A1594 - end of helix removed outlier: 4.195A pdb=" N VAL A1598 " --> pdb=" O PRO A1594 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE A1601 " --> pdb=" O ILE A1597 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A1602 " --> pdb=" O VAL A1598 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A1603 " --> pdb=" O VAL A1599 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A1605 " --> pdb=" O ILE A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1618 through 1631 removed outlier: 5.080A pdb=" N GLY A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRP A1628 " --> pdb=" O LEU A1624 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A1631 " --> pdb=" O GLY A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1632 through 1638 removed outlier: 3.715A pdb=" N TYR A1635 " --> pdb=" O PRO A1632 " (cutoff:3.500A) Proline residue: A1636 - end of helix No H-bonds generated for 'chain 'A' and resid 1632 through 1638' Processing helix chain 'A' and resid 1647 through 1667 removed outlier: 4.091A pdb=" N THR A1666 " --> pdb=" O GLY A1662 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A1667 " --> pdb=" O SER A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1677 through 1689 removed outlier: 3.563A pdb=" N PHE A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1719 removed outlier: 4.677A pdb=" N MET A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1740 Processing helix chain 'A' and resid 1742 through 1755 removed outlier: 3.699A pdb=" N HIS A1753 " --> pdb=" O LEU A1749 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1842 Processing helix chain 'A' and resid 1861 through 1868 Processing helix chain 'A' and resid 1884 through 1893 removed outlier: 4.000A pdb=" N LEU A1888 " --> pdb=" O GLY A1884 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1913 removed outlier: 3.668A pdb=" N GLN A1904 " --> pdb=" O ALA A1900 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1913 " --> pdb=" O GLY A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1914 through 1917 removed outlier: 4.001A pdb=" N TRP A1917 " --> pdb=" O GLY A1914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1914 through 1917' Processing helix chain 'A' and resid 1928 through 1940 Processing helix chain 'A' and resid 1957 through 1972 removed outlier: 3.977A pdb=" N ARG A1961 " --> pdb=" O ASP A1957 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A1963 " --> pdb=" O SER A1959 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU A1969 " --> pdb=" O TRP A1965 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A1972 " --> pdb=" O LEU A1968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 1991 removed outlier: 3.731A pdb=" N LEU A1991 " --> pdb=" O GLU A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 2008 through 2016 Processing helix chain 'A' and resid 2027 through 2042 removed outlier: 4.666A pdb=" N GLN A2032 " --> pdb=" O ALA A2028 " (cutoff:3.500A) Proline residue: A2033 - end of helix Processing helix chain 'A' and resid 2062 through 2066 Processing helix chain 'A' and resid 2069 through 2077 Processing helix chain 'A' and resid 2096 through 2102 removed outlier: 3.955A pdb=" N PHE A2100 " --> pdb=" O VAL A2096 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.672A pdb=" N TYR A 528 " --> pdb=" O ILE A1473 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A1475 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN A 530 " --> pdb=" O PHE A1475 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.872A pdb=" N LYS A 294 " --> pdb=" O TRP A 435 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY A 437 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 296 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 462 " --> pdb=" O THR A1511 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU A1513 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE A 464 " --> pdb=" O LEU A1513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 960 through 961 Processing sheet with id=AA5, first strand: chain 'A' and resid 1010 through 1012 removed outlier: 5.436A pdb=" N ALA A1012 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1090 through 1094 removed outlier: 7.124A pdb=" N VAL A1100 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A1099 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A1035 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1279 through 1283 removed outlier: 3.510A pdb=" N GLN A1380 " --> pdb=" O SER A1281 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1793 through 1794 removed outlier: 3.558A pdb=" N LEU A1793 " --> pdb=" O ILE A1817 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A1817 " --> pdb=" O LEU A1793 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1824 through 1825 removed outlier: 7.292A pdb=" N GLY A1824 " --> pdb=" O ALA A1996 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2046 through 2051 removed outlier: 4.969A pdb=" N LEU A2047 " --> pdb=" O GLN A2058 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN A2058 " --> pdb=" O LEU A2047 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A2049 " --> pdb=" O ARG A2056 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A2025 " --> pdb=" O ASP A2085 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP A2085 " --> pdb=" O ARG A2025 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1485 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: 5.59 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 4451 1.34 - 1.48: 3980 1.48 - 1.61: 5852 1.61 - 1.75: 7 1.75 - 1.89: 91 Bond restraints: 14381 Sorted by residual: bond pdb=" C17 17F A2202 " pdb=" O9 17F A2202 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C17 17F A2201 " pdb=" O9 17F A2201 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C7 17F A2202 " pdb=" O7 17F A2202 " ideal model delta sigma weight residual 1.335 1.454 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C7 17F A2201 " pdb=" O7 17F A2201 " ideal model delta sigma weight residual 1.335 1.454 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" O2 17F A2202 " pdb=" P1 17F A2202 " ideal model delta sigma weight residual 1.498 1.610 -0.112 2.00e-02 2.50e+03 3.15e+01 ... (remaining 14376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 18962 3.80 - 7.61: 476 7.61 - 11.41: 76 11.41 - 15.22: 22 15.22 - 19.02: 2 Bond angle restraints: 19538 Sorted by residual: angle pdb=" CA TYR A 744 " pdb=" CB TYR A 744 " pdb=" CG TYR A 744 " ideal model delta sigma weight residual 113.90 127.05 -13.15 1.80e+00 3.09e-01 5.34e+01 angle pdb=" CA CYS A 81 " pdb=" CB CYS A 81 " pdb=" SG CYS A 81 " ideal model delta sigma weight residual 114.40 129.87 -15.47 2.30e+00 1.89e-01 4.53e+01 angle pdb=" CB MET A1275 " pdb=" CG MET A1275 " pdb=" SD MET A1275 " ideal model delta sigma weight residual 112.70 131.72 -19.02 3.00e+00 1.11e-01 4.02e+01 angle pdb=" CA CYS A 536 " pdb=" CB CYS A 536 " pdb=" SG CYS A 536 " ideal model delta sigma weight residual 114.40 128.58 -14.18 2.30e+00 1.89e-01 3.80e+01 angle pdb=" CA GLU A 572 " pdb=" CB GLU A 572 " pdb=" CG GLU A 572 " ideal model delta sigma weight residual 114.10 124.26 -10.16 2.00e+00 2.50e-01 2.58e+01 ... (remaining 19533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.65: 8348 33.65 - 67.30: 212 67.30 - 100.95: 20 100.95 - 134.61: 1 134.61 - 168.26: 1 Dihedral angle restraints: 8582 sinusoidal: 3449 harmonic: 5133 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 81 " pdb=" CB CYS A 81 " ideal model delta sinusoidal sigma weight residual 93.00 10.73 82.27 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CA THR A1274 " pdb=" C THR A1274 " pdb=" N MET A1275 " pdb=" CA MET A1275 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA GLY A 863 " pdb=" C GLY A 863 " pdb=" N SER A 864 " pdb=" CA SER A 864 " ideal model delta harmonic sigma weight residual -180.00 -151.84 -28.16 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 8579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1811 0.090 - 0.180: 345 0.180 - 0.271: 46 0.271 - 0.361: 5 0.361 - 0.451: 8 Chirality restraints: 2215 Sorted by residual: chirality pdb=" CB VAL A 719 " pdb=" CA VAL A 719 " pdb=" CG1 VAL A 719 " pdb=" CG2 VAL A 719 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CB ILE A 836 " pdb=" CA ILE A 836 " pdb=" CG1 ILE A 836 " pdb=" CG2 ILE A 836 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CB VAL A 504 " pdb=" CA VAL A 504 " pdb=" CG1 VAL A 504 " pdb=" CG2 VAL A 504 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 2212 not shown) Planarity restraints: 2497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 415 " 0.100 5.00e-02 4.00e+02 1.51e-01 3.66e+01 pdb=" N PRO A 416 " -0.262 5.00e-02 4.00e+02 pdb=" CA PRO A 416 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO A 416 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 744 " 0.060 2.00e-02 2.50e+03 4.27e-02 3.65e+01 pdb=" CG TYR A 744 " -0.102 2.00e-02 2.50e+03 pdb=" CD1 TYR A 744 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 744 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 744 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 744 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 744 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 744 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A1265 " -0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C HIS A1265 " 0.085 2.00e-02 2.50e+03 pdb=" O HIS A1265 " -0.032 2.00e-02 2.50e+03 pdb=" N TYR A1266 " -0.028 2.00e-02 2.50e+03 ... (remaining 2494 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 223 2.65 - 3.21: 11865 3.21 - 3.77: 20910 3.77 - 4.34: 26769 4.34 - 4.90: 45131 Nonbonded interactions: 104898 Sorted by model distance: nonbonded pdb=" NE2 GLN A 24 " pdb=" O6 17F A2201 " model vdw 2.087 3.120 nonbonded pdb=" OH TYR A1276 " pdb=" O GLY A1479 " model vdw 2.124 3.040 nonbonded pdb=" OD2 ASP A1587 " pdb=" OH TYR A1635 " model vdw 2.225 3.040 nonbonded pdb=" OE1 GLN A 642 " pdb=" OH TYR A 744 " model vdw 2.284 3.040 nonbonded pdb=" O LEU A 290 " pdb=" NZ LYS A 411 " model vdw 2.322 3.120 ... (remaining 104893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.990 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 47.010 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.016 0.736 14387 Z= 0.851 Angle : 1.488 19.023 19548 Z= 0.734 Chirality : 0.076 0.451 2215 Planarity : 0.011 0.151 2497 Dihedral : 15.635 168.257 5263 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: -4.54 (0.16), residues: 1783 helix: -3.04 (0.13), residues: 895 sheet: -2.79 (0.38), residues: 156 loop : -2.81 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A1336 HIS 0.018 0.003 HIS A1508 PHE 0.046 0.004 PHE A 297 TYR 0.102 0.004 TYR A 744 ARG 0.028 0.004 ARG A1349 Details of bonding type rmsd hydrogen bonds : bond 0.16421 ( 511) hydrogen bonds : angle 7.39944 ( 1485) SS BOND : bond 0.02116 ( 5) SS BOND : angle 4.26564 ( 10) covalent geometry : bond 0.01441 (14381) covalent geometry : angle 1.48541 (19538) Misc. bond : bond 0.73642 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: A 1275 MET cc_start: 0.7134 (ptp) cc_final: 0.6855 (ptp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2375 time to fit residues: 36.0919 Evaluate side-chains 87 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 119 HIS A1077 GLN ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1488 ASN ** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.230913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.184217 restraints weight = 30223.601| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.81 r_work: 0.3151 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14387 Z= 0.185 Angle : 0.790 10.942 19548 Z= 0.387 Chirality : 0.045 0.268 2215 Planarity : 0.007 0.104 2497 Dihedral : 10.738 164.582 2055 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.34 % Allowed : 5.15 % Favored : 94.51 % 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: -3.55 (0.18), residues: 1783 helix: -2.00 (0.15), residues: 896 sheet: -2.53 (0.39), residues: 149 loop : -2.63 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 500 HIS 0.011 0.001 HIS A 119 PHE 0.027 0.002 PHE A1240 TYR 0.039 0.002 TYR A 744 ARG 0.005 0.000 ARG A1838 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 511) hydrogen bonds : angle 5.32389 ( 1485) SS BOND : bond 0.00782 ( 5) SS BOND : angle 2.07576 ( 10) covalent geometry : bond 0.00445 (14381) covalent geometry : angle 0.78836 (19538) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.7622 (tmm) cc_final: 0.7259 (tmm) REVERT: A 522 ASN cc_start: 0.9093 (t0) cc_final: 0.8670 (p0) REVERT: A 1275 MET cc_start: 0.7113 (ptp) cc_final: 0.6674 (ptp) outliers start: 5 outliers final: 2 residues processed: 103 average time/residue: 0.2239 time to fit residues: 36.5497 Evaluate side-chains 91 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 1284 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 112 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 181 HIS A 766 ASN ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1693 HIS ** 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 = 0.4484 r_free = 0.4484 target = 0.229811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180705 restraints weight = 30018.687| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 4.03 r_work: 0.3106 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14387 Z= 0.207 Angle : 0.771 10.395 19548 Z= 0.373 Chirality : 0.046 0.263 2215 Planarity : 0.006 0.081 2497 Dihedral : 10.179 161.150 2055 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 0.47 % Allowed : 8.40 % Favored : 91.12 % 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: -3.12 (0.19), residues: 1783 helix: -1.55 (0.16), residues: 890 sheet: -2.32 (0.41), residues: 149 loop : -2.55 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 500 HIS 0.017 0.001 HIS A 119 PHE 0.025 0.002 PHE A1240 TYR 0.039 0.002 TYR A 744 ARG 0.005 0.000 ARG A1705 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 511) hydrogen bonds : angle 4.99543 ( 1485) SS BOND : bond 0.00961 ( 5) SS BOND : angle 2.38188 ( 10) covalent geometry : bond 0.00504 (14381) covalent geometry : angle 0.76881 (19538) Misc. bond : bond 0.00293 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7681 (tmm) cc_final: 0.7402 (tmm) REVERT: A 522 ASN cc_start: 0.9083 (t0) cc_final: 0.8769 (p0) REVERT: A 965 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 1275 MET cc_start: 0.7422 (ptp) cc_final: 0.6504 (ptp) REVERT: A 1703 MET cc_start: 0.7376 (mmt) cc_final: 0.7123 (mmt) outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.2413 time to fit residues: 39.5331 Evaluate side-chains 102 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1284 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 50.0000 chunk 19 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 54 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 181 HIS A 766 ASN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1693 HIS ** 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 = 0.4570 r_free = 0.4570 target = 0.235482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.196813 restraints weight = 34712.050| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 3.27 r_work: 0.3717 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14387 Z= 0.210 Angle : 0.748 10.432 19548 Z= 0.361 Chirality : 0.045 0.260 2215 Planarity : 0.006 0.069 2497 Dihedral : 9.828 160.814 2055 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 0.61 % Allowed : 10.57 % Favored : 88.82 % 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: -2.84 (0.19), residues: 1783 helix: -1.29 (0.17), residues: 886 sheet: -2.22 (0.42), residues: 149 loop : -2.47 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 500 HIS 0.021 0.001 HIS A 119 PHE 0.024 0.002 PHE A1486 TYR 0.036 0.002 TYR A 744 ARG 0.004 0.000 ARG A1705 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 511) hydrogen bonds : angle 4.82827 ( 1485) SS BOND : bond 0.00928 ( 5) SS BOND : angle 2.34952 ( 10) covalent geometry : bond 0.00512 (14381) covalent geometry : angle 0.74632 (19538) Misc. bond : bond 0.00240 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.7568 (tmm) cc_final: 0.7141 (tmm) REVERT: A 522 ASN cc_start: 0.9067 (t0) cc_final: 0.8725 (p0) REVERT: A 1275 MET cc_start: 0.7043 (ptp) cc_final: 0.5792 (ptp) REVERT: A 1839 MET cc_start: 0.3170 (ptp) cc_final: 0.2960 (ptp) outliers start: 9 outliers final: 7 residues processed: 107 average time/residue: 0.2308 time to fit residues: 39.0386 Evaluate side-chains 101 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1524 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 28 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 163 optimal weight: 50.0000 chunk 56 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 181 HIS A 766 ASN ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1693 HIS ** 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 = 0.4555 r_free = 0.4555 target = 0.233787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.189808 restraints weight = 26277.075| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 3.42 r_work: 0.3671 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14387 Z= 0.253 Angle : 0.770 11.247 19548 Z= 0.372 Chirality : 0.046 0.261 2215 Planarity : 0.006 0.064 2497 Dihedral : 9.773 159.997 2055 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 0.95 % Allowed : 12.33 % Favored : 86.72 % 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: -2.76 (0.19), residues: 1783 helix: -1.21 (0.17), residues: 889 sheet: -2.15 (0.42), residues: 149 loop : -2.45 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 500 HIS 0.018 0.001 HIS A 181 PHE 0.026 0.002 PHE A1486 TYR 0.040 0.002 TYR A 744 ARG 0.004 0.000 ARG A 120 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 511) hydrogen bonds : angle 4.79754 ( 1485) SS BOND : bond 0.01047 ( 5) SS BOND : angle 2.55987 ( 10) covalent geometry : bond 0.00620 (14381) covalent geometry : angle 0.76795 (19538) Misc. bond : bond 0.00201 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.7552 (tmm) cc_final: 0.7083 (tmm) REVERT: A 522 ASN cc_start: 0.9070 (t0) cc_final: 0.8755 (p0) REVERT: A 1275 MET cc_start: 0.7021 (ptp) cc_final: 0.6462 (ptp) REVERT: A 1382 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (mt) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.2237 time to fit residues: 36.1197 Evaluate side-chains 98 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1336 TRP Chi-restraints excluded: chain A residue 1382 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 50.0000 chunk 133 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 766 ASN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 HIS ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1693 HIS ** 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 = 0.4571 r_free = 0.4571 target = 0.235649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.193652 restraints weight = 32041.180| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 3.60 r_work: 0.3668 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14387 Z= 0.168 Angle : 0.693 10.554 19548 Z= 0.334 Chirality : 0.043 0.249 2215 Planarity : 0.005 0.062 2497 Dihedral : 9.326 162.539 2055 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.88 % Allowed : 12.94 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.47 (0.20), residues: 1783 helix: -0.95 (0.17), residues: 885 sheet: -1.93 (0.43), residues: 149 loop : -2.34 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 500 HIS 0.004 0.001 HIS A1508 PHE 0.020 0.001 PHE A1240 TYR 0.028 0.001 TYR A 744 ARG 0.007 0.000 ARG A1434 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 511) hydrogen bonds : angle 4.57343 ( 1485) SS BOND : bond 0.00724 ( 5) SS BOND : angle 1.99410 ( 10) covalent geometry : bond 0.00409 (14381) covalent geometry : angle 0.69213 (19538) Misc. bond : bond 0.00187 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: A 522 ASN cc_start: 0.9089 (t0) cc_final: 0.8846 (p0) REVERT: A 1275 MET cc_start: 0.6786 (ptp) cc_final: 0.6198 (ptp) REVERT: A 1382 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7965 (mt) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.2023 time to fit residues: 35.9494 Evaluate side-chains 102 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1336 TRP Chi-restraints excluded: chain A residue 1382 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 179 optimal weight: 20.0000 chunk 166 optimal weight: 40.0000 chunk 175 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 167 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 766 ASN ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1693 HIS ** 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 = 0.4551 r_free = 0.4551 target = 0.233354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.193228 restraints weight = 29001.684| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 3.22 r_work: 0.3704 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14387 Z= 0.259 Angle : 0.770 10.486 19548 Z= 0.372 Chirality : 0.046 0.247 2215 Planarity : 0.006 0.062 2497 Dihedral : 9.524 159.386 2055 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 1.15 % Allowed : 13.62 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.50 (0.20), residues: 1783 helix: -0.98 (0.17), residues: 888 sheet: -1.85 (0.47), residues: 135 loop : -2.39 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 500 HIS 0.006 0.001 HIS A1508 PHE 0.027 0.002 PHE A1486 TYR 0.041 0.002 TYR A 744 ARG 0.005 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 511) hydrogen bonds : angle 4.67622 ( 1485) SS BOND : bond 0.01067 ( 5) SS BOND : angle 2.59736 ( 10) covalent geometry : bond 0.00637 (14381) covalent geometry : angle 0.76766 (19538) Misc. bond : bond 0.00165 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8068 (tt) REVERT: A 522 ASN cc_start: 0.9037 (t0) cc_final: 0.8787 (p0) REVERT: A 1275 MET cc_start: 0.6862 (ptp) cc_final: 0.6010 (ptp) REVERT: A 1382 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8044 (mt) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.2399 time to fit residues: 39.7237 Evaluate side-chains 101 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1336 TRP Chi-restraints excluded: chain A residue 1382 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 135 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 179 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 152 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 766 ASN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 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 = 0.4573 r_free = 0.4573 target = 0.235951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.195925 restraints weight = 40249.058| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.51 r_work: 0.3585 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14387 Z= 0.152 Angle : 0.694 10.603 19548 Z= 0.334 Chirality : 0.043 0.268 2215 Planarity : 0.005 0.061 2497 Dihedral : 9.218 161.765 2055 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 1.15 % Allowed : 14.02 % Favored : 84.82 % 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: -2.32 (0.20), residues: 1783 helix: -0.82 (0.17), residues: 887 sheet: -1.81 (0.44), residues: 149 loop : -2.30 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 500 HIS 0.024 0.001 HIS A 181 PHE 0.019 0.001 PHE A1240 TYR 0.029 0.001 TYR A 744 ARG 0.004 0.000 ARG A1007 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 511) hydrogen bonds : angle 4.52405 ( 1485) SS BOND : bond 0.00706 ( 5) SS BOND : angle 1.99268 ( 10) covalent geometry : bond 0.00368 (14381) covalent geometry : angle 0.69276 (19538) Misc. bond : bond 0.00162 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 965 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 1275 MET cc_start: 0.6630 (ptp) cc_final: 0.5896 (ptp) REVERT: A 1382 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7947 (mt) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.2163 time to fit residues: 37.7764 Evaluate side-chains 105 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 390 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1336 TRP Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1508 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 10.0000 chunk 113 optimal weight: 0.0050 chunk 161 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 642 GLN A 766 ASN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 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 = 0.4595 r_free = 0.4595 target = 0.238638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.197838 restraints weight = 35004.680| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 3.52 r_work: 0.3548 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14387 Z= 0.114 Angle : 0.652 10.155 19548 Z= 0.313 Chirality : 0.042 0.261 2215 Planarity : 0.005 0.060 2497 Dihedral : 8.780 164.880 2055 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.81 % Allowed : 14.43 % Favored : 84.76 % 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: -2.02 (0.20), residues: 1783 helix: -0.55 (0.18), residues: 880 sheet: -1.52 (0.45), residues: 147 loop : -2.21 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1480 HIS 0.004 0.001 HIS A 181 PHE 0.020 0.001 PHE A1240 TYR 0.015 0.001 TYR A 744 ARG 0.006 0.000 ARG A1705 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 511) hydrogen bonds : angle 4.33735 ( 1485) SS BOND : bond 0.00435 ( 5) SS BOND : angle 1.48108 ( 10) covalent geometry : bond 0.00268 (14381) covalent geometry : angle 0.65084 (19538) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7584 (tt) REVERT: A 749 TRP cc_start: 0.7530 (m100) cc_final: 0.6228 (t60) REVERT: A 766 ASN cc_start: 0.5890 (m-40) cc_final: 0.5652 (m110) REVERT: A 1275 MET cc_start: 0.6224 (ptp) cc_final: 0.5508 (ptp) REVERT: A 1869 MET cc_start: 0.2089 (tpt) cc_final: 0.1770 (tpt) outliers start: 12 outliers final: 10 residues processed: 108 average time/residue: 0.2162 time to fit residues: 37.5756 Evaluate side-chains 104 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 390 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1336 TRP Chi-restraints excluded: chain A residue 1508 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 69 optimal weight: 0.0470 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 0.3980 chunk 53 optimal weight: 0.0470 chunk 63 optimal weight: 0.0870 chunk 168 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1693 HIS ** 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 = 0.4605 r_free = 0.4605 target = 0.239818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.200874 restraints weight = 43415.384| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 3.59 r_work: 0.3742 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 14387 Z= 0.105 Angle : 0.648 9.821 19548 Z= 0.308 Chirality : 0.041 0.262 2215 Planarity : 0.005 0.058 2497 Dihedral : 8.587 166.064 2055 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.61 % Allowed : 14.84 % Favored : 84.55 % 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: -1.82 (0.20), residues: 1783 helix: -0.39 (0.18), residues: 877 sheet: -1.19 (0.46), residues: 146 loop : -2.16 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 979 HIS 0.019 0.001 HIS A 181 PHE 0.022 0.001 PHE A1240 TYR 0.012 0.001 TYR A 744 ARG 0.005 0.000 ARG A1705 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 511) hydrogen bonds : angle 4.24952 ( 1485) SS BOND : bond 0.00341 ( 5) SS BOND : angle 1.25441 ( 10) covalent geometry : bond 0.00246 (14381) covalent geometry : angle 0.64709 (19538) Misc. bond : bond 0.00127 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7340 (tt) REVERT: A 749 TRP cc_start: 0.7524 (m100) cc_final: 0.6197 (t60) REVERT: A 1869 MET cc_start: 0.2464 (tpt) cc_final: 0.2249 (tpt) outliers start: 9 outliers final: 7 residues processed: 102 average time/residue: 0.2347 time to fit residues: 38.3863 Evaluate side-chains 101 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 390 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1336 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 0.0040 chunk 168 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 111 optimal weight: 0.1980 chunk 65 optimal weight: 0.0980 chunk 86 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.238841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.198886 restraints weight = 40048.347| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.75 r_work: 0.3770 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14387 Z= 0.188 Angle : 0.704 11.108 19548 Z= 0.336 Chirality : 0.044 0.259 2215 Planarity : 0.005 0.059 2497 Dihedral : 8.850 162.133 2055 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 0.81 % Allowed : 15.24 % Favored : 83.94 % 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: -1.94 (0.20), residues: 1783 helix: -0.51 (0.18), residues: 882 sheet: -1.35 (0.47), residues: 136 loop : -2.18 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 500 HIS 0.005 0.001 HIS A1508 PHE 0.025 0.001 PHE A1486 TYR 0.021 0.001 TYR A 744 ARG 0.004 0.000 ARG A1007 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 511) hydrogen bonds : angle 4.32400 ( 1485) SS BOND : bond 0.00828 ( 5) SS BOND : angle 2.12607 ( 10) covalent geometry : bond 0.00460 (14381) covalent geometry : angle 0.70255 (19538) Misc. bond : bond 0.00133 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6333.70 seconds wall clock time: 110 minutes 26.67 seconds (6626.67 seconds total)