Starting phenix.real_space_refine on Fri Sep 27 10:24:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/09_2024/7e7q_31002_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/09_2024/7e7q_31002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/09_2024/7e7q_31002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/09_2024/7e7q_31002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/09_2024/7e7q_31002_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e7q_31002/09_2024/7e7q_31002_neut.cif" } resolution = 3.3 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 85 5.16 5 C 9819 2.51 5 N 2558 2.21 5 O 2809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15279 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 14995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1958, 14995 Classifications: {'peptide': 1958} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PTRANS': 103, 'TRANS': 1854} Chain breaks: 15 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 641 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 527 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 13, 'GLU:plan': 21, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 381 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {' MG': 2, 'ATP': 2, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 9.02, per 1000 atoms: 0.59 Number of scatterers: 15279 At special positions: 0 Unit cell: (113.4, 93.96, 236.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 6 15.00 Mg 2 11.99 O 2809 8.00 N 2558 7.00 C 9819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.02 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=1.89 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1455 " distance=2.05 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA D 3 " - " BMA D 4 " " BMA M 3 " - " BMA M 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " BETA1-6 " BMA D 3 " - " BMA D 5 " " BMA M 3 " - " BMA M 5 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 444 " " NAG A2303 " - " ASN A 504 " " NAG A2304 " - " ASN A1457 " " NAG A2305 " - " ASN A1469 " " NAG A2306 " - " ASN A1588 " " NAG A2307 " - " ASN A1662 " " NAG D 1 " - " ASN A 415 " " NAG M 1 " - " ASN A1529 " Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 2.1 seconds 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3662 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 13 sheets defined 51.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 1 through 22 removed outlier: 3.762A pdb=" N ARG A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 32 through 35 removed outlier: 3.526A pdb=" N LEU A 35 " --> pdb=" O PRO A 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 35' Processing helix chain 'A' and resid 36 through 45 removed outlier: 3.699A pdb=" N ASN A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 76 Processing helix chain 'A' and resid 100 through 112 removed outlier: 3.809A pdb=" N TYR A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.585A pdb=" N GLN A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.035A pdb=" N LEU A 260 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 removed outlier: 3.660A pdb=" N MET A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Proline residue: A 282 - end of helix removed outlier: 3.658A pdb=" N GLN A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 314 through 324 Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 383 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'A' and resid 415 through 430 removed outlier: 4.184A pdb=" N VAL A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 461 through 470 removed outlier: 3.523A pdb=" N ARG A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.751A pdb=" N ILE A 502 " --> pdb=" O TRP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 518 removed outlier: 3.847A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 545 removed outlier: 4.131A pdb=" N GLU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.683A pdb=" N VAL A 578 " --> pdb=" O ILE A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 607 through 623 removed outlier: 3.696A pdb=" N GLN A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 Proline residue: A 656 - end of helix Processing helix chain 'A' and resid 663 through 680 removed outlier: 3.508A pdb=" N VAL A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 689 removed outlier: 3.624A pdb=" N THR A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 722 removed outlier: 3.962A pdb=" N ILE A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 711 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 753 removed outlier: 3.534A pdb=" N LEU A 733 " --> pdb=" O ASP A 729 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 763 removed outlier: 3.642A pdb=" N ALA A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 773 through 778 Processing helix chain 'A' and resid 787 through 795 Processing helix chain 'A' and resid 797 through 815 removed outlier: 3.586A pdb=" N TYR A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.577A pdb=" N SER A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 844 " --> pdb=" O MET A 840 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 845 " --> pdb=" O GLN A 841 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 859 " --> pdb=" O TRP A 855 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 974 Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1019 through 1031 removed outlier: 4.028A pdb=" N GLN A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A1031 " --> pdb=" O TYR A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1050 removed outlier: 3.778A pdb=" N GLU A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1077 removed outlier: 3.535A pdb=" N VAL A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A1075 " --> pdb=" O SER A1071 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 removed outlier: 3.542A pdb=" N TYR A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1126 removed outlier: 3.765A pdb=" N ASP A1124 " --> pdb=" O MET A1120 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A1125 " --> pdb=" O ASP A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1152 Processing helix chain 'A' and resid 1205 through 1212 Processing helix chain 'A' and resid 1240 through 1253 removed outlier: 3.889A pdb=" N GLU A1252 " --> pdb=" O ARG A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1278 removed outlier: 4.338A pdb=" N ILE A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A1273 " --> pdb=" O LEU A1269 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A1276 " --> pdb=" O ILE A1272 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1277 " --> pdb=" O PHE A1273 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1369 removed outlier: 3.548A pdb=" N GLN A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A1368 " --> pdb=" O GLN A1364 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A1369 " --> pdb=" O HIS A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1391 removed outlier: 3.666A pdb=" N PHE A1373 " --> pdb=" O SER A1369 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Proline residue: A1380 - end of helix Processing helix chain 'A' and resid 1406 through 1410 removed outlier: 3.847A pdb=" N TYR A1410 " --> pdb=" O PRO A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1477 removed outlier: 3.559A pdb=" N THR A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A1475 " --> pdb=" O THR A1471 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A1477 " --> pdb=" O LEU A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1544 Proline residue: A1539 - end of helix removed outlier: 3.614A pdb=" N SER A1544 " --> pdb=" O ALA A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1588 removed outlier: 3.728A pdb=" N VAL A1577 " --> pdb=" O GLY A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1599 removed outlier: 3.983A pdb=" N GLU A1597 " --> pdb=" O PRO A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1606 Processing helix chain 'A' and resid 1625 through 1641 removed outlier: 3.590A pdb=" N SER A1629 " --> pdb=" O HIS A1625 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A1630 " --> pdb=" O ALA A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1652 removed outlier: 3.836A pdb=" N TYR A1652 " --> pdb=" O PRO A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1691 removed outlier: 3.623A pdb=" N VAL A1673 " --> pdb=" O SER A1669 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A1681 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A1683 " --> pdb=" O ASP A1679 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1696 Processing helix chain 'A' and resid 1697 through 1706 removed outlier: 4.134A pdb=" N LEU A1701 " --> pdb=" O PHE A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1716 removed outlier: 3.688A pdb=" N SER A1716 " --> pdb=" O LEU A1712 " (cutoff:3.500A) Processing helix chain 'A' and resid 1719 through 1750 removed outlier: 4.029A pdb=" N TYR A1723 " --> pdb=" O SER A1719 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET A1733 " --> pdb=" O LEU A1729 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A1737 " --> pdb=" O MET A1733 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A1738 " --> pdb=" O ASN A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1775 removed outlier: 3.601A pdb=" N LEU A1769 " --> pdb=" O ALA A1765 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP A1772 " --> pdb=" O LEU A1768 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1784 removed outlier: 4.823A pdb=" N TYR A1779 " --> pdb=" O PRO A1776 " (cutoff:3.500A) Proline residue: A1780 - end of helix removed outlier: 3.627A pdb=" N PHE A1783 " --> pdb=" O PRO A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1787 through 1806 Processing helix chain 'A' and resid 1808 through 1814 removed outlier: 3.575A pdb=" N GLU A1814 " --> pdb=" O THR A1810 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1833 removed outlier: 3.879A pdb=" N ARG A1824 " --> pdb=" O ARG A1820 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A1825 " --> pdb=" O THR A1821 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A1831 " --> pdb=" O ALA A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1857 removed outlier: 4.016A pdb=" N GLY A1844 " --> pdb=" O CYS A1840 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A1846 " --> pdb=" O GLY A1842 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A1849 " --> pdb=" O LEU A1845 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A1853 " --> pdb=" O ALA A1849 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1854 " --> pdb=" O LEU A1850 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N THR A1855 " --> pdb=" O SER A1851 " (cutoff:3.500A) Processing helix chain 'A' and resid 1858 through 1861 Processing helix chain 'A' and resid 1875 through 1901 removed outlier: 3.992A pdb=" N VAL A1883 " --> pdb=" O LEU A1879 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1884 " --> pdb=" O PHE A1880 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1887 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A1890 " --> pdb=" O GLY A1886 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1891 " --> pdb=" O VAL A1887 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A1898 " --> pdb=" O LEU A1894 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS A1899 " --> pdb=" O LEU A1895 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A1900 " --> pdb=" O VAL A1896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1987 removed outlier: 3.619A pdb=" N THR A1981 " --> pdb=" O GLY A1977 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A1982 " --> pdb=" O LYS A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 2009 through 2012 removed outlier: 3.809A pdb=" N GLN A2012 " --> pdb=" O GLU A2009 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2009 through 2012' Processing helix chain 'A' and resid 2028 through 2039 removed outlier: 3.782A pdb=" N HIS A2032 " --> pdb=" O THR A2028 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A2033 " --> pdb=" O GLY A2029 " (cutoff:3.500A) Processing helix chain 'A' and resid 2046 through 2059 removed outlier: 3.547A pdb=" N VAL A2050 " --> pdb=" O GLU A2046 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A2058 " --> pdb=" O SER A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2071 Processing helix chain 'A' and resid 2074 through 2083 removed outlier: 3.648A pdb=" N LYS A2078 " --> pdb=" O GLY A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2118 removed outlier: 3.687A pdb=" N ARG A2107 " --> pdb=" O PRO A2103 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET A2108 " --> pdb=" O GLN A2104 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2134 removed outlier: 3.813A pdb=" N CYS A2133 " --> pdb=" O SER A2129 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A2134 " --> pdb=" O MET A2130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2129 through 2134' Processing helix chain 'A' and resid 2153 through 2161 removed outlier: 3.767A pdb=" N LEU A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A2160 " --> pdb=" O HIS A2156 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2190 removed outlier: 3.746A pdb=" N PHE A2189 " --> pdb=" O GLU A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2215 through 2220 Processing helix chain 'A' and resid 2221 through 2223 No H-bonds generated for 'chain 'A' and resid 2221 through 2223' Processing helix chain 'A' and resid 2240 through 2251 removed outlier: 3.979A pdb=" N GLN A2251 " --> pdb=" O ASN A2247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.863A pdb=" N TYR A 49 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.634A pdb=" N LYS A1616 " --> pdb=" O SER A1561 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 527 removed outlier: 5.765A pdb=" N LYS A 397 " --> pdb=" O TRP A 548 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLY A 550 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 399 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 552 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 944 through 947 removed outlier: 3.737A pdb=" N VAL A 946 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 944 through 947 removed outlier: 3.737A pdb=" N VAL A 946 " --> pdb=" O LYS A 936 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU A 934 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER A 984 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1005 through 1008 removed outlier: 6.139A pdb=" N GLY A1006 " --> pdb=" O ILE A1084 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASP A1086 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS A1008 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A1116 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR A 959 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS A1140 " --> pdb=" O ILE A1132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1155 through 1157 Processing sheet with id=AA8, first strand: chain 'A' and resid 1159 through 1161 removed outlier: 5.728A pdb=" N VAL A1160 " --> pdb=" O SER A1260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1414 through 1417 removed outlier: 3.666A pdb=" N PHE A1417 " --> pdb=" O GLN A1523 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1961 through 1962 Processing sheet with id=AB2, first strand: chain 'A' and resid 1943 through 1945 removed outlier: 5.799A pdb=" N LEU A1943 " --> pdb=" O ARG A1957 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A1957 " --> pdb=" O LEU A1943 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1967 through 1968 removed outlier: 6.299A pdb=" N GLY A2015 " --> pdb=" O LEU A2093 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2140 through 2143 removed outlier: 6.009A pdb=" N LEU A2140 " --> pdb=" O MET A2151 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET A2151 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A2142 " --> pdb=" O ARG A2149 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1755 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: 5.88 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4617 1.33 - 1.46: 3167 1.46 - 1.58: 7703 1.58 - 1.70: 10 1.70 - 1.82: 135 Bond restraints: 15632 Sorted by residual: bond pdb=" C4 ATP A2309 " pdb=" C5 ATP A2309 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.88e+01 bond pdb=" C4 ATP A2308 " pdb=" C5 ATP A2308 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.45e+01 bond pdb=" C5 ATP A2309 " pdb=" C6 ATP A2309 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.04e+01 bond pdb=" C4 ATP A2308 " pdb=" N9 ATP A2308 " ideal model delta sigma weight residual 1.374 1.316 0.058 1.00e-02 1.00e+04 3.39e+01 bond pdb=" C4 ATP A2309 " pdb=" N9 ATP A2309 " ideal model delta sigma weight residual 1.374 1.317 0.057 1.00e-02 1.00e+04 3.24e+01 ... (remaining 15627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 21140 4.69 - 9.38: 128 9.38 - 14.07: 7 14.07 - 18.75: 2 18.75 - 23.44: 2 Bond angle restraints: 21279 Sorted by residual: angle pdb=" PB ATP A2309 " pdb=" O3B ATP A2309 " pdb=" PG ATP A2309 " ideal model delta sigma weight residual 139.87 116.43 23.44 1.00e+00 1.00e+00 5.50e+02 angle pdb=" PB ATP A2308 " pdb=" O3B ATP A2308 " pdb=" PG ATP A2308 " ideal model delta sigma weight residual 139.87 119.55 20.32 1.00e+00 1.00e+00 4.13e+02 angle pdb=" PA ATP A2309 " pdb=" O3A ATP A2309 " pdb=" PB ATP A2309 " ideal model delta sigma weight residual 136.83 121.41 15.42 1.00e+00 1.00e+00 2.38e+02 angle pdb=" PA ATP A2308 " pdb=" O3A ATP A2308 " pdb=" PB ATP A2308 " ideal model delta sigma weight residual 136.83 122.11 14.72 1.00e+00 1.00e+00 2.17e+02 angle pdb=" C5 ATP A2308 " pdb=" C4 ATP A2308 " pdb=" N3 ATP A2308 " ideal model delta sigma weight residual 126.80 119.03 7.77 1.00e+00 1.00e+00 6.04e+01 ... (remaining 21274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 8714 22.39 - 44.77: 617 44.77 - 67.16: 97 67.16 - 89.55: 53 89.55 - 111.93: 25 Dihedral angle restraints: 9506 sinusoidal: 3846 harmonic: 5660 Sorted by residual: dihedral pdb=" CB CYS A1444 " pdb=" SG CYS A1444 " pdb=" SG CYS A1455 " pdb=" CB CYS A1455 " ideal model delta sinusoidal sigma weight residual -86.00 -164.95 78.95 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CA GLY A 924 " pdb=" C GLY A 924 " pdb=" N TRP A 925 " pdb=" CA TRP A 925 " ideal model delta harmonic sigma weight residual -180.00 -143.63 -36.37 0 5.00e+00 4.00e-02 5.29e+01 dihedral pdb=" CB CYS A 641 " pdb=" SG CYS A 641 " pdb=" SG CYS A1490 " pdb=" CB CYS A1490 " ideal model delta sinusoidal sigma weight residual -86.00 -144.78 58.78 1 1.00e+01 1.00e-02 4.62e+01 ... (remaining 9503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2322 0.109 - 0.217: 153 0.217 - 0.326: 8 0.326 - 0.434: 2 0.434 - 0.543: 2 Chirality restraints: 2487 Sorted by residual: chirality pdb=" C1 NAG A2304 " pdb=" ND2 ASN A1457 " pdb=" C2 NAG A2304 " pdb=" O5 NAG A2304 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C1 NAG A2302 " pdb=" ND2 ASN A 444 " pdb=" C2 NAG A2302 " pdb=" O5 NAG A2302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" CB THR A2028 " pdb=" CA THR A2028 " pdb=" OG1 THR A2028 " pdb=" CG2 THR A2028 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 2484 not shown) Planarity restraints: 2675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 380 " 0.091 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO A 381 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 961 " 0.028 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE A 961 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 961 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 961 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 961 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 961 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 961 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1735 " 0.023 2.00e-02 2.50e+03 2.16e-02 9.36e+00 pdb=" CG TYR A1735 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR A1735 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A1735 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A1735 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A1735 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A1735 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A1735 " -0.001 2.00e-02 2.50e+03 ... (remaining 2672 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 38 2.33 - 2.97: 7806 2.97 - 3.61: 20645 3.61 - 4.26: 31518 4.26 - 4.90: 55423 Nonbonded interactions: 115430 Sorted by model distance: nonbonded pdb=" O GLY A1226 " pdb=" O ALA A2135 " model vdw 1.683 3.040 nonbonded pdb=" O GLY A1154 " pdb=" O ASP A1266 " model vdw 1.738 3.040 nonbonded pdb=" O2G ATP A2309 " pdb="MG MG A2311 " model vdw 1.855 2.170 nonbonded pdb=" O3G ATP A2308 " pdb="MG MG A2310 " model vdw 1.920 2.170 nonbonded pdb=" OE1 GLN A2019 " pdb="MG MG A2311 " model vdw 1.962 2.170 ... (remaining 115425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 37.270 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.083 15632 Z= 0.698 Angle : 1.076 23.442 21279 Z= 0.624 Chirality : 0.062 0.543 2487 Planarity : 0.006 0.138 2666 Dihedral : 17.665 111.933 5826 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.16 % Favored : 88.37 % Rotamer: Outliers : 1.16 % Allowed : 1.29 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.87 (0.18), residues: 1926 helix: -0.75 (0.17), residues: 911 sheet: -1.98 (0.39), residues: 155 loop : -3.24 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 31 HIS 0.011 0.002 HIS A1118 PHE 0.055 0.003 PHE A 961 TYR 0.051 0.003 TYR A1735 ARG 0.022 0.001 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1527 ASP cc_start: 0.8008 (t70) cc_final: 0.7751 (t0) REVERT: A 1566 LEU cc_start: 0.8289 (pt) cc_final: 0.8057 (pt) REVERT: A 2048 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7310 (tm-30) outliers start: 18 outliers final: 14 residues processed: 204 average time/residue: 0.2785 time to fit residues: 84.4516 Evaluate side-chains 178 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1261 SER Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1267 THR Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1275 LYS Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1489 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 HIS A1053 HIS A1826 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15632 Z= 0.204 Angle : 0.705 10.284 21279 Z= 0.351 Chirality : 0.047 0.395 2487 Planarity : 0.005 0.105 2666 Dihedral : 13.958 101.101 2522 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.31 % Favored : 91.54 % Rotamer: Outliers : 1.55 % Allowed : 8.12 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.25 (0.19), residues: 1926 helix: -0.12 (0.17), residues: 931 sheet: -1.90 (0.39), residues: 172 loop : -3.10 (0.19), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 871 HIS 0.005 0.001 HIS A1838 PHE 0.024 0.001 PHE A1839 TYR 0.016 0.001 TYR A2063 ARG 0.008 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.6638 (t80) cc_final: 0.6417 (t80) REVERT: A 1045 MET cc_start: 0.8825 (ttm) cc_final: 0.8586 (ttt) REVERT: A 1233 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7147 (pp) REVERT: A 1259 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6300 (mt) REVERT: A 1271 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: A 1527 ASP cc_start: 0.7941 (t70) cc_final: 0.7706 (t0) REVERT: A 1831 LYS cc_start: 0.8163 (mttp) cc_final: 0.7574 (mtpp) REVERT: A 2086 ILE cc_start: 0.8755 (mm) cc_final: 0.8509 (mm) outliers start: 24 outliers final: 11 residues processed: 207 average time/residue: 0.2891 time to fit residues: 88.5195 Evaluate side-chains 189 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1267 THR Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1489 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 175 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 HIS A1119 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15632 Z= 0.355 Angle : 0.740 11.410 21279 Z= 0.364 Chirality : 0.050 0.380 2487 Planarity : 0.005 0.084 2666 Dihedral : 12.434 102.342 2515 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.35 % Favored : 90.55 % Rotamer: Outliers : 1.93 % Allowed : 11.73 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.08 (0.19), residues: 1926 helix: -0.00 (0.18), residues: 933 sheet: -1.57 (0.40), residues: 163 loop : -3.04 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 871 HIS 0.008 0.001 HIS A 922 PHE 0.027 0.002 PHE A 961 TYR 0.015 0.002 TYR A 400 ARG 0.005 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.6636 (t80) cc_final: 0.6410 (t80) REVERT: A 1259 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6561 (mt) REVERT: A 1271 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: A 1527 ASP cc_start: 0.7899 (t70) cc_final: 0.7642 (t0) REVERT: A 1735 TYR cc_start: 0.8876 (t80) cc_final: 0.8570 (t80) REVERT: A 1831 LYS cc_start: 0.8190 (mttp) cc_final: 0.7594 (mtpp) REVERT: A 2063 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.7117 (p90) outliers start: 30 outliers final: 16 residues processed: 201 average time/residue: 0.2821 time to fit residues: 84.2018 Evaluate side-chains 185 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1259 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1267 THR Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 2063 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 84 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 HIS ** A1442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15632 Z= 0.173 Angle : 0.634 9.770 21279 Z= 0.311 Chirality : 0.046 0.366 2487 Planarity : 0.005 0.070 2666 Dihedral : 10.503 103.640 2507 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.37 % Rotamer: Outliers : 2.13 % Allowed : 14.05 % Favored : 83.83 % 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: -1.76 (0.19), residues: 1926 helix: 0.27 (0.18), residues: 944 sheet: -1.40 (0.40), residues: 172 loop : -2.94 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 871 HIS 0.029 0.001 HIS A1119 PHE 0.025 0.001 PHE A 287 TYR 0.013 0.001 TYR A 400 ARG 0.003 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 190 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TYR cc_start: 0.6532 (t80) cc_final: 0.6306 (t80) REVERT: A 689 GLN cc_start: 0.7575 (mp10) cc_final: 0.7288 (mp10) REVERT: A 922 HIS cc_start: 0.5382 (t70) cc_final: 0.5058 (t-170) REVERT: A 1085 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8801 (pp) REVERT: A 1271 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: A 1274 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8292 (mm) REVERT: A 1527 ASP cc_start: 0.7831 (t70) cc_final: 0.7597 (t70) REVERT: A 1735 TYR cc_start: 0.8744 (t80) cc_final: 0.8398 (t80) REVERT: A 1831 LYS cc_start: 0.8168 (mttp) cc_final: 0.7546 (mtpp) REVERT: A 2063 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.7062 (p90) REVERT: A 2086 ILE cc_start: 0.8779 (mm) cc_final: 0.8550 (mm) REVERT: A 2205 MET cc_start: 0.6065 (mmp) cc_final: 0.5527 (mmm) outliers start: 33 outliers final: 18 residues processed: 217 average time/residue: 0.2598 time to fit residues: 85.0844 Evaluate side-chains 198 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1267 THR Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain A residue 2200 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 0.3980 chunk 77 optimal weight: 0.0670 chunk 160 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 169 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 overall best weight: 0.4520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 HIS ** A1442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1608 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15632 Z= 0.156 Angle : 0.594 9.833 21279 Z= 0.291 Chirality : 0.045 0.344 2487 Planarity : 0.004 0.059 2666 Dihedral : 9.289 104.771 2504 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.68 % Rotamer: Outliers : 2.38 % Allowed : 15.01 % Favored : 82.60 % 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: -1.46 (0.20), residues: 1926 helix: 0.49 (0.18), residues: 951 sheet: -1.16 (0.40), residues: 171 loop : -2.82 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 871 HIS 0.003 0.001 HIS A 922 PHE 0.029 0.001 PHE A1839 TYR 0.013 0.001 TYR A 400 ARG 0.004 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.6546 (t80) cc_final: 0.6281 (t80) REVERT: A 89 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: A 508 ARG cc_start: 0.7134 (tpt90) cc_final: 0.6847 (ttm110) REVERT: A 573 MET cc_start: 0.9396 (mtm) cc_final: 0.9002 (mtm) REVERT: A 689 GLN cc_start: 0.7561 (mp10) cc_final: 0.7306 (mp10) REVERT: A 1085 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8769 (pp) REVERT: A 1271 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6473 (mp0) REVERT: A 1735 TYR cc_start: 0.8630 (t80) cc_final: 0.8352 (t80) REVERT: A 1814 GLU cc_start: 0.7742 (pp20) cc_final: 0.7473 (pp20) REVERT: A 1831 LYS cc_start: 0.8173 (mttp) cc_final: 0.7564 (mtpp) REVERT: A 2048 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7398 (tm-30) REVERT: A 2063 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7049 (p90) REVERT: A 2086 ILE cc_start: 0.8744 (mm) cc_final: 0.8538 (mm) REVERT: A 2205 MET cc_start: 0.6050 (mmp) cc_final: 0.5701 (mmm) outliers start: 37 outliers final: 16 residues processed: 221 average time/residue: 0.2640 time to fit residues: 88.0353 Evaluate side-chains 197 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 2063 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15632 Z= 0.200 Angle : 0.611 9.667 21279 Z= 0.299 Chirality : 0.045 0.332 2487 Planarity : 0.005 0.067 2666 Dihedral : 9.103 104.898 2501 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.37 % Rotamer: Outliers : 2.19 % Allowed : 16.04 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1926 helix: 0.54 (0.18), residues: 953 sheet: -0.95 (0.42), residues: 166 loop : -2.76 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 871 HIS 0.004 0.001 HIS A1118 PHE 0.016 0.001 PHE A 836 TYR 0.015 0.001 TYR A 400 ARG 0.003 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.6509 (t80) cc_final: 0.6303 (t80) REVERT: A 89 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8646 (pt0) REVERT: A 508 ARG cc_start: 0.7125 (tpt90) cc_final: 0.6839 (ttm110) REVERT: A 689 GLN cc_start: 0.7597 (mp10) cc_final: 0.7285 (mp10) REVERT: A 922 HIS cc_start: 0.5252 (t70) cc_final: 0.4896 (t-170) REVERT: A 1085 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8762 (pp) REVERT: A 1151 PHE cc_start: 0.7406 (m-80) cc_final: 0.7168 (m-80) REVERT: A 1271 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: A 1735 TYR cc_start: 0.8695 (t80) cc_final: 0.8345 (t80) REVERT: A 1814 GLU cc_start: 0.7733 (pp20) cc_final: 0.7451 (pp20) REVERT: A 1831 LYS cc_start: 0.8168 (mttp) cc_final: 0.7566 (mtpp) REVERT: A 2048 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7414 (tm-30) REVERT: A 2063 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7024 (p90) REVERT: A 2086 ILE cc_start: 0.8765 (mm) cc_final: 0.8551 (mm) REVERT: A 2205 MET cc_start: 0.6095 (mmp) cc_final: 0.5729 (mmm) outliers start: 34 outliers final: 18 residues processed: 209 average time/residue: 0.2787 time to fit residues: 87.6941 Evaluate side-chains 195 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 2063 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2075 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15632 Z= 0.419 Angle : 0.732 10.375 21279 Z= 0.360 Chirality : 0.050 0.363 2487 Planarity : 0.005 0.066 2666 Dihedral : 9.549 105.752 2499 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.93 % Favored : 91.02 % Rotamer: Outliers : 2.32 % Allowed : 17.01 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.19), residues: 1926 helix: 0.27 (0.18), residues: 941 sheet: -0.98 (0.42), residues: 162 loop : -2.85 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1772 HIS 0.006 0.001 HIS A1118 PHE 0.022 0.002 PHE A 961 TYR 0.017 0.002 TYR A 400 ARG 0.004 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8706 (pt0) REVERT: A 113 LEU cc_start: 0.7444 (mm) cc_final: 0.7227 (mp) REVERT: A 508 ARG cc_start: 0.7152 (tpt90) cc_final: 0.6859 (ttm110) REVERT: A 689 GLN cc_start: 0.7674 (mp10) cc_final: 0.7313 (mp10) REVERT: A 718 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: A 1085 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8828 (pp) REVERT: A 1271 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: A 1735 TYR cc_start: 0.8923 (t80) cc_final: 0.8679 (t80) REVERT: A 1814 GLU cc_start: 0.7766 (pp20) cc_final: 0.7473 (pp20) REVERT: A 1831 LYS cc_start: 0.8193 (mttp) cc_final: 0.7623 (mtpp) REVERT: A 2048 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7469 (tm-30) REVERT: A 2063 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6808 (p90) REVERT: A 2204 ASN cc_start: 0.5703 (m110) cc_final: 0.5231 (m110) outliers start: 36 outliers final: 23 residues processed: 207 average time/residue: 0.2715 time to fit residues: 84.9477 Evaluate side-chains 200 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1617 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1769 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain A residue 2067 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 119 optimal weight: 0.0570 chunk 128 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 50.0000 chunk 147 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15632 Z= 0.171 Angle : 0.611 10.019 21279 Z= 0.300 Chirality : 0.045 0.344 2487 Planarity : 0.005 0.067 2666 Dihedral : 8.990 104.790 2499 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.06 % Allowed : 17.33 % Favored : 80.61 % 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: -1.37 (0.20), residues: 1926 helix: 0.52 (0.18), residues: 946 sheet: -0.78 (0.43), residues: 161 loop : -2.75 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 871 HIS 0.003 0.001 HIS A 922 PHE 0.014 0.001 PHE A 836 TYR 0.021 0.001 TYR A 49 ARG 0.003 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8684 (pt0) REVERT: A 508 ARG cc_start: 0.7141 (tpt90) cc_final: 0.6846 (ttm110) REVERT: A 599 GLU cc_start: 0.7930 (pm20) cc_final: 0.7723 (mp0) REVERT: A 689 GLN cc_start: 0.7668 (mp10) cc_final: 0.7315 (mp10) REVERT: A 922 HIS cc_start: 0.5333 (t70) cc_final: 0.5045 (t-170) REVERT: A 1085 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8760 (pp) REVERT: A 1271 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: A 1735 TYR cc_start: 0.8746 (t80) cc_final: 0.8428 (t80) REVERT: A 1814 GLU cc_start: 0.7717 (pp20) cc_final: 0.7442 (pp20) REVERT: A 1831 LYS cc_start: 0.8144 (mttp) cc_final: 0.7554 (mtpp) REVERT: A 2063 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.6548 (p90) REVERT: A 2086 ILE cc_start: 0.8805 (mm) cc_final: 0.8580 (mm) outliers start: 32 outliers final: 23 residues processed: 207 average time/residue: 0.2808 time to fit residues: 87.4136 Evaluate side-chains 206 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1617 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1769 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain A residue 2067 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15632 Z= 0.177 Angle : 0.620 11.135 21279 Z= 0.302 Chirality : 0.045 0.332 2487 Planarity : 0.005 0.068 2666 Dihedral : 8.724 102.783 2498 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.06 % Allowed : 17.85 % Favored : 80.09 % 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: -1.24 (0.20), residues: 1926 helix: 0.63 (0.18), residues: 945 sheet: -0.82 (0.43), residues: 166 loop : -2.67 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 871 HIS 0.003 0.001 HIS A1118 PHE 0.029 0.001 PHE A1839 TYR 0.020 0.001 TYR A 49 ARG 0.005 0.000 ARG A1596 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 178 time to evaluate : 1.740 Fit side-chains revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8625 (pt0) REVERT: A 508 ARG cc_start: 0.7149 (tpt90) cc_final: 0.6857 (ttm110) REVERT: A 689 GLN cc_start: 0.7653 (mp10) cc_final: 0.7353 (mp10) REVERT: A 922 HIS cc_start: 0.5254 (t70) cc_final: 0.4954 (t-170) REVERT: A 1085 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8767 (pp) REVERT: A 1271 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: A 1735 TYR cc_start: 0.8719 (t80) cc_final: 0.8377 (t80) REVERT: A 1814 GLU cc_start: 0.7718 (pp20) cc_final: 0.7444 (pp20) REVERT: A 1831 LYS cc_start: 0.8130 (mttp) cc_final: 0.7555 (mtpp) REVERT: A 2063 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.6520 (p90) REVERT: A 2086 ILE cc_start: 0.8805 (mm) cc_final: 0.8584 (mm) REVERT: A 2204 ASN cc_start: 0.5501 (m110) cc_final: 0.5175 (m110) outliers start: 32 outliers final: 24 residues processed: 206 average time/residue: 0.2730 time to fit residues: 85.0285 Evaluate side-chains 203 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1617 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1769 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain A residue 2067 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 178 optimal weight: 0.0020 chunk 154 optimal weight: 0.6980 chunk 16 optimal weight: 0.0020 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15632 Z= 0.171 Angle : 0.609 10.306 21279 Z= 0.297 Chirality : 0.044 0.329 2487 Planarity : 0.005 0.070 2666 Dihedral : 8.488 99.818 2498 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.00 % Allowed : 17.72 % Favored : 80.28 % 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: -1.15 (0.20), residues: 1926 helix: 0.70 (0.18), residues: 951 sheet: -0.67 (0.43), residues: 161 loop : -2.67 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 871 HIS 0.003 0.001 HIS A1023 PHE 0.016 0.001 PHE A 836 TYR 0.014 0.001 TYR A 400 ARG 0.004 0.000 ARG A1596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.715 Fit side-chains revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8592 (pt0) REVERT: A 508 ARG cc_start: 0.7123 (tpt90) cc_final: 0.6838 (ttm110) REVERT: A 689 GLN cc_start: 0.7651 (mp10) cc_final: 0.7349 (mp10) REVERT: A 922 HIS cc_start: 0.5262 (t70) cc_final: 0.4950 (t-170) REVERT: A 1085 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8771 (pp) REVERT: A 1271 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: A 1735 TYR cc_start: 0.8669 (t80) cc_final: 0.8332 (t80) REVERT: A 1814 GLU cc_start: 0.7728 (pp20) cc_final: 0.7450 (pp20) REVERT: A 1831 LYS cc_start: 0.8146 (mttp) cc_final: 0.7577 (mtpp) REVERT: A 2063 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.6430 (p90) REVERT: A 2086 ILE cc_start: 0.8790 (mm) cc_final: 0.8565 (mm) REVERT: A 2204 ASN cc_start: 0.5223 (m110) cc_final: 0.4925 (m110) outliers start: 31 outliers final: 24 residues processed: 207 average time/residue: 0.2742 time to fit residues: 85.2825 Evaluate side-chains 210 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 925 TRP Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1119 HIS Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1264 ILE Chi-restraints excluded: chain A residue 1270 GLU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1490 CYS Chi-restraints excluded: chain A residue 1617 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1769 LEU Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 2063 TYR Chi-restraints excluded: chain A residue 2067 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 0.2980 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 957 GLN ** A1442 ASN ** 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 = 0.3707 r_free = 0.3707 target = 0.144485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109825 restraints weight = 21359.763| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.63 r_work: 0.2977 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15632 Z= 0.158 Angle : 0.597 9.704 21279 Z= 0.290 Chirality : 0.044 0.321 2487 Planarity : 0.004 0.069 2666 Dihedral : 8.194 95.016 2498 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.68 % Allowed : 17.98 % Favored : 80.35 % 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: -1.01 (0.20), residues: 1926 helix: 0.84 (0.18), residues: 950 sheet: -0.65 (0.43), residues: 161 loop : -2.61 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 871 HIS 0.003 0.001 HIS A1023 PHE 0.015 0.001 PHE A 836 TYR 0.024 0.001 TYR A 49 ARG 0.003 0.000 ARG A1596 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3287.41 seconds wall clock time: 59 minutes 17.91 seconds (3557.91 seconds total)