Starting phenix.real_space_refine on Fri Feb 6 05:55:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g41_51021/02_2026/9g41_51021.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g41_51021/02_2026/9g41_51021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g41_51021/02_2026/9g41_51021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g41_51021/02_2026/9g41_51021.map" model { file = "/net/cci-nas-00/data/ceres_data/9g41_51021/02_2026/9g41_51021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g41_51021/02_2026/9g41_51021.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 14106 2.51 5 N 3789 2.21 5 O 4306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22273 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1370, 10973 Classifications: {'peptide': 1370} Link IDs: {'PTRANS': 49, 'TRANS': 1320} Chain breaks: 2 Chain: "B" Number of atoms: 10973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1370, 10973 Classifications: {'peptide': 1370} Link IDs: {'PTRANS': 49, 'TRANS': 1320} Chain breaks: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.86, per 1000 atoms: 0.22 Number of scatterers: 22273 At special positions: 0 Unit cell: (187.06, 111.86, 130.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 4306 8.00 N 3789 7.00 C 14106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A2801 " - " ASN A1764 " " NAG A2802 " - " ASN A1984 " " NAG A2803 " - " ASN A1703 " " NAG A2804 " - " ASN A2639 " " NAG A2805 " - " ASN A1798 " " NAG B2801 " - " ASN B1764 " " NAG B2802 " - " ASN B1984 " " NAG B2803 " - " ASN B2639 " " NAG B2804 " - " ASN B1798 " " NAG C 1 " - " ASN A1607 " " NAG D 1 " - " ASN A2328 " " NAG E 1 " - " ASN A1883 " " NAG F 1 " - " ASN B1607 " " NAG G 1 " - " ASN B2328 " " NAG H 1 " - " ASN B1883 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5064 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 23 sheets defined 9.7% alpha, 53.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 1065 through 1067 No H-bonds generated for 'chain 'A' and resid 1065 through 1067' Processing helix chain 'A' and resid 2401 through 2405 Processing helix chain 'A' and resid 2432 through 2434 No H-bonds generated for 'chain 'A' and resid 2432 through 2434' Processing helix chain 'A' and resid 2435 through 2442 removed outlier: 3.519A pdb=" N VAL A2439 " --> pdb=" O MET A2435 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY A2440 " --> pdb=" O TRP A2436 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS A2441 " --> pdb=" O ARG A2437 " (cutoff:3.500A) Processing helix chain 'A' and resid 2451 through 2455 Processing helix chain 'A' and resid 2469 through 2477 Processing helix chain 'A' and resid 2480 through 2485 removed outlier: 4.285A pdb=" N ILE A2484 " --> pdb=" O GLN A2480 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2507 Processing helix chain 'A' and resid 2515 through 2529 Processing helix chain 'A' and resid 2581 through 2592 removed outlier: 3.582A pdb=" N ASN A2592 " --> pdb=" O ALA A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2626 removed outlier: 3.636A pdb=" N LEU A2622 " --> pdb=" O ALA A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2707 removed outlier: 3.573A pdb=" N GLN A2692 " --> pdb=" O ASP A2688 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A2693 " --> pdb=" O GLN A2689 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A2697 " --> pdb=" O ARG A2693 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A2698 " --> pdb=" O ALA A2694 " (cutoff:3.500A) Processing helix chain 'A' and resid 2717 through 2727 Processing helix chain 'A' and resid 2744 through 2749 removed outlier: 3.590A pdb=" N LEU A2747 " --> pdb=" O TYR A2744 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A2748 " --> pdb=" O PRO A2745 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP A2749 " --> pdb=" O GLU A2746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2744 through 2749' Processing helix chain 'A' and resid 2750 through 2752 No H-bonds generated for 'chain 'A' and resid 2750 through 2752' Processing helix chain 'B' and resid 1065 through 1067 No H-bonds generated for 'chain 'B' and resid 1065 through 1067' Processing helix chain 'B' and resid 2401 through 2405 removed outlier: 3.510A pdb=" N GLY B2404 " --> pdb=" O GLY B2401 " (cutoff:3.500A) Processing helix chain 'B' and resid 2435 through 2442 removed outlier: 4.097A pdb=" N GLY B2440 " --> pdb=" O TRP B2436 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS B2441 " --> pdb=" O ARG B2437 " (cutoff:3.500A) Processing helix chain 'B' and resid 2451 through 2455 Processing helix chain 'B' and resid 2469 through 2477 Processing helix chain 'B' and resid 2480 through 2485 removed outlier: 4.224A pdb=" N ILE B2484 " --> pdb=" O GLN B2480 " (cutoff:3.500A) Processing helix chain 'B' and resid 2499 through 2507 Processing helix chain 'B' and resid 2515 through 2529 Processing helix chain 'B' and resid 2581 through 2592 removed outlier: 3.521A pdb=" N ASN B2592 " --> pdb=" O ALA B2588 " (cutoff:3.500A) Processing helix chain 'B' and resid 2618 through 2626 Processing helix chain 'B' and resid 2677 through 2707 removed outlier: 3.518A pdb=" N ARG B2693 " --> pdb=" O GLN B2689 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B2697 " --> pdb=" O ARG B2693 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B2698 " --> pdb=" O ALA B2694 " (cutoff:3.500A) Processing helix chain 'B' and resid 2717 through 2727 Processing helix chain 'B' and resid 2744 through 2749 removed outlier: 3.585A pdb=" N LEU B2747 " --> pdb=" O TYR B2744 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B2748 " --> pdb=" O PRO B2745 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP B2749 " --> pdb=" O GLU B2746 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2744 through 2749' Processing helix chain 'B' and resid 2750 through 2752 No H-bonds generated for 'chain 'B' and resid 2750 through 2752' Processing sheet with id=AA1, first strand: chain 'A' and resid 1021 through 1024 Processing sheet with id=AA2, first strand: chain 'A' and resid 1040 through 1041 Processing sheet with id=AA3, first strand: chain 'A' and resid 1099 through 1105 removed outlier: 3.591A pdb=" N VAL A1094 " --> pdb=" O PHE A1101 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A1103 " --> pdb=" O LEU A1092 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1177 through 1179 Processing sheet with id=AA5, first strand: chain 'A' and resid 1574 through 1578 removed outlier: 6.025A pdb=" N GLN A1594 " --> pdb=" O PHE A1608 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER A1598 " --> pdb=" O TYR A1604 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR A1604 " --> pdb=" O SER A1598 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A1605 " --> pdb=" O ASP A1621 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP A1621 " --> pdb=" O LEU A1605 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A1607 " --> pdb=" O LEU A1619 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A1619 " --> pdb=" O ASN A1607 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A1609 " --> pdb=" O THR A1617 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR A1617 " --> pdb=" O ILE A1629 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG A1638 " --> pdb=" O LEU A1650 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS A1659 " --> pdb=" O MET A1671 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A1681 " --> pdb=" O TYR A1693 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR A1702 " --> pdb=" O LEU A1714 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR A1766 " --> pdb=" O CYS A1762 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A1776 " --> pdb=" O ILE A1799 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A1799 " --> pdb=" O ALA A1776 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER A1778 " --> pdb=" O CYS A1797 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS A1797 " --> pdb=" O SER A1778 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS A1780 " --> pdb=" O GLY A1795 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N THR A1793 " --> pdb=" O LEU A1814 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N LEU A1814 " --> pdb=" O THR A1793 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY A1795 " --> pdb=" O TRP A1812 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER A1809 " --> pdb=" O VAL A1832 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL A1832 " --> pdb=" O SER A1809 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU A1811 " --> pdb=" O LEU A1830 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A1830 " --> pdb=" O GLU A1811 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG A1813 " --> pdb=" O ARG A1828 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A1828 " --> pdb=" O ARG A1813 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG A1815 " --> pdb=" O PHE A1826 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE A1826 " --> pdb=" O ARG A1815 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A1817 " --> pdb=" O THR A1824 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A1838 " --> pdb=" O LEU A1830 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A1832 " --> pdb=" O ASN A1836 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASN A1836 " --> pdb=" O VAL A1832 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE A1871 " --> pdb=" O VAL A1884 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A1893 " --> pdb=" O THR A1904 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER A1901 " --> pdb=" O PHE A1917 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N PHE A1917 " --> pdb=" O SER A1901 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG A1903 " --> pdb=" O ARG A1915 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG A1915 " --> pdb=" O ARG A1903 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A1905 " --> pdb=" O VAL A1913 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL A1913 " --> pdb=" O TYR A1925 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS A1953 " --> pdb=" O MET A1965 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU A1998 " --> pdb=" O TYR A2011 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER A2020 " --> pdb=" O PHE A2031 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYS A2041 " --> pdb=" O TYR A2056 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL A2059 " --> pdb=" O VAL A2063 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL A2063 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 11.927A pdb=" N LEU A2062 " --> pdb=" O TYR A2084 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N TYR A2084 " --> pdb=" O LEU A2062 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP A2064 " --> pdb=" O TYR A2082 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG A2079 " --> pdb=" O PRO A2096 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP A2081 " --> pdb=" O ILE A2094 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A2094 " --> pdb=" O ASP A2081 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A2083 " --> pdb=" O ALA A2092 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A2098 " --> pdb=" O THR A2101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1574 through 1578 removed outlier: 6.025A pdb=" N GLN A1594 " --> pdb=" O PHE A1608 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER A1598 " --> pdb=" O TYR A1604 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR A1604 " --> pdb=" O SER A1598 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A1605 " --> pdb=" O ASP A1621 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP A1621 " --> pdb=" O LEU A1605 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A1607 " --> pdb=" O LEU A1619 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A1619 " --> pdb=" O ASN A1607 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A1609 " --> pdb=" O THR A1617 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR A1617 " --> pdb=" O ILE A1629 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG A1638 " --> pdb=" O LEU A1650 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS A1659 " --> pdb=" O MET A1671 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A1681 " --> pdb=" O TYR A1693 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR A1702 " --> pdb=" O LEU A1714 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR A1766 " --> pdb=" O CYS A1762 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A1776 " --> pdb=" O ILE A1799 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A1799 " --> pdb=" O ALA A1776 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER A1778 " --> pdb=" O CYS A1797 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS A1797 " --> pdb=" O SER A1778 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS A1780 " --> pdb=" O GLY A1795 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N THR A1793 " --> pdb=" O LEU A1814 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N LEU A1814 " --> pdb=" O THR A1793 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY A1795 " --> pdb=" O TRP A1812 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER A1809 " --> pdb=" O VAL A1832 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL A1832 " --> pdb=" O SER A1809 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU A1811 " --> pdb=" O LEU A1830 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A1830 " --> pdb=" O GLU A1811 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG A1813 " --> pdb=" O ARG A1828 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A1828 " --> pdb=" O ARG A1813 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG A1815 " --> pdb=" O PHE A1826 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE A1826 " --> pdb=" O ARG A1815 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A1817 " --> pdb=" O THR A1824 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A1838 " --> pdb=" O LEU A1830 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A1832 " --> pdb=" O ASN A1836 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASN A1836 " --> pdb=" O VAL A1832 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE A1871 " --> pdb=" O VAL A1884 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A1893 " --> pdb=" O THR A1904 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER A1901 " --> pdb=" O PHE A1917 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N PHE A1917 " --> pdb=" O SER A1901 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG A1903 " --> pdb=" O ARG A1915 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG A1915 " --> pdb=" O ARG A1903 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A1905 " --> pdb=" O VAL A1913 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL A1913 " --> pdb=" O TYR A1925 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS A1953 " --> pdb=" O MET A1965 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU A1998 " --> pdb=" O TYR A2011 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER A2020 " --> pdb=" O PHE A2031 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYS A2041 " --> pdb=" O TYR A2056 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL A2059 " --> pdb=" O VAL A2063 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL A2063 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 11.927A pdb=" N LEU A2062 " --> pdb=" O TYR A2084 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N TYR A2084 " --> pdb=" O LEU A2062 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP A2064 " --> pdb=" O TYR A2082 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG A2079 " --> pdb=" O PRO A2096 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP A2081 " --> pdb=" O ILE A2094 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A2094 " --> pdb=" O ASP A2081 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A2083 " --> pdb=" O ALA A2092 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ALA A2092 " --> pdb=" O TYR A2108 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A2107 " --> pdb=" O PHE A2120 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A2120 " --> pdb=" O LEU A2107 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG A2109 " --> pdb=" O GLU A2118 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU A2118 " --> pdb=" O VAL A2125 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYS A2152 " --> pdb=" O VAL A2168 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET A2158 " --> pdb=" O LEU A2162 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU A2162 " --> pdb=" O MET A2158 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE A2177 " --> pdb=" O TYR A2194 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A2207 " --> pdb=" O PRO A2211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2216 through 2217 removed outlier: 6.464A pdb=" N SER A2216 " --> pdb=" O HIS A2224 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS A2224 " --> pdb=" O LEU A2237 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU A2248 " --> pdb=" O PRO A2236 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG A2238 " --> pdb=" O THR A2246 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR A2246 " --> pdb=" O TYR A2253 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN A2252 " --> pdb=" O ARG A2264 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG A2264 " --> pdb=" O GLN A2252 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS A2254 " --> pdb=" O CYS A2262 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N CYS A2262 " --> pdb=" O PHE A2269 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR A2278 " --> pdb=" O TYR A2291 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER A2288 " --> pdb=" O THR A2304 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A2304 " --> pdb=" O SER A2288 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLN A2290 " --> pdb=" O TYR A2302 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR A2302 " --> pdb=" O GLN A2290 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG A2292 " --> pdb=" O ALA A2300 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA A2300 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A2347 " --> pdb=" O TYR A2338 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE A2346 " --> pdb=" O VAL A2358 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR A2357 " --> pdb=" O VAL A2369 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A2369 " --> pdb=" O TYR A2357 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA A2359 " --> pdb=" O LEU A2367 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU A2367 " --> pdb=" O LEU A2380 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN A2379 " --> pdb=" O ASP A2391 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP A2391 " --> pdb=" O GLN A2379 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLN A2381 " --> pdb=" O TYR A2389 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2406 through 2408 removed outlier: 3.721A pdb=" N LEU A2413 " --> pdb=" O ASP A2408 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A2427 " --> pdb=" O ASP A2422 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2563 through 2568 removed outlier: 3.615A pdb=" N ALA A2594 " --> pdb=" O VAL A2572 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2563 through 2568 removed outlier: 3.615A pdb=" N ALA A2594 " --> pdb=" O VAL A2572 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASP A2608 " --> pdb=" O LEU A2667 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER A2669 " --> pdb=" O ASP A2608 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N HIS A2610 " --> pdb=" O SER A2669 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG A2671 " --> pdb=" O HIS A2610 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE A2612 " --> pdb=" O ARG A2671 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N GLY A2673 " --> pdb=" O PHE A2612 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS A2614 " --> pdb=" O GLY A2673 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A2642 " --> pdb=" O GLY A2630 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A2630 " --> pdb=" O VAL A2642 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2733 through 2737 Processing sheet with id=AB3, first strand: chain 'B' and resid 1021 through 1024 Processing sheet with id=AB4, first strand: chain 'B' and resid 1040 through 1041 Processing sheet with id=AB5, first strand: chain 'B' and resid 1099 through 1105 removed outlier: 3.571A pdb=" N VAL B1094 " --> pdb=" O PHE B1101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B1103 " --> pdb=" O LEU B1092 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1177 through 1179 Processing sheet with id=AB7, first strand: chain 'B' and resid 1574 through 1578 removed outlier: 6.075A pdb=" N GLN B1594 " --> pdb=" O PHE B1608 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER B1598 " --> pdb=" O TYR B1604 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR B1604 " --> pdb=" O SER B1598 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B1605 " --> pdb=" O ASP B1621 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP B1621 " --> pdb=" O LEU B1605 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN B1607 " --> pdb=" O LEU B1619 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU B1619 " --> pdb=" O ASN B1607 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1609 " --> pdb=" O THR B1617 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR B1617 " --> pdb=" O ILE B1629 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ARG B1638 " --> pdb=" O LEU B1650 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS B1659 " --> pdb=" O MET B1671 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA B1681 " --> pdb=" O TYR B1693 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N THR B1702 " --> pdb=" O LEU B1714 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B1776 " --> pdb=" O ILE B1799 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE B1799 " --> pdb=" O ALA B1776 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER B1778 " --> pdb=" O CYS B1797 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS B1797 " --> pdb=" O SER B1778 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS B1780 " --> pdb=" O GLY B1795 " (cutoff:3.500A) removed outlier: 11.265A pdb=" N THR B1793 " --> pdb=" O LEU B1814 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU B1814 " --> pdb=" O THR B1793 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY B1795 " --> pdb=" O TRP B1812 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER B1809 " --> pdb=" O VAL B1832 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B1832 " --> pdb=" O SER B1809 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU B1811 " --> pdb=" O LEU B1830 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B1830 " --> pdb=" O GLU B1811 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ARG B1813 " --> pdb=" O ARG B1828 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG B1828 " --> pdb=" O ARG B1813 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARG B1815 " --> pdb=" O PHE B1826 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE B1826 " --> pdb=" O ARG B1815 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU B1817 " --> pdb=" O THR B1824 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B1838 " --> pdb=" O LEU B1830 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B1832 " --> pdb=" O ASN B1836 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASN B1836 " --> pdb=" O VAL B1832 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE B1871 " --> pdb=" O VAL B1884 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B1894 " --> pdb=" O SER B1885 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1902 through 1906 removed outlier: 3.829A pdb=" N SER B1914 " --> pdb=" O ASP B1905 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL B1913 " --> pdb=" O TYR B1925 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N HIS B1953 " --> pdb=" O MET B1965 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE B1988 " --> pdb=" O THR B2000 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B2000 " --> pdb=" O ILE B1988 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B1990 " --> pdb=" O LEU B1998 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU B1998 " --> pdb=" O TYR B2011 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B2007 " --> pdb=" O PHE B2002 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER B2020 " --> pdb=" O PHE B2031 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS B2041 " --> pdb=" O TYR B2056 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL B2059 " --> pdb=" O VAL B2063 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL B2063 " --> pdb=" O VAL B2059 " (cutoff:3.500A) removed outlier: 11.823A pdb=" N LEU B2062 " --> pdb=" O TYR B2084 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N TYR B2084 " --> pdb=" O LEU B2062 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP B2064 " --> pdb=" O TYR B2082 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B2098 " --> pdb=" O THR B2101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1902 through 1906 removed outlier: 3.829A pdb=" N SER B1914 " --> pdb=" O ASP B1905 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL B1913 " --> pdb=" O TYR B1925 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N HIS B1953 " --> pdb=" O MET B1965 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE B1988 " --> pdb=" O THR B2000 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B2000 " --> pdb=" O ILE B1988 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B1990 " --> pdb=" O LEU B1998 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU B1998 " --> pdb=" O TYR B2011 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B2007 " --> pdb=" O PHE B2002 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER B2020 " --> pdb=" O PHE B2031 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS B2041 " --> pdb=" O TYR B2056 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL B2059 " --> pdb=" O VAL B2063 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL B2063 " --> pdb=" O VAL B2059 " (cutoff:3.500A) removed outlier: 11.823A pdb=" N LEU B2062 " --> pdb=" O TYR B2084 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N TYR B2084 " --> pdb=" O LEU B2062 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASP B2064 " --> pdb=" O TYR B2082 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA B2092 " --> pdb=" O TYR B2108 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B2107 " --> pdb=" O PHE B2120 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE B2120 " --> pdb=" O LEU B2107 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG B2109 " --> pdb=" O GLU B2118 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU B2118 " --> pdb=" O VAL B2125 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B2132 " --> pdb=" O LYS B2143 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS B2152 " --> pdb=" O VAL B2168 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET B2158 " --> pdb=" O LEU B2162 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B2162 " --> pdb=" O MET B2158 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE B2177 " --> pdb=" O TYR B2194 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B2207 " --> pdb=" O PRO B2211 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 2216 through 2217 removed outlier: 6.471A pdb=" N SER B2216 " --> pdb=" O HIS B2224 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N HIS B2224 " --> pdb=" O LEU B2237 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU B2248 " --> pdb=" O PRO B2236 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG B2238 " --> pdb=" O THR B2246 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B2246 " --> pdb=" O TYR B2253 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN B2252 " --> pdb=" O ARG B2264 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG B2264 " --> pdb=" O GLN B2252 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS B2254 " --> pdb=" O CYS B2262 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N CYS B2262 " --> pdb=" O PHE B2269 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR B2278 " --> pdb=" O TYR B2291 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B2292 " --> pdb=" O SER B2301 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA B2300 " --> pdb=" O TYR B2312 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B2347 " --> pdb=" O TYR B2338 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE B2346 " --> pdb=" O VAL B2358 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU B2367 " --> pdb=" O LEU B2380 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLN B2379 " --> pdb=" O ASP B2391 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP B2391 " --> pdb=" O GLN B2379 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN B2381 " --> pdb=" O TYR B2389 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 2406 through 2408 removed outlier: 3.698A pdb=" N LEU B2413 " --> pdb=" O ASP B2408 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B2427 " --> pdb=" O ASP B2422 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 2563 through 2568 removed outlier: 3.739A pdb=" N ALA B2594 " --> pdb=" O VAL B2572 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 2563 through 2568 removed outlier: 3.739A pdb=" N ALA B2594 " --> pdb=" O VAL B2572 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASP B2608 " --> pdb=" O LEU B2667 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER B2669 " --> pdb=" O ASP B2608 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS B2610 " --> pdb=" O SER B2669 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ARG B2671 " --> pdb=" O HIS B2610 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE B2612 " --> pdb=" O ARG B2671 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N GLY B2673 " --> pdb=" O PHE B2612 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS B2614 " --> pdb=" O GLY B2673 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B2642 " --> pdb=" O GLY B2630 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B2630 " --> pdb=" O VAL B2642 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 2733 through 2737 1165 hydrogen bonds defined for protein. 3174 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: 7.00 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7190 1.34 - 1.46: 4298 1.46 - 1.57: 11155 1.57 - 1.69: 0 1.69 - 1.81: 134 Bond restraints: 22777 Sorted by residual: bond pdb=" C1 NAG A2801 " pdb=" O5 NAG A2801 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C1 NAG B2801 " pdb=" O5 NAG B2801 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 ... (remaining 22772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 30369 2.05 - 4.10: 451 4.10 - 6.16: 49 6.16 - 8.21: 11 8.21 - 10.26: 2 Bond angle restraints: 30882 Sorted by residual: angle pdb=" CB MET A2435 " pdb=" CG MET A2435 " pdb=" SD MET A2435 " ideal model delta sigma weight residual 112.70 122.96 -10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C PRO B1981 " pdb=" N GLU B1982 " pdb=" CA GLU B1982 " ideal model delta sigma weight residual 122.46 127.16 -4.70 1.41e+00 5.03e-01 1.11e+01 angle pdb=" CA MET A2435 " pdb=" CB MET A2435 " pdb=" CG MET A2435 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N GLY B2014 " pdb=" CA GLY B2014 " pdb=" C GLY B2014 " ideal model delta sigma weight residual 112.13 116.39 -4.26 1.34e+00 5.57e-01 1.01e+01 angle pdb=" CB ARG B2437 " pdb=" CG ARG B2437 " pdb=" CD ARG B2437 " ideal model delta sigma weight residual 111.30 118.06 -6.76 2.30e+00 1.89e-01 8.64e+00 ... (remaining 30877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.89: 12219 20.89 - 41.79: 1212 41.79 - 62.68: 289 62.68 - 83.58: 60 83.58 - 104.47: 18 Dihedral angle restraints: 13798 sinusoidal: 5828 harmonic: 7970 Sorted by residual: dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -175.76 104.47 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -175.60 104.31 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" C3 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual 47.62 -55.14 102.76 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 13795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2770 0.059 - 0.119: 608 0.119 - 0.178: 62 0.178 - 0.238: 1 0.238 - 0.297: 3 Chirality restraints: 3444 Sorted by residual: chirality pdb=" C1 NAG A2803 " pdb=" ND2 ASN A1703 " pdb=" C2 NAG A2803 " pdb=" O5 NAG A2803 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 3441 not shown) Planarity restraints: 3960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B2490 " -0.401 9.50e-02 1.11e+02 1.81e-01 2.58e+01 pdb=" NE ARG B2490 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B2490 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG B2490 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B2490 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B1017 " 0.064 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO B1018 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B1018 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B1018 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2437 " -0.239 9.50e-02 1.11e+02 1.08e-01 9.27e+00 pdb=" NE ARG A2437 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A2437 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A2437 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A2437 " -0.000 2.00e-02 2.50e+03 ... (remaining 3957 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4875 2.79 - 3.32: 17340 3.32 - 3.85: 36613 3.85 - 4.37: 42631 4.37 - 4.90: 76150 Nonbonded interactions: 177609 Sorted by model distance: nonbonded pdb=" OG SER A1742 " pdb=" O GLU A1745 " model vdw 2.264 3.040 nonbonded pdb=" O LEU B2223 " pdb=" OH TYR B2239 " model vdw 2.266 3.040 nonbonded pdb=" OG SER B1742 " pdb=" O GLU B1745 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR A1766 " pdb=" O7 NAG A2801 " model vdw 2.275 3.040 nonbonded pdb=" O SER A1938 " pdb=" OG SER A1938 " model vdw 2.277 3.040 ... (remaining 177604 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 'A' and resid 1015 through 2804) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.200 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.004 0.050 22801 Z= 0.178 Angle : 0.637 10.261 30954 Z= 0.328 Chirality : 0.049 0.297 3444 Planarity : 0.006 0.181 3945 Dihedral : 17.814 104.470 8734 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.67 % Allowed : 26.04 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2728 helix: -2.82 (0.23), residues: 216 sheet: 1.21 (0.18), residues: 914 loop : -0.79 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG B2490 TYR 0.021 0.002 TYR B2339 PHE 0.021 0.002 PHE A2346 TRP 0.021 0.002 TRP B1689 HIS 0.020 0.002 HIS B1953 Details of bonding type rmsd covalent geometry : bond 0.00378 (22777) covalent geometry : angle 0.62037 (30882) hydrogen bonds : bond 0.21797 ( 874) hydrogen bonds : angle 8.41110 ( 3174) link_ALPHA1-3 : bond 0.00933 ( 1) link_ALPHA1-3 : angle 1.81049 ( 3) link_BETA1-4 : bond 0.01017 ( 8) link_BETA1-4 : angle 1.99903 ( 24) link_NAG-ASN : bond 0.00552 ( 15) link_NAG-ASN : angle 3.52409 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 797 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1032 SER cc_start: 0.8083 (t) cc_final: 0.7736 (m) REVERT: A 1056 THR cc_start: 0.7745 (t) cc_final: 0.7512 (t) REVERT: A 1114 THR cc_start: 0.7985 (m) cc_final: 0.7778 (t) REVERT: A 1118 ASP cc_start: 0.7902 (p0) cc_final: 0.7663 (p0) REVERT: A 1121 ASP cc_start: 0.7025 (p0) cc_final: 0.6808 (p0) REVERT: A 1173 ASP cc_start: 0.7655 (t0) cc_final: 0.7241 (t0) REVERT: A 1180 VAL cc_start: 0.8826 (m) cc_final: 0.8577 (p) REVERT: A 1600 VAL cc_start: 0.8213 (t) cc_final: 0.7956 (m) REVERT: A 1618 GLU cc_start: 0.7157 (tt0) cc_final: 0.6916 (tt0) REVERT: A 1620 ILE cc_start: 0.7743 (mt) cc_final: 0.7319 (mt) REVERT: A 1621 ASP cc_start: 0.7841 (p0) cc_final: 0.6519 (p0) REVERT: A 1639 HIS cc_start: 0.7814 (p-80) cc_final: 0.7490 (p-80) REVERT: A 1710 VAL cc_start: 0.8859 (t) cc_final: 0.8438 (m) REVERT: A 1713 SER cc_start: 0.8374 (m) cc_final: 0.7854 (t) REVERT: A 1723 THR cc_start: 0.8493 (m) cc_final: 0.8192 (p) REVERT: A 1738 ILE cc_start: 0.8556 (mt) cc_final: 0.8307 (mm) REVERT: A 1748 TYR cc_start: 0.8262 (m-80) cc_final: 0.8029 (m-80) REVERT: A 1842 TYR cc_start: 0.7915 (t80) cc_final: 0.7566 (t80) REVERT: A 1855 HIS cc_start: 0.7386 (m-70) cc_final: 0.6982 (m-70) REVERT: A 1871 PHE cc_start: 0.7724 (p90) cc_final: 0.7494 (p90) REVERT: A 1879 LEU cc_start: 0.8139 (mt) cc_final: 0.7939 (mp) REVERT: A 1900 MET cc_start: 0.8334 (mtt) cc_final: 0.7968 (mtp) REVERT: A 1970 SER cc_start: 0.8750 (t) cc_final: 0.8547 (p) REVERT: A 1975 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7707 (ttm110) REVERT: A 1994 ASP cc_start: 0.7907 (p0) cc_final: 0.7683 (p0) REVERT: A 1996 ARG cc_start: 0.7863 (mmt90) cc_final: 0.7192 (mtm110) REVERT: A 2019 LEU cc_start: 0.8387 (tp) cc_final: 0.8152 (tp) REVERT: A 2023 VAL cc_start: 0.8705 (t) cc_final: 0.8262 (m) REVERT: A 2042 MET cc_start: 0.8259 (ttm) cc_final: 0.8045 (ttp) REVERT: A 2053 THR cc_start: 0.8188 (m) cc_final: 0.7751 (p) REVERT: A 2065 LYS cc_start: 0.8307 (ttpt) cc_final: 0.7917 (ttmm) REVERT: A 2079 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7232 (ttm110) REVERT: A 2095 LYS cc_start: 0.7974 (tptm) cc_final: 0.7746 (tptm) REVERT: A 2116 LYS cc_start: 0.8082 (mttt) cc_final: 0.7783 (mttt) REVERT: A 2138 VAL cc_start: 0.8192 (t) cc_final: 0.7913 (p) REVERT: A 2139 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7039 (ptp) REVERT: A 2190 THR cc_start: 0.8002 (m) cc_final: 0.7667 (p) REVERT: A 2213 TRP cc_start: 0.8150 (m-90) cc_final: 0.7924 (m-90) REVERT: A 2241 LEU cc_start: 0.8237 (tp) cc_final: 0.8013 (tp) REVERT: A 2273 SER cc_start: 0.8149 (m) cc_final: 0.7899 (t) REVERT: A 2274 LYS cc_start: 0.8506 (tptp) cc_final: 0.8255 (tptt) REVERT: A 2292 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7836 (ttm-80) REVERT: A 2301 SER cc_start: 0.8526 (t) cc_final: 0.8262 (p) REVERT: A 2303 LYS cc_start: 0.8317 (tttt) cc_final: 0.7990 (mtpt) REVERT: A 2322 ARG cc_start: 0.8420 (ttm170) cc_final: 0.7970 (ttp-170) REVERT: A 2408 ASP cc_start: 0.7814 (t70) cc_final: 0.7578 (t0) REVERT: A 2453 ASN cc_start: 0.8081 (m-40) cc_final: 0.7816 (m110) REVERT: A 2480 GLN cc_start: 0.7800 (tp40) cc_final: 0.7544 (mm110) REVERT: A 2517 VAL cc_start: 0.8619 (p) cc_final: 0.8417 (t) REVERT: A 2524 HIS cc_start: 0.7824 (m90) cc_final: 0.7620 (m90) REVERT: A 2526 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7514 (tp40) REVERT: A 2554 THR cc_start: 0.8510 (m) cc_final: 0.8179 (m) REVERT: A 2599 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7675 (mmmt) REVERT: A 2602 TYR cc_start: 0.8240 (m-80) cc_final: 0.7903 (m-80) REVERT: A 2604 ILE cc_start: 0.8374 (mt) cc_final: 0.8069 (tt) REVERT: A 2614 LYS cc_start: 0.7598 (mtpt) cc_final: 0.7319 (ttmm) REVERT: A 2682 GLU cc_start: 0.7558 (tp30) cc_final: 0.6976 (tp30) REVERT: A 2730 VAL cc_start: 0.8380 (m) cc_final: 0.8157 (t) REVERT: B 1032 SER cc_start: 0.7953 (t) cc_final: 0.7651 (m) REVERT: B 1044 THR cc_start: 0.7468 (p) cc_final: 0.7028 (p) REVERT: B 1092 LEU cc_start: 0.8215 (tp) cc_final: 0.8002 (tp) REVERT: B 1115 PHE cc_start: 0.8441 (t80) cc_final: 0.8162 (t80) REVERT: B 1173 ASP cc_start: 0.7698 (t0) cc_final: 0.7254 (t0) REVERT: B 1180 VAL cc_start: 0.8707 (m) cc_final: 0.8491 (p) REVERT: B 1601 THR cc_start: 0.8382 (m) cc_final: 0.8089 (t) REVERT: B 1606 TYR cc_start: 0.8127 (m-80) cc_final: 0.7876 (m-80) REVERT: B 1608 PHE cc_start: 0.7353 (m-80) cc_final: 0.7106 (m-80) REVERT: B 1614 ASN cc_start: 0.7940 (m-40) cc_final: 0.7669 (m110) REVERT: B 1618 GLU cc_start: 0.7227 (tt0) cc_final: 0.6998 (tt0) REVERT: B 1621 ASP cc_start: 0.7812 (p0) cc_final: 0.7598 (p0) REVERT: B 1710 VAL cc_start: 0.8793 (t) cc_final: 0.8394 (m) REVERT: B 1713 SER cc_start: 0.8354 (m) cc_final: 0.7763 (t) REVERT: B 1723 THR cc_start: 0.8527 (m) cc_final: 0.8294 (p) REVERT: B 1740 ASN cc_start: 0.7107 (m110) cc_final: 0.6889 (m110) REVERT: B 1770 MET cc_start: 0.7738 (tpt) cc_final: 0.7489 (tpp) REVERT: B 1813 ARG cc_start: 0.7143 (mtt180) cc_final: 0.6829 (mtt90) REVERT: B 1829 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7310 (ttmm) REVERT: B 1854 ASP cc_start: 0.7972 (m-30) cc_final: 0.7594 (m-30) REVERT: B 1905 ASP cc_start: 0.7343 (m-30) cc_final: 0.7085 (m-30) REVERT: B 1919 ASP cc_start: 0.7543 (p0) cc_final: 0.7266 (p0) REVERT: B 1922 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8157 (m) REVERT: B 1965 MET cc_start: 0.8347 (mpt) cc_final: 0.7910 (mpp) REVERT: B 1996 ARG cc_start: 0.8007 (mmt90) cc_final: 0.7070 (mtm110) REVERT: B 2019 LEU cc_start: 0.8405 (tp) cc_final: 0.8122 (tp) REVERT: B 2023 VAL cc_start: 0.8649 (t) cc_final: 0.8159 (m) REVERT: B 2053 THR cc_start: 0.8139 (m) cc_final: 0.7734 (p) REVERT: B 2057 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7810 (ttp80) REVERT: B 2112 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7235 (mt-10) REVERT: B 2138 VAL cc_start: 0.8288 (t) cc_final: 0.7934 (p) REVERT: B 2139 MET cc_start: 0.7992 (ppp) cc_final: 0.7324 (ptm) REVERT: B 2163 MET cc_start: 0.7339 (mtp) cc_final: 0.6999 (mtp) REVERT: B 2170 TYR cc_start: 0.8361 (m-80) cc_final: 0.8002 (m-80) REVERT: B 2182 LYS cc_start: 0.7988 (tttm) cc_final: 0.7759 (ptmt) REVERT: B 2190 THR cc_start: 0.8043 (m) cc_final: 0.7724 (p) REVERT: B 2213 TRP cc_start: 0.8153 (m-90) cc_final: 0.7846 (m-90) REVERT: B 2223 LEU cc_start: 0.7318 (tp) cc_final: 0.6935 (tp) REVERT: B 2274 LYS cc_start: 0.8284 (tptp) cc_final: 0.8008 (tptp) REVERT: B 2279 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7399 (mtp85) REVERT: B 2292 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7755 (ttm-80) REVERT: B 2346 PHE cc_start: 0.7988 (p90) cc_final: 0.7729 (p90) REVERT: B 2408 ASP cc_start: 0.7707 (t70) cc_final: 0.7445 (t0) REVERT: B 2418 GLN cc_start: 0.7404 (mt0) cc_final: 0.7155 (mt0) REVERT: B 2429 THR cc_start: 0.7780 (p) cc_final: 0.7439 (t) REVERT: B 2435 MET cc_start: 0.7385 (ppp) cc_final: 0.7012 (ptt) REVERT: B 2437 ARG cc_start: 0.6873 (ttp-110) cc_final: 0.6611 (ptm-80) REVERT: B 2453 ASN cc_start: 0.8125 (m-40) cc_final: 0.7837 (m110) REVERT: B 2454 ASN cc_start: 0.8432 (m-40) cc_final: 0.8153 (m-40) REVERT: B 2467 VAL cc_start: 0.8639 (t) cc_final: 0.8371 (t) REVERT: B 2501 GLU cc_start: 0.7735 (pm20) cc_final: 0.7410 (pm20) REVERT: B 2539 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7692 (mmtp) REVERT: B 2541 HIS cc_start: 0.7405 (p90) cc_final: 0.6493 (p90) REVERT: B 2554 THR cc_start: 0.8395 (m) cc_final: 0.8093 (m) REVERT: B 2561 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7356 (mtpp) REVERT: B 2564 MET cc_start: 0.8376 (tmt) cc_final: 0.7790 (ttp) REVERT: B 2589 SER cc_start: 0.8403 (t) cc_final: 0.8071 (p) REVERT: B 2604 ILE cc_start: 0.8249 (mt) cc_final: 0.7867 (tt) REVERT: B 2613 VAL cc_start: 0.8107 (m) cc_final: 0.7663 (p) REVERT: B 2671 ARG cc_start: 0.6644 (ttt180) cc_final: 0.6342 (ttt180) REVERT: B 2682 GLU cc_start: 0.7483 (tp30) cc_final: 0.6974 (tp30) REVERT: B 2691 ARG cc_start: 0.7652 (ttt-90) cc_final: 0.7444 (ttt-90) REVERT: B 2695 LEU cc_start: 0.7823 (mt) cc_final: 0.7562 (mp) outliers start: 16 outliers final: 5 residues processed: 808 average time/residue: 0.1682 time to fit residues: 200.0614 Evaluate side-chains 670 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 662 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 2139 MET Chi-restraints excluded: chain A residue 2398 MET Chi-restraints excluded: chain A residue 2550 HIS Chi-restraints excluded: chain B residue 1829 LYS Chi-restraints excluded: chain B residue 1922 VAL Chi-restraints excluded: chain B residue 1960 VAL Chi-restraints excluded: chain B residue 2550 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN A1740 ASN ** A1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2220 ASN A2224 HIS A2753 ASN B1166 ASN B1582 GLN B1639 HIS B1780 HIS ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2085 HIS B2220 ASN B2753 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107986 restraints weight = 32982.678| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.44 r_work: 0.3150 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22801 Z= 0.166 Angle : 0.584 7.230 30954 Z= 0.306 Chirality : 0.046 0.272 3444 Planarity : 0.004 0.065 3945 Dihedral : 7.373 71.927 3578 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.54 % Allowed : 25.12 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2728 helix: -0.28 (0.32), residues: 224 sheet: 1.37 (0.18), residues: 876 loop : -0.66 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2247 TYR 0.020 0.002 TYR B2068 PHE 0.016 0.002 PHE A2370 TRP 0.013 0.001 TRP A2287 HIS 0.009 0.001 HIS B1639 Details of bonding type rmsd covalent geometry : bond 0.00366 (22777) covalent geometry : angle 0.57345 (30882) hydrogen bonds : bond 0.04520 ( 874) hydrogen bonds : angle 5.67663 ( 3174) link_ALPHA1-3 : bond 0.01325 ( 1) link_ALPHA1-3 : angle 0.85666 ( 3) link_BETA1-4 : bond 0.00465 ( 8) link_BETA1-4 : angle 1.90539 ( 24) link_NAG-ASN : bond 0.00339 ( 15) link_NAG-ASN : angle 2.65568 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 658 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1032 SER cc_start: 0.8408 (t) cc_final: 0.8034 (m) REVERT: A 1056 THR cc_start: 0.7967 (t) cc_final: 0.7750 (t) REVERT: A 1059 LYS cc_start: 0.8369 (mtmt) cc_final: 0.8086 (ptpt) REVERT: A 1101 PHE cc_start: 0.7327 (t80) cc_final: 0.6685 (t80) REVERT: A 1125 GLN cc_start: 0.7314 (mp10) cc_final: 0.6642 (pm20) REVERT: A 1173 ASP cc_start: 0.7989 (t0) cc_final: 0.7590 (t0) REVERT: A 1174 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7950 (mmtm) REVERT: A 1575 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6960 (mm-30) REVERT: A 1600 VAL cc_start: 0.8216 (t) cc_final: 0.7997 (m) REVERT: A 1614 ASN cc_start: 0.7995 (m-40) cc_final: 0.7794 (m-40) REVERT: A 1618 GLU cc_start: 0.7633 (tt0) cc_final: 0.7353 (tt0) REVERT: A 1620 ILE cc_start: 0.7807 (mt) cc_final: 0.7585 (mt) REVERT: A 1639 HIS cc_start: 0.7667 (p-80) cc_final: 0.7438 (p-80) REVERT: A 1674 ASP cc_start: 0.7981 (t70) cc_final: 0.7719 (t70) REVERT: A 1693 TYR cc_start: 0.8420 (m-80) cc_final: 0.8122 (m-80) REVERT: A 1710 VAL cc_start: 0.8848 (t) cc_final: 0.8443 (m) REVERT: A 1713 SER cc_start: 0.8324 (m) cc_final: 0.7769 (t) REVERT: A 1723 THR cc_start: 0.8714 (m) cc_final: 0.8233 (p) REVERT: A 1731 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7536 (mtt90) REVERT: A 1738 ILE cc_start: 0.8630 (mt) cc_final: 0.8224 (mm) REVERT: A 1745 GLU cc_start: 0.6192 (mt-10) cc_final: 0.5871 (mp0) REVERT: A 1768 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7341 (mtp85) REVERT: A 1808 ASN cc_start: 0.7517 (m-40) cc_final: 0.7307 (m110) REVERT: A 1835 ARG cc_start: 0.7548 (mtm180) cc_final: 0.7274 (mtm180) REVERT: A 1842 TYR cc_start: 0.8079 (t80) cc_final: 0.7755 (t80) REVERT: A 1865 ASP cc_start: 0.7556 (t0) cc_final: 0.6441 (t70) REVERT: A 1866 GLN cc_start: 0.7705 (pm20) cc_final: 0.7082 (pm20) REVERT: A 1879 LEU cc_start: 0.7949 (mt) cc_final: 0.7742 (mp) REVERT: A 1885 SER cc_start: 0.8156 (t) cc_final: 0.7949 (t) REVERT: A 1900 MET cc_start: 0.8065 (mtt) cc_final: 0.7701 (mtp) REVERT: A 1903 ARG cc_start: 0.7768 (mtt90) cc_final: 0.7319 (mtt-85) REVERT: A 1905 ASP cc_start: 0.7834 (m-30) cc_final: 0.7485 (m-30) REVERT: A 1970 SER cc_start: 0.8586 (t) cc_final: 0.8305 (p) REVERT: A 1975 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7662 (ttm110) REVERT: A 1994 ASP cc_start: 0.8234 (p0) cc_final: 0.7778 (p0) REVERT: A 1996 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7072 (mtm110) REVERT: A 2013 TYR cc_start: 0.8333 (m-80) cc_final: 0.8068 (m-80) REVERT: A 2019 LEU cc_start: 0.8295 (tp) cc_final: 0.7965 (tp) REVERT: A 2057 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7579 (ttp-170) REVERT: A 2065 LYS cc_start: 0.8268 (ttpt) cc_final: 0.7742 (ttmm) REVERT: A 2079 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7699 (ttm110) REVERT: A 2095 LYS cc_start: 0.8133 (tptm) cc_final: 0.7825 (tptm) REVERT: A 2109 ARG cc_start: 0.7678 (ttt90) cc_final: 0.7358 (ttm-80) REVERT: A 2116 LYS cc_start: 0.8360 (mttt) cc_final: 0.8103 (mttt) REVERT: A 2138 VAL cc_start: 0.8239 (t) cc_final: 0.7888 (p) REVERT: A 2155 GLN cc_start: 0.8001 (mt0) cc_final: 0.7800 (mt0) REVERT: A 2190 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7495 (p) REVERT: A 2213 TRP cc_start: 0.8069 (m-90) cc_final: 0.7674 (m-90) REVERT: A 2235 MET cc_start: 0.7536 (mtp) cc_final: 0.7329 (mtm) REVERT: A 2251 VAL cc_start: 0.8082 (p) cc_final: 0.7749 (m) REVERT: A 2273 SER cc_start: 0.8334 (m) cc_final: 0.8057 (p) REVERT: A 2274 LYS cc_start: 0.8633 (tptp) cc_final: 0.8095 (tptt) REVERT: A 2292 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8081 (ttm-80) REVERT: A 2301 SER cc_start: 0.8550 (t) cc_final: 0.8308 (p) REVERT: A 2303 LYS cc_start: 0.8428 (tttt) cc_final: 0.8003 (mtpt) REVERT: A 2348 MET cc_start: 0.8336 (mtp) cc_final: 0.8043 (mtm) REVERT: A 2349 GLU cc_start: 0.8056 (tt0) cc_final: 0.7801 (tt0) REVERT: A 2453 ASN cc_start: 0.8298 (m-40) cc_final: 0.8060 (m110) REVERT: A 2501 GLU cc_start: 0.7708 (pm20) cc_final: 0.7355 (pm20) REVERT: A 2526 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7247 (tp40) REVERT: A 2554 THR cc_start: 0.8592 (m) cc_final: 0.8312 (m) REVERT: A 2574 THR cc_start: 0.7975 (m) cc_final: 0.7654 (t) REVERT: A 2599 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7752 (mmmt) REVERT: A 2604 ILE cc_start: 0.8187 (mt) cc_final: 0.7877 (tt) REVERT: A 2613 VAL cc_start: 0.7802 (OUTLIER) cc_final: 0.7545 (p) REVERT: A 2614 LYS cc_start: 0.7497 (mtpt) cc_final: 0.7221 (ttmm) REVERT: A 2699 TRP cc_start: 0.8047 (m100) cc_final: 0.7722 (m100) REVERT: B 1032 SER cc_start: 0.8275 (t) cc_final: 0.7893 (m) REVERT: B 1043 GLU cc_start: 0.8068 (mp0) cc_final: 0.7861 (mp0) REVERT: B 1073 LEU cc_start: 0.8776 (mt) cc_final: 0.8554 (mp) REVERT: B 1092 LEU cc_start: 0.8182 (tp) cc_final: 0.7967 (tp) REVERT: B 1115 PHE cc_start: 0.8372 (t80) cc_final: 0.8081 (t80) REVERT: B 1125 GLN cc_start: 0.7835 (mp10) cc_final: 0.7187 (mp10) REVERT: B 1173 ASP cc_start: 0.7974 (t0) cc_final: 0.7437 (t0) REVERT: B 1174 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7878 (mmtp) REVERT: B 1180 VAL cc_start: 0.8562 (m) cc_final: 0.8350 (p) REVERT: B 1593 HIS cc_start: 0.7578 (t-170) cc_final: 0.6987 (t-90) REVERT: B 1599 LEU cc_start: 0.8219 (mt) cc_final: 0.7996 (mp) REVERT: B 1606 TYR cc_start: 0.7883 (m-80) cc_final: 0.7605 (m-80) REVERT: B 1608 PHE cc_start: 0.7701 (m-80) cc_final: 0.7207 (m-80) REVERT: B 1666 LEU cc_start: 0.7827 (mt) cc_final: 0.7618 (mt) REVERT: B 1710 VAL cc_start: 0.8744 (t) cc_final: 0.8352 (m) REVERT: B 1723 THR cc_start: 0.8709 (m) cc_final: 0.8338 (p) REVERT: B 1731 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7732 (mtt-85) REVERT: B 1740 ASN cc_start: 0.7591 (m110) cc_final: 0.7213 (m110) REVERT: B 1760 GLN cc_start: 0.8037 (tt0) cc_final: 0.7649 (mm110) REVERT: B 1770 MET cc_start: 0.8030 (tpt) cc_final: 0.7805 (tpp) REVERT: B 1799 ILE cc_start: 0.8479 (mp) cc_final: 0.8253 (mt) REVERT: B 1813 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7367 (mmm-85) REVERT: B 1854 ASP cc_start: 0.8069 (m-30) cc_final: 0.7783 (m-30) REVERT: B 1903 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7448 (mtt-85) REVERT: B 1919 ASP cc_start: 0.7675 (p0) cc_final: 0.7359 (p0) REVERT: B 1965 MET cc_start: 0.8489 (mpt) cc_final: 0.7858 (mpp) REVERT: B 1975 ARG cc_start: 0.7979 (ttt90) cc_final: 0.7608 (ttt180) REVERT: B 1994 ASP cc_start: 0.8101 (p0) cc_final: 0.7646 (p0) REVERT: B 1996 ARG cc_start: 0.7960 (mmt90) cc_final: 0.6481 (mtm110) REVERT: B 2013 TYR cc_start: 0.8353 (m-80) cc_final: 0.8084 (m-80) REVERT: B 2019 LEU cc_start: 0.8241 (tp) cc_final: 0.7957 (tp) REVERT: B 2057 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.7456 (ttp80) REVERT: B 2112 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7718 (tp30) REVERT: B 2138 VAL cc_start: 0.8330 (t) cc_final: 0.7948 (p) REVERT: B 2158 MET cc_start: 0.7340 (ptm) cc_final: 0.7058 (ptp) REVERT: B 2163 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6780 (mtp) REVERT: B 2182 LYS cc_start: 0.8102 (tttm) cc_final: 0.7793 (ptmt) REVERT: B 2190 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7494 (p) REVERT: B 2193 THR cc_start: 0.8462 (m) cc_final: 0.7977 (p) REVERT: B 2213 TRP cc_start: 0.8094 (m-90) cc_final: 0.7626 (m-90) REVERT: B 2251 VAL cc_start: 0.8064 (p) cc_final: 0.7757 (m) REVERT: B 2279 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7572 (ttt-90) REVERT: B 2292 ARG cc_start: 0.8258 (tpp80) cc_final: 0.7994 (ttm-80) REVERT: B 2303 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7896 (mtpt) REVERT: B 2418 GLN cc_start: 0.7753 (mt0) cc_final: 0.7223 (mt0) REVERT: B 2429 THR cc_start: 0.7878 (p) cc_final: 0.7478 (t) REVERT: B 2453 ASN cc_start: 0.8265 (m-40) cc_final: 0.8051 (m110) REVERT: B 2501 GLU cc_start: 0.7762 (pm20) cc_final: 0.7559 (pm20) REVERT: B 2541 HIS cc_start: 0.7622 (p90) cc_final: 0.7407 (p90) REVERT: B 2554 THR cc_start: 0.8446 (m) cc_final: 0.8138 (m) REVERT: B 2589 SER cc_start: 0.8430 (t) cc_final: 0.7974 (p) REVERT: B 2604 ILE cc_start: 0.7937 (mt) cc_final: 0.7535 (tt) REVERT: B 2605 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: B 2613 VAL cc_start: 0.7862 (m) cc_final: 0.7474 (p) REVERT: B 2671 ARG cc_start: 0.6829 (ttt180) cc_final: 0.6482 (ttt180) REVERT: B 2682 GLU cc_start: 0.7612 (tp30) cc_final: 0.7326 (tp30) outliers start: 61 outliers final: 26 residues processed: 696 average time/residue: 0.1734 time to fit residues: 177.4579 Evaluate side-chains 647 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 616 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1616 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1684 SER Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1846 ILE Chi-restraints excluded: chain A residue 1892 LEU Chi-restraints excluded: chain A residue 2020 SER Chi-restraints excluded: chain A residue 2113 ILE Chi-restraints excluded: chain A residue 2139 MET Chi-restraints excluded: chain A residue 2144 HIS Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain A residue 2475 VAL Chi-restraints excluded: chain A residue 2550 HIS Chi-restraints excluded: chain A residue 2613 VAL Chi-restraints excluded: chain A residue 2746 GLU Chi-restraints excluded: chain B residue 1567 VAL Chi-restraints excluded: chain B residue 1616 VAL Chi-restraints excluded: chain B residue 1739 THR Chi-restraints excluded: chain B residue 1926 SER Chi-restraints excluded: chain B residue 1977 ILE Chi-restraints excluded: chain B residue 2163 MET Chi-restraints excluded: chain B residue 2190 THR Chi-restraints excluded: chain B residue 2375 LEU Chi-restraints excluded: chain B residue 2430 SER Chi-restraints excluded: chain B residue 2475 VAL Chi-restraints excluded: chain B residue 2550 HIS Chi-restraints excluded: chain B residue 2605 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 216 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 204 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 198 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2524 HIS A2703 GLN B1582 GLN ** B1808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1963 HIS B2085 HIS B2438 ASN B2524 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105837 restraints weight = 33223.541| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.45 r_work: 0.3179 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22801 Z= 0.150 Angle : 0.547 8.833 30954 Z= 0.287 Chirality : 0.046 0.224 3444 Planarity : 0.004 0.054 3945 Dihedral : 6.344 56.750 3569 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.00 % Allowed : 24.71 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2728 helix: 0.73 (0.35), residues: 224 sheet: 1.25 (0.17), residues: 880 loop : -0.55 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2247 TYR 0.020 0.002 TYR A2068 PHE 0.018 0.002 PHE A1871 TRP 0.009 0.001 TRP A2287 HIS 0.007 0.001 HIS A1175 Details of bonding type rmsd covalent geometry : bond 0.00331 (22777) covalent geometry : angle 0.53549 (30882) hydrogen bonds : bond 0.04116 ( 874) hydrogen bonds : angle 5.21410 ( 3174) link_ALPHA1-3 : bond 0.01083 ( 1) link_ALPHA1-3 : angle 0.96981 ( 3) link_BETA1-4 : bond 0.00670 ( 8) link_BETA1-4 : angle 1.90646 ( 24) link_NAG-ASN : bond 0.00412 ( 15) link_NAG-ASN : angle 2.68958 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 651 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1032 SER cc_start: 0.8337 (t) cc_final: 0.7929 (m) REVERT: A 1101 PHE cc_start: 0.7206 (t80) cc_final: 0.6609 (t80) REVERT: A 1115 PHE cc_start: 0.8395 (t80) cc_final: 0.8149 (t80) REVERT: A 1125 GLN cc_start: 0.7441 (mp10) cc_final: 0.7103 (pm20) REVERT: A 1151 GLU cc_start: 0.7985 (tp30) cc_final: 0.7147 (tm-30) REVERT: A 1173 ASP cc_start: 0.7907 (t0) cc_final: 0.7541 (t0) REVERT: A 1174 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8033 (mmtm) REVERT: A 1575 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7091 (mm-30) REVERT: A 1599 LEU cc_start: 0.8283 (mt) cc_final: 0.8069 (mp) REVERT: A 1618 GLU cc_start: 0.7581 (tt0) cc_final: 0.7378 (tt0) REVERT: A 1620 ILE cc_start: 0.7928 (mt) cc_final: 0.7675 (mt) REVERT: A 1674 ASP cc_start: 0.7961 (t70) cc_final: 0.7725 (t70) REVERT: A 1693 TYR cc_start: 0.8375 (m-80) cc_final: 0.8061 (m-80) REVERT: A 1710 VAL cc_start: 0.8836 (t) cc_final: 0.8480 (m) REVERT: A 1713 SER cc_start: 0.8340 (m) cc_final: 0.7860 (t) REVERT: A 1720 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7359 (ptpp) REVERT: A 1723 THR cc_start: 0.8723 (m) cc_final: 0.8287 (p) REVERT: A 1731 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7460 (mtt90) REVERT: A 1738 ILE cc_start: 0.8666 (mt) cc_final: 0.8299 (mm) REVERT: A 1835 ARG cc_start: 0.7569 (mtm180) cc_final: 0.7304 (mtm180) REVERT: A 1842 TYR cc_start: 0.8122 (t80) cc_final: 0.7786 (t80) REVERT: A 1865 ASP cc_start: 0.7700 (t0) cc_final: 0.6810 (t70) REVERT: A 1866 GLN cc_start: 0.7797 (pm20) cc_final: 0.7394 (pm20) REVERT: A 1885 SER cc_start: 0.8216 (t) cc_final: 0.8008 (t) REVERT: A 1900 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7860 (mtp) REVERT: A 1903 ARG cc_start: 0.7752 (mtt90) cc_final: 0.7334 (mtt-85) REVERT: A 1905 ASP cc_start: 0.7806 (m-30) cc_final: 0.7492 (m-30) REVERT: A 1932 MET cc_start: 0.7849 (tmm) cc_final: 0.7084 (ttm) REVERT: A 1975 ARG cc_start: 0.7948 (ttm170) cc_final: 0.7738 (ttm110) REVERT: A 1994 ASP cc_start: 0.8193 (p0) cc_final: 0.7732 (p0) REVERT: A 1996 ARG cc_start: 0.8131 (mmt90) cc_final: 0.7017 (mtm110) REVERT: A 2013 TYR cc_start: 0.8374 (m-80) cc_final: 0.8078 (m-80) REVERT: A 2057 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7713 (ttp-170) REVERT: A 2065 LYS cc_start: 0.8317 (ttpt) cc_final: 0.7811 (ttmm) REVERT: A 2079 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7739 (ttm110) REVERT: A 2095 LYS cc_start: 0.8121 (tptm) cc_final: 0.7850 (tptm) REVERT: A 2109 ARG cc_start: 0.7742 (ttt90) cc_final: 0.7502 (ttm-80) REVERT: A 2116 LYS cc_start: 0.8398 (mttt) cc_final: 0.8187 (mttm) REVERT: A 2138 VAL cc_start: 0.8250 (t) cc_final: 0.7856 (p) REVERT: A 2190 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7599 (p) REVERT: A 2213 TRP cc_start: 0.8096 (m-90) cc_final: 0.7808 (m-90) REVERT: A 2251 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7810 (m) REVERT: A 2273 SER cc_start: 0.8345 (m) cc_final: 0.7969 (t) REVERT: A 2274 LYS cc_start: 0.8556 (tptp) cc_final: 0.8180 (tptp) REVERT: A 2292 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8084 (ttm-80) REVERT: A 2301 SER cc_start: 0.8528 (t) cc_final: 0.8281 (p) REVERT: A 2303 LYS cc_start: 0.8439 (tttt) cc_final: 0.8030 (mtpt) REVERT: A 2322 ARG cc_start: 0.8431 (ttm170) cc_final: 0.8193 (ttp-170) REVERT: A 2348 MET cc_start: 0.8391 (mtp) cc_final: 0.8102 (mtt) REVERT: A 2349 GLU cc_start: 0.8039 (tt0) cc_final: 0.7767 (tt0) REVERT: A 2408 ASP cc_start: 0.8030 (t0) cc_final: 0.7576 (m-30) REVERT: A 2418 GLN cc_start: 0.7572 (tt0) cc_final: 0.7345 (tt0) REVERT: A 2453 ASN cc_start: 0.8321 (m-40) cc_final: 0.8087 (m110) REVERT: A 2455 ASN cc_start: 0.8307 (t0) cc_final: 0.8027 (t0) REVERT: A 2501 GLU cc_start: 0.7786 (pm20) cc_final: 0.7561 (pm20) REVERT: A 2526 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7344 (tp40) REVERT: A 2550 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7472 (m90) REVERT: A 2552 PHE cc_start: 0.8416 (m-80) cc_final: 0.8036 (m-80) REVERT: A 2554 THR cc_start: 0.8568 (m) cc_final: 0.8329 (m) REVERT: A 2574 THR cc_start: 0.8047 (m) cc_final: 0.7813 (t) REVERT: A 2599 LYS cc_start: 0.8206 (mtmm) cc_final: 0.8005 (mmmt) REVERT: A 2604 ILE cc_start: 0.8316 (mt) cc_final: 0.7966 (tt) REVERT: A 2613 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7558 (p) REVERT: A 2682 GLU cc_start: 0.7788 (tp30) cc_final: 0.7228 (tp30) REVERT: A 2689 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: A 2699 TRP cc_start: 0.8106 (m100) cc_final: 0.7872 (m100) REVERT: A 2711 GLU cc_start: 0.7688 (tt0) cc_final: 0.7283 (tp30) REVERT: B 1032 SER cc_start: 0.8223 (t) cc_final: 0.7832 (m) REVERT: B 1043 GLU cc_start: 0.8061 (mp0) cc_final: 0.7812 (mp0) REVERT: B 1058 VAL cc_start: 0.8773 (t) cc_final: 0.8567 (p) REVERT: B 1115 PHE cc_start: 0.8493 (t80) cc_final: 0.8199 (t80) REVERT: B 1125 GLN cc_start: 0.7705 (mp10) cc_final: 0.7393 (mp10) REVERT: B 1173 ASP cc_start: 0.7926 (t0) cc_final: 0.7427 (t0) REVERT: B 1174 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7918 (mmtp) REVERT: B 1184 ILE cc_start: 0.8013 (mm) cc_final: 0.7509 (mt) REVERT: B 1593 HIS cc_start: 0.7624 (t-170) cc_final: 0.7027 (t-90) REVERT: B 1599 LEU cc_start: 0.8272 (mt) cc_final: 0.8052 (mp) REVERT: B 1608 PHE cc_start: 0.7782 (m-80) cc_final: 0.7240 (m-80) REVERT: B 1614 ASN cc_start: 0.8048 (m-40) cc_final: 0.7825 (m-40) REVERT: B 1621 ASP cc_start: 0.7796 (p0) cc_final: 0.7559 (p0) REVERT: B 1625 ASN cc_start: 0.8590 (m-40) cc_final: 0.8312 (m110) REVERT: B 1710 VAL cc_start: 0.8726 (t) cc_final: 0.8364 (m) REVERT: B 1723 THR cc_start: 0.8718 (m) cc_final: 0.8383 (p) REVERT: B 1731 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7652 (mtt-85) REVERT: B 1740 ASN cc_start: 0.7644 (m110) cc_final: 0.7296 (m110) REVERT: B 1760 GLN cc_start: 0.8000 (tt0) cc_final: 0.7722 (mm110) REVERT: B 1770 MET cc_start: 0.7933 (tpt) cc_final: 0.7686 (tpp) REVERT: B 1775 MET cc_start: 0.8306 (ttt) cc_final: 0.8078 (ttp) REVERT: B 1796 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7539 (mtm-85) REVERT: B 1799 ILE cc_start: 0.8616 (mp) cc_final: 0.8306 (mt) REVERT: B 1813 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7340 (mmm-85) REVERT: B 1854 ASP cc_start: 0.8131 (m-30) cc_final: 0.7834 (m-30) REVERT: B 1903 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7529 (mtt-85) REVERT: B 1922 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8114 (m) REVERT: B 1965 MET cc_start: 0.8512 (mpt) cc_final: 0.7909 (mpp) REVERT: B 1990 ASP cc_start: 0.7792 (m-30) cc_final: 0.7589 (m-30) REVERT: B 1994 ASP cc_start: 0.7931 (p0) cc_final: 0.7617 (p0) REVERT: B 1996 ARG cc_start: 0.7959 (mmt90) cc_final: 0.6764 (mtm110) REVERT: B 2013 TYR cc_start: 0.8419 (m-80) cc_final: 0.8188 (m-80) REVERT: B 2057 ARG cc_start: 0.8004 (ttp-170) cc_final: 0.7654 (ttp80) REVERT: B 2112 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7717 (tp30) REVERT: B 2138 VAL cc_start: 0.8365 (t) cc_final: 0.7968 (p) REVERT: B 2163 MET cc_start: 0.7852 (mtp) cc_final: 0.7094 (mtp) REVERT: B 2190 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7586 (p) REVERT: B 2193 THR cc_start: 0.8473 (m) cc_final: 0.8001 (p) REVERT: B 2213 TRP cc_start: 0.8107 (m-90) cc_final: 0.7664 (m-10) REVERT: B 2251 VAL cc_start: 0.8186 (p) cc_final: 0.7875 (m) REVERT: B 2274 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8092 (tptp) REVERT: B 2292 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8075 (ttm-80) REVERT: B 2303 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7923 (mtpt) REVERT: B 2337 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7628 (mt) REVERT: B 2403 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.8149 (m90) REVERT: B 2418 GLN cc_start: 0.7749 (mt0) cc_final: 0.7264 (mt0) REVERT: B 2427 ARG cc_start: 0.8453 (ptp-170) cc_final: 0.7992 (mtp-110) REVERT: B 2467 VAL cc_start: 0.8478 (t) cc_final: 0.8269 (m) REVERT: B 2508 SER cc_start: 0.8470 (p) cc_final: 0.8146 (t) REVERT: B 2541 HIS cc_start: 0.7631 (p90) cc_final: 0.7418 (p90) REVERT: B 2550 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7738 (m90) REVERT: B 2554 THR cc_start: 0.8472 (m) cc_final: 0.8231 (m) REVERT: B 2569 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 2589 SER cc_start: 0.8481 (t) cc_final: 0.8089 (p) REVERT: B 2604 ILE cc_start: 0.8084 (mt) cc_final: 0.7587 (tt) REVERT: B 2605 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: B 2613 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7563 (p) REVERT: B 2671 ARG cc_start: 0.6915 (ttt180) cc_final: 0.6495 (ttt180) REVERT: B 2682 GLU cc_start: 0.7519 (tp30) cc_final: 0.7174 (tp30) REVERT: B 2685 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6940 (ttp80) outliers start: 72 outliers final: 41 residues processed: 690 average time/residue: 0.1707 time to fit residues: 173.7272 Evaluate side-chains 683 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 627 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1892 LEU Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1909 GLN Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2015 LYS Chi-restraints excluded: chain A residue 2020 SER Chi-restraints excluded: chain A residue 2042 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2113 ILE Chi-restraints excluded: chain A residue 2139 MET Chi-restraints excluded: chain A residue 2144 HIS Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2204 SER Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2225 LEU Chi-restraints excluded: chain A residue 2251 VAL Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain A residue 2441 LYS Chi-restraints excluded: chain A residue 2550 HIS Chi-restraints excluded: chain A residue 2613 VAL Chi-restraints excluded: chain A residue 2689 GLN Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1181 LYS Chi-restraints excluded: chain B residue 1567 VAL Chi-restraints excluded: chain B residue 1568 LEU Chi-restraints excluded: chain B residue 1647 ILE Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1738 ILE Chi-restraints excluded: chain B residue 1739 THR Chi-restraints excluded: chain B residue 1922 VAL Chi-restraints excluded: chain B residue 1932 MET Chi-restraints excluded: chain B residue 1977 ILE Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2093 SER Chi-restraints excluded: chain B residue 2125 VAL Chi-restraints excluded: chain B residue 2140 THR Chi-restraints excluded: chain B residue 2190 THR Chi-restraints excluded: chain B residue 2224 HIS Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2375 LEU Chi-restraints excluded: chain B residue 2403 HIS Chi-restraints excluded: chain B residue 2475 VAL Chi-restraints excluded: chain B residue 2550 HIS Chi-restraints excluded: chain B residue 2555 THR Chi-restraints excluded: chain B residue 2605 GLU Chi-restraints excluded: chain B residue 2613 VAL Chi-restraints excluded: chain B residue 2685 ARG Chi-restraints excluded: chain B residue 2752 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 118 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 233 optimal weight: 0.3980 chunk 151 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1639 HIS A1963 HIS A2325 HIS A2524 HIS B1102 GLN B1582 GLN B1808 ASN B2085 HIS B2252 GLN B2524 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106412 restraints weight = 33262.689| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.43 r_work: 0.3152 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22801 Z= 0.247 Angle : 0.626 18.814 30954 Z= 0.323 Chirality : 0.049 0.545 3444 Planarity : 0.004 0.056 3945 Dihedral : 6.283 59.181 3569 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.24 % Allowed : 24.42 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2728 helix: 0.86 (0.35), residues: 224 sheet: 1.16 (0.17), residues: 878 loop : -0.68 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B2490 TYR 0.025 0.002 TYR A2068 PHE 0.028 0.002 PHE B2370 TRP 0.012 0.002 TRP A1689 HIS 0.010 0.002 HIS A1639 Details of bonding type rmsd covalent geometry : bond 0.00552 (22777) covalent geometry : angle 0.60279 (30882) hydrogen bonds : bond 0.04426 ( 874) hydrogen bonds : angle 5.24458 ( 3174) link_ALPHA1-3 : bond 0.01070 ( 1) link_ALPHA1-3 : angle 1.06260 ( 3) link_BETA1-4 : bond 0.00519 ( 8) link_BETA1-4 : angle 2.05626 ( 24) link_NAG-ASN : bond 0.00584 ( 15) link_NAG-ASN : angle 4.24874 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 647 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1032 SER cc_start: 0.8315 (t) cc_final: 0.7853 (m) REVERT: A 1101 PHE cc_start: 0.7246 (t80) cc_final: 0.6774 (t80) REVERT: A 1125 GLN cc_start: 0.7487 (mp10) cc_final: 0.7150 (pm20) REVERT: A 1151 GLU cc_start: 0.7942 (tp30) cc_final: 0.7050 (tm-30) REVERT: A 1173 ASP cc_start: 0.7788 (t0) cc_final: 0.7414 (t0) REVERT: A 1174 LYS cc_start: 0.8242 (mmtt) cc_final: 0.8032 (mmtm) REVERT: A 1575 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7138 (mm-30) REVERT: A 1599 LEU cc_start: 0.8344 (mt) cc_final: 0.8008 (mp) REVERT: A 1618 GLU cc_start: 0.7647 (tt0) cc_final: 0.7398 (tt0) REVERT: A 1693 TYR cc_start: 0.8309 (m-80) cc_final: 0.7921 (m-80) REVERT: A 1700 ARG cc_start: 0.8331 (mmt90) cc_final: 0.7784 (mmt-90) REVERT: A 1710 VAL cc_start: 0.8861 (t) cc_final: 0.8507 (m) REVERT: A 1713 SER cc_start: 0.8359 (m) cc_final: 0.7829 (t) REVERT: A 1720 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7388 (ptpp) REVERT: A 1723 THR cc_start: 0.8753 (m) cc_final: 0.8312 (p) REVERT: A 1731 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7489 (mtt90) REVERT: A 1738 ILE cc_start: 0.8691 (mt) cc_final: 0.8326 (mm) REVERT: A 1745 GLU cc_start: 0.6260 (mp0) cc_final: 0.5985 (mp0) REVERT: A 1816 LYS cc_start: 0.7476 (ttmt) cc_final: 0.7213 (ttmt) REVERT: A 1835 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7193 (mtm180) REVERT: A 1842 TYR cc_start: 0.8219 (t80) cc_final: 0.7516 (t80) REVERT: A 1865 ASP cc_start: 0.7917 (t0) cc_final: 0.7313 (t70) REVERT: A 1866 GLN cc_start: 0.7812 (pm20) cc_final: 0.7584 (pm20) REVERT: A 1885 SER cc_start: 0.8320 (t) cc_final: 0.8108 (t) REVERT: A 1900 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7920 (mtp) REVERT: A 1903 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7350 (mtt-85) REVERT: A 1905 ASP cc_start: 0.7820 (m-30) cc_final: 0.7510 (m-30) REVERT: A 1932 MET cc_start: 0.7864 (tmm) cc_final: 0.7061 (ttm) REVERT: A 1975 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7847 (ttm110) REVERT: A 1994 ASP cc_start: 0.8200 (p0) cc_final: 0.7559 (p0) REVERT: A 1996 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7096 (mtm180) REVERT: A 2000 THR cc_start: 0.8336 (m) cc_final: 0.7994 (t) REVERT: A 2057 ARG cc_start: 0.8094 (ttp-170) cc_final: 0.7739 (ttp-170) REVERT: A 2065 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7779 (ttmm) REVERT: A 2079 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7744 (ttm110) REVERT: A 2095 LYS cc_start: 0.8174 (tptm) cc_final: 0.7879 (tptm) REVERT: A 2109 ARG cc_start: 0.7827 (ttt90) cc_final: 0.7569 (ttm-80) REVERT: A 2116 LYS cc_start: 0.8499 (mttt) cc_final: 0.8295 (mttm) REVERT: A 2138 VAL cc_start: 0.8300 (t) cc_final: 0.7884 (p) REVERT: A 2139 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7277 (ptm) REVERT: A 2190 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7572 (p) REVERT: A 2251 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7846 (m) REVERT: A 2254 LYS cc_start: 0.8057 (tttt) cc_final: 0.7631 (ttpt) REVERT: A 2273 SER cc_start: 0.8345 (m) cc_final: 0.8008 (t) REVERT: A 2274 LYS cc_start: 0.8561 (tptp) cc_final: 0.8221 (tptp) REVERT: A 2292 ARG cc_start: 0.8432 (tpp80) cc_final: 0.8166 (ttm-80) REVERT: A 2303 LYS cc_start: 0.8472 (tttt) cc_final: 0.8061 (mttm) REVERT: A 2322 ARG cc_start: 0.8447 (ttm170) cc_final: 0.8205 (ttp-170) REVERT: A 2348 MET cc_start: 0.8438 (mtp) cc_final: 0.8163 (mtt) REVERT: A 2349 GLU cc_start: 0.8038 (tt0) cc_final: 0.7753 (tt0) REVERT: A 2418 GLN cc_start: 0.7630 (tt0) cc_final: 0.7395 (tt0) REVERT: A 2427 ARG cc_start: 0.8479 (ptp-110) cc_final: 0.7973 (mtp-110) REVERT: A 2453 ASN cc_start: 0.8326 (m-40) cc_final: 0.8098 (m110) REVERT: A 2526 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7670 (tp40) REVERT: A 2554 THR cc_start: 0.8579 (m) cc_final: 0.8327 (m) REVERT: A 2571 ARG cc_start: 0.8159 (mtp180) cc_final: 0.7363 (mtp180) REVERT: A 2599 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8076 (mmmt) REVERT: A 2604 ILE cc_start: 0.8354 (mt) cc_final: 0.7965 (tt) REVERT: A 2682 GLU cc_start: 0.7817 (tp30) cc_final: 0.7439 (tp30) REVERT: A 2699 TRP cc_start: 0.8154 (m100) cc_final: 0.7852 (m100) REVERT: A 2711 GLU cc_start: 0.7684 (tt0) cc_final: 0.7273 (tp30) REVERT: B 1032 SER cc_start: 0.8236 (t) cc_final: 0.7817 (m) REVERT: B 1043 GLU cc_start: 0.8108 (mp0) cc_final: 0.7828 (mp0) REVERT: B 1058 VAL cc_start: 0.8754 (t) cc_final: 0.8540 (p) REVERT: B 1101 PHE cc_start: 0.7265 (t80) cc_final: 0.6844 (t80) REVERT: B 1125 GLN cc_start: 0.7781 (mp10) cc_final: 0.7480 (mp10) REVERT: B 1173 ASP cc_start: 0.7876 (t0) cc_final: 0.7485 (t0) REVERT: B 1184 ILE cc_start: 0.8136 (mm) cc_final: 0.7666 (mt) REVERT: B 1599 LEU cc_start: 0.8232 (mt) cc_final: 0.8018 (mp) REVERT: B 1614 ASN cc_start: 0.8034 (m-40) cc_final: 0.7799 (m-40) REVERT: B 1650 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 1693 TYR cc_start: 0.8412 (m-80) cc_final: 0.8196 (m-80) REVERT: B 1710 VAL cc_start: 0.8743 (t) cc_final: 0.8390 (m) REVERT: B 1723 THR cc_start: 0.8717 (m) cc_final: 0.8371 (p) REVERT: B 1731 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7725 (mtt-85) REVERT: B 1740 ASN cc_start: 0.7727 (m110) cc_final: 0.7379 (m110) REVERT: B 1770 MET cc_start: 0.7916 (tpt) cc_final: 0.7690 (tpp) REVERT: B 1784 HIS cc_start: 0.7885 (t70) cc_final: 0.7539 (t70) REVERT: B 1796 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7545 (mtm-85) REVERT: B 1799 ILE cc_start: 0.8626 (mp) cc_final: 0.8371 (mt) REVERT: B 1808 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7274 (m-40) REVERT: B 1813 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7317 (mmm-85) REVERT: B 1854 ASP cc_start: 0.8156 (m-30) cc_final: 0.7822 (m-30) REVERT: B 1900 MET cc_start: 0.8053 (mtp) cc_final: 0.7827 (mtp) REVERT: B 1903 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7578 (mtt-85) REVERT: B 1919 ASP cc_start: 0.7791 (p0) cc_final: 0.7491 (p0) REVERT: B 1922 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8134 (m) REVERT: B 1994 ASP cc_start: 0.7926 (p0) cc_final: 0.7610 (p0) REVERT: B 1996 ARG cc_start: 0.8041 (mmt90) cc_final: 0.6918 (mtm110) REVERT: B 1999 LYS cc_start: 0.8423 (tttt) cc_final: 0.8160 (tttp) REVERT: B 2013 TYR cc_start: 0.8458 (m-80) cc_final: 0.8179 (m-80) REVERT: B 2057 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7670 (ttp80) REVERT: B 2112 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7728 (tp30) REVERT: B 2163 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6888 (mtt) REVERT: B 2190 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7543 (p) REVERT: B 2193 THR cc_start: 0.8492 (m) cc_final: 0.7998 (p) REVERT: B 2213 TRP cc_start: 0.8149 (m-90) cc_final: 0.7911 (m-10) REVERT: B 2251 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7867 (m) REVERT: B 2273 SER cc_start: 0.8123 (m) cc_final: 0.7784 (t) REVERT: B 2292 ARG cc_start: 0.8326 (tpp80) cc_final: 0.8113 (ttm-80) REVERT: B 2303 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7939 (mtpt) REVERT: B 2337 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7763 (mt) REVERT: B 2418 GLN cc_start: 0.7755 (mt0) cc_final: 0.7251 (mt0) REVERT: B 2427 ARG cc_start: 0.8515 (ptp-170) cc_final: 0.7981 (mtp-110) REVERT: B 2467 VAL cc_start: 0.8485 (t) cc_final: 0.8250 (m) REVERT: B 2508 SER cc_start: 0.8475 (p) cc_final: 0.8209 (t) REVERT: B 2550 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7543 (m90) REVERT: B 2554 THR cc_start: 0.8537 (m) cc_final: 0.8298 (m) REVERT: B 2582 GLU cc_start: 0.6891 (tt0) cc_final: 0.6600 (tt0) REVERT: B 2589 SER cc_start: 0.8525 (t) cc_final: 0.8100 (p) REVERT: B 2590 VAL cc_start: 0.8239 (t) cc_final: 0.7943 (t) REVERT: B 2604 ILE cc_start: 0.8121 (mt) cc_final: 0.7588 (tt) REVERT: B 2605 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: B 2671 ARG cc_start: 0.6966 (ttt180) cc_final: 0.6496 (ttt-90) REVERT: B 2682 GLU cc_start: 0.7532 (tp30) cc_final: 0.7221 (tp30) outliers start: 102 outliers final: 70 residues processed: 706 average time/residue: 0.1763 time to fit residues: 183.3093 Evaluate side-chains 706 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 622 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1756 ARG Chi-restraints excluded: chain A residue 1846 ILE Chi-restraints excluded: chain A residue 1851 ILE Chi-restraints excluded: chain A residue 1892 LEU Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1926 SER Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2001 SER Chi-restraints excluded: chain A residue 2015 LYS Chi-restraints excluded: chain A residue 2019 LEU Chi-restraints excluded: chain A residue 2020 SER Chi-restraints excluded: chain A residue 2042 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2113 ILE Chi-restraints excluded: chain A residue 2139 MET Chi-restraints excluded: chain A residue 2163 MET Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2204 SER Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2225 LEU Chi-restraints excluded: chain A residue 2240 ASP Chi-restraints excluded: chain A residue 2251 VAL Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain A residue 2398 MET Chi-restraints excluded: chain A residue 2439 VAL Chi-restraints excluded: chain A residue 2441 LYS Chi-restraints excluded: chain A residue 2471 LYS Chi-restraints excluded: chain A residue 2503 SER Chi-restraints excluded: chain A residue 2550 HIS Chi-restraints excluded: chain A residue 2689 GLN Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1181 LYS Chi-restraints excluded: chain B residue 1567 VAL Chi-restraints excluded: chain B residue 1616 VAL Chi-restraints excluded: chain B residue 1647 ILE Chi-restraints excluded: chain B residue 1650 LEU Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1738 ILE Chi-restraints excluded: chain B residue 1739 THR Chi-restraints excluded: chain B residue 1768 ARG Chi-restraints excluded: chain B residue 1808 ASN Chi-restraints excluded: chain B residue 1816 LYS Chi-restraints excluded: chain B residue 1823 VAL Chi-restraints excluded: chain B residue 1851 ILE Chi-restraints excluded: chain B residue 1922 VAL Chi-restraints excluded: chain B residue 1932 MET Chi-restraints excluded: chain B residue 1977 ILE Chi-restraints excluded: chain B residue 1982 GLU Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2019 LEU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2093 SER Chi-restraints excluded: chain B residue 2140 THR Chi-restraints excluded: chain B residue 2163 MET Chi-restraints excluded: chain B residue 2190 THR Chi-restraints excluded: chain B residue 2224 HIS Chi-restraints excluded: chain B residue 2240 ASP Chi-restraints excluded: chain B residue 2246 THR Chi-restraints excluded: chain B residue 2251 VAL Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2375 LEU Chi-restraints excluded: chain B residue 2430 SER Chi-restraints excluded: chain B residue 2437 ARG Chi-restraints excluded: chain B residue 2475 VAL Chi-restraints excluded: chain B residue 2550 HIS Chi-restraints excluded: chain B residue 2555 THR Chi-restraints excluded: chain B residue 2574 THR Chi-restraints excluded: chain B residue 2593 ASN Chi-restraints excluded: chain B residue 2605 GLU Chi-restraints excluded: chain B residue 2657 THR Chi-restraints excluded: chain B residue 2752 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 273 optimal weight: 0.5980 chunk 169 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 267 optimal weight: 0.6980 chunk 232 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2325 HIS A2524 HIS B1582 GLN B1808 ASN B2085 HIS B2453 ASN B2524 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108058 restraints weight = 32894.157| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.42 r_work: 0.3150 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22801 Z= 0.140 Angle : 0.557 14.055 30954 Z= 0.290 Chirality : 0.047 0.516 3444 Planarity : 0.004 0.043 3945 Dihedral : 5.936 59.833 3569 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.54 % Allowed : 25.79 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 2728 helix: 1.12 (0.36), residues: 224 sheet: 1.12 (0.17), residues: 882 loop : -0.63 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2490 TYR 0.018 0.002 TYR B2056 PHE 0.026 0.002 PHE A1826 TRP 0.016 0.001 TRP A2436 HIS 0.009 0.001 HIS B1593 Details of bonding type rmsd covalent geometry : bond 0.00309 (22777) covalent geometry : angle 0.53860 (30882) hydrogen bonds : bond 0.03772 ( 874) hydrogen bonds : angle 5.05011 ( 3174) link_ALPHA1-3 : bond 0.01328 ( 1) link_ALPHA1-3 : angle 1.37931 ( 3) link_BETA1-4 : bond 0.00615 ( 8) link_BETA1-4 : angle 1.94610 ( 24) link_NAG-ASN : bond 0.00406 ( 15) link_NAG-ASN : angle 3.44988 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 633 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1032 SER cc_start: 0.8306 (t) cc_final: 0.7862 (m) REVERT: A 1101 PHE cc_start: 0.7198 (t80) cc_final: 0.6720 (t80) REVERT: A 1125 GLN cc_start: 0.7444 (mp10) cc_final: 0.7063 (pm20) REVERT: A 1151 GLU cc_start: 0.7941 (tp30) cc_final: 0.7099 (tm-30) REVERT: A 1153 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7010 (tpp80) REVERT: A 1173 ASP cc_start: 0.7782 (t0) cc_final: 0.7433 (t0) REVERT: A 1174 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7974 (mmtm) REVERT: A 1575 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 1599 LEU cc_start: 0.8084 (mt) cc_final: 0.7851 (mp) REVERT: A 1618 GLU cc_start: 0.7698 (tt0) cc_final: 0.7401 (tt0) REVERT: A 1693 TYR cc_start: 0.8275 (m-80) cc_final: 0.7868 (m-80) REVERT: A 1698 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: A 1710 VAL cc_start: 0.8842 (t) cc_final: 0.8442 (m) REVERT: A 1713 SER cc_start: 0.8271 (m) cc_final: 0.7798 (t) REVERT: A 1720 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7375 (ptpp) REVERT: A 1723 THR cc_start: 0.8765 (m) cc_final: 0.8321 (p) REVERT: A 1731 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7590 (mtt90) REVERT: A 1738 ILE cc_start: 0.8654 (mt) cc_final: 0.8261 (mm) REVERT: A 1745 GLU cc_start: 0.6375 (mp0) cc_final: 0.5993 (mp0) REVERT: A 1842 TYR cc_start: 0.8124 (t80) cc_final: 0.7439 (t80) REVERT: A 1850 LYS cc_start: 0.8142 (tttt) cc_final: 0.7870 (ttmm) REVERT: A 1865 ASP cc_start: 0.7749 (t0) cc_final: 0.7195 (t70) REVERT: A 1885 SER cc_start: 0.8270 (t) cc_final: 0.8060 (t) REVERT: A 1887 PHE cc_start: 0.8292 (m-80) cc_final: 0.7865 (m-80) REVERT: A 1900 MET cc_start: 0.8111 (mtt) cc_final: 0.7822 (mtp) REVERT: A 1903 ARG cc_start: 0.7697 (mtt90) cc_final: 0.7233 (mtt-85) REVERT: A 1905 ASP cc_start: 0.7793 (m-30) cc_final: 0.7458 (m-30) REVERT: A 1932 MET cc_start: 0.7843 (tmm) cc_final: 0.7038 (ttm) REVERT: A 1994 ASP cc_start: 0.8119 (p0) cc_final: 0.7565 (p0) REVERT: A 1996 ARG cc_start: 0.8086 (mmt90) cc_final: 0.7027 (mtm110) REVERT: A 2000 THR cc_start: 0.8287 (m) cc_final: 0.7968 (t) REVERT: A 2013 TYR cc_start: 0.8357 (m-80) cc_final: 0.8121 (m-80) REVERT: A 2015 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8290 (ttpp) REVERT: A 2065 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7746 (ttmm) REVERT: A 2079 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7698 (ttm110) REVERT: A 2095 LYS cc_start: 0.8172 (tptm) cc_final: 0.7851 (tptm) REVERT: A 2109 ARG cc_start: 0.7713 (ttt90) cc_final: 0.7440 (ttm-80) REVERT: A 2116 LYS cc_start: 0.8500 (mttt) cc_final: 0.8283 (mttm) REVERT: A 2138 VAL cc_start: 0.8271 (t) cc_final: 0.7846 (p) REVERT: A 2139 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7394 (ptm) REVERT: A 2190 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7521 (p) REVERT: A 2213 TRP cc_start: 0.8027 (m-90) cc_final: 0.7586 (m-10) REVERT: A 2251 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7721 (m) REVERT: A 2273 SER cc_start: 0.8300 (m) cc_final: 0.7974 (t) REVERT: A 2292 ARG cc_start: 0.8412 (tpp80) cc_final: 0.8099 (ttm-80) REVERT: A 2303 LYS cc_start: 0.8431 (tttt) cc_final: 0.7992 (mtpt) REVERT: A 2348 MET cc_start: 0.8368 (mtp) cc_final: 0.8113 (mtt) REVERT: A 2349 GLU cc_start: 0.8020 (tt0) cc_final: 0.7704 (tt0) REVERT: A 2418 GLN cc_start: 0.7578 (tt0) cc_final: 0.7346 (tt0) REVERT: A 2427 ARG cc_start: 0.8414 (ptp-110) cc_final: 0.7869 (mtp-110) REVERT: A 2453 ASN cc_start: 0.8303 (m-40) cc_final: 0.8079 (m110) REVERT: A 2526 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7621 (tp40) REVERT: A 2554 THR cc_start: 0.8567 (m) cc_final: 0.8308 (m) REVERT: A 2571 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7223 (mtp180) REVERT: A 2574 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8089 (p) REVERT: A 2599 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8019 (mmmt) REVERT: A 2604 ILE cc_start: 0.8274 (mt) cc_final: 0.7928 (tt) REVERT: A 2682 GLU cc_start: 0.7739 (tp30) cc_final: 0.7352 (tp30) REVERT: A 2699 TRP cc_start: 0.8060 (m100) cc_final: 0.7768 (m100) REVERT: A 2711 GLU cc_start: 0.7678 (tt0) cc_final: 0.7238 (tp30) REVERT: B 1032 SER cc_start: 0.8235 (t) cc_final: 0.7805 (m) REVERT: B 1043 GLU cc_start: 0.8129 (mp0) cc_final: 0.7875 (mp0) REVERT: B 1101 PHE cc_start: 0.7254 (t80) cc_final: 0.6858 (t80) REVERT: B 1125 GLN cc_start: 0.7805 (mp10) cc_final: 0.7412 (mp10) REVERT: B 1173 ASP cc_start: 0.7894 (t0) cc_final: 0.7488 (t0) REVERT: B 1174 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7841 (mmtp) REVERT: B 1184 ILE cc_start: 0.8065 (mm) cc_final: 0.7579 (mt) REVERT: B 1599 LEU cc_start: 0.8181 (mt) cc_final: 0.7962 (mp) REVERT: B 1614 ASN cc_start: 0.8046 (m-40) cc_final: 0.7814 (m-40) REVERT: B 1693 TYR cc_start: 0.8378 (m-80) cc_final: 0.8153 (m-80) REVERT: B 1710 VAL cc_start: 0.8717 (t) cc_final: 0.8341 (m) REVERT: B 1723 THR cc_start: 0.8714 (m) cc_final: 0.8333 (p) REVERT: B 1770 MET cc_start: 0.7941 (tpt) cc_final: 0.7718 (tpp) REVERT: B 1784 HIS cc_start: 0.7735 (t70) cc_final: 0.7453 (t70) REVERT: B 1796 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7542 (mtm-85) REVERT: B 1799 ILE cc_start: 0.8534 (mp) cc_final: 0.8269 (mt) REVERT: B 1813 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7271 (mmm-85) REVERT: B 1842 TYR cc_start: 0.8133 (t80) cc_final: 0.7896 (t80) REVERT: B 1854 ASP cc_start: 0.8172 (m-30) cc_final: 0.7835 (m-30) REVERT: B 1900 MET cc_start: 0.7973 (mtp) cc_final: 0.7717 (mtp) REVERT: B 1903 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7495 (mtt-85) REVERT: B 1919 ASP cc_start: 0.7774 (p0) cc_final: 0.7477 (p0) REVERT: B 1922 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8096 (m) REVERT: B 1950 ASP cc_start: 0.8107 (m-30) cc_final: 0.7794 (t0) REVERT: B 1965 MET cc_start: 0.8625 (mpp) cc_final: 0.7925 (mpp) REVERT: B 1990 ASP cc_start: 0.7749 (m-30) cc_final: 0.7402 (m-30) REVERT: B 1996 ARG cc_start: 0.7931 (mmt90) cc_final: 0.6807 (mtm110) REVERT: B 1999 LYS cc_start: 0.8401 (tttt) cc_final: 0.8152 (tttp) REVERT: B 2013 TYR cc_start: 0.8401 (m-80) cc_final: 0.8123 (m-80) REVERT: B 2057 ARG cc_start: 0.7955 (ttp-170) cc_final: 0.7630 (ttp80) REVERT: B 2112 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7741 (tp30) REVERT: B 2190 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7528 (p) REVERT: B 2193 THR cc_start: 0.8432 (m) cc_final: 0.7901 (p) REVERT: B 2251 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7725 (m) REVERT: B 2273 SER cc_start: 0.7895 (m) cc_final: 0.7680 (t) REVERT: B 2303 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7893 (mtpt) REVERT: B 2337 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7713 (mt) REVERT: B 2418 GLN cc_start: 0.7677 (mt0) cc_final: 0.7136 (mt0) REVERT: B 2427 ARG cc_start: 0.8465 (ptp-170) cc_final: 0.7954 (mtp-110) REVERT: B 2467 VAL cc_start: 0.8484 (t) cc_final: 0.8257 (m) REVERT: B 2508 SER cc_start: 0.8451 (p) cc_final: 0.8204 (t) REVERT: B 2550 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7840 (m90) REVERT: B 2554 THR cc_start: 0.8530 (m) cc_final: 0.8291 (m) REVERT: B 2561 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7506 (mtpp) REVERT: B 2582 GLU cc_start: 0.6821 (tt0) cc_final: 0.6541 (tt0) REVERT: B 2589 SER cc_start: 0.8416 (t) cc_final: 0.7989 (p) REVERT: B 2590 VAL cc_start: 0.8150 (t) cc_final: 0.7850 (t) REVERT: B 2604 ILE cc_start: 0.8057 (mt) cc_final: 0.7590 (tt) REVERT: B 2605 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: B 2671 ARG cc_start: 0.6890 (ttt180) cc_final: 0.6392 (ttt-90) REVERT: B 2682 GLU cc_start: 0.7349 (tp30) cc_final: 0.7149 (tp30) outliers start: 85 outliers final: 54 residues processed: 675 average time/residue: 0.1762 time to fit residues: 174.4762 Evaluate side-chains 687 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 620 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1698 GLU Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1851 ILE Chi-restraints excluded: chain A residue 1892 LEU Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2015 LYS Chi-restraints excluded: chain A residue 2019 LEU Chi-restraints excluded: chain A residue 2042 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2113 ILE Chi-restraints excluded: chain A residue 2139 MET Chi-restraints excluded: chain A residue 2144 HIS Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2204 SER Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2251 VAL Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain A residue 2398 MET Chi-restraints excluded: chain A residue 2430 SER Chi-restraints excluded: chain A residue 2441 LYS Chi-restraints excluded: chain A residue 2471 LYS Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2503 SER Chi-restraints excluded: chain A residue 2550 HIS Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1181 LYS Chi-restraints excluded: chain B residue 1567 VAL Chi-restraints excluded: chain B residue 1647 ILE Chi-restraints excluded: chain B residue 1650 LEU Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1739 THR Chi-restraints excluded: chain B residue 1768 ARG Chi-restraints excluded: chain B residue 1816 LYS Chi-restraints excluded: chain B residue 1851 ILE Chi-restraints excluded: chain B residue 1909 GLN Chi-restraints excluded: chain B residue 1922 VAL Chi-restraints excluded: chain B residue 1932 MET Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2019 LEU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2085 HIS Chi-restraints excluded: chain B residue 2093 SER Chi-restraints excluded: chain B residue 2190 THR Chi-restraints excluded: chain B residue 2224 HIS Chi-restraints excluded: chain B residue 2240 ASP Chi-restraints excluded: chain B residue 2251 VAL Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2375 LEU Chi-restraints excluded: chain B residue 2430 SER Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 2550 HIS Chi-restraints excluded: chain B residue 2574 THR Chi-restraints excluded: chain B residue 2593 ASN Chi-restraints excluded: chain B residue 2605 GLU Chi-restraints excluded: chain B residue 2752 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 262 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 132 optimal weight: 0.0270 chunk 208 optimal weight: 0.5980 chunk 183 optimal weight: 0.0370 chunk 257 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1614 ASN A2329 HIS A2524 HIS B1582 GLN B1740 ASN B2085 HIS B2318 HIS B2524 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.126906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107248 restraints weight = 33058.603| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.42 r_work: 0.3101 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22801 Z= 0.198 Angle : 0.590 15.366 30954 Z= 0.306 Chirality : 0.048 0.604 3444 Planarity : 0.004 0.064 3945 Dihedral : 5.953 59.999 3569 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.20 % Allowed : 25.50 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2728 helix: 1.13 (0.36), residues: 224 sheet: 1.05 (0.17), residues: 882 loop : -0.69 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B2490 TYR 0.021 0.002 TYR B1595 PHE 0.022 0.002 PHE B2370 TRP 0.013 0.002 TRP A2436 HIS 0.018 0.002 HIS B2085 Details of bonding type rmsd covalent geometry : bond 0.00445 (22777) covalent geometry : angle 0.56935 (30882) hydrogen bonds : bond 0.03996 ( 874) hydrogen bonds : angle 5.07003 ( 3174) link_ALPHA1-3 : bond 0.01271 ( 1) link_ALPHA1-3 : angle 1.30660 ( 3) link_BETA1-4 : bond 0.00423 ( 8) link_BETA1-4 : angle 1.93574 ( 24) link_NAG-ASN : bond 0.00497 ( 15) link_NAG-ASN : angle 3.82385 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 641 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1032 SER cc_start: 0.8319 (t) cc_final: 0.7847 (m) REVERT: A 1101 PHE cc_start: 0.7228 (t80) cc_final: 0.6711 (t80) REVERT: A 1125 GLN cc_start: 0.7384 (mp10) cc_final: 0.6806 (mp10) REVERT: A 1153 ARG cc_start: 0.7896 (tpp80) cc_final: 0.7149 (tpp80) REVERT: A 1173 ASP cc_start: 0.7799 (t0) cc_final: 0.7425 (t0) REVERT: A 1174 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7942 (mmtm) REVERT: A 1575 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7130 (mm-30) REVERT: A 1599 LEU cc_start: 0.8040 (mt) cc_final: 0.7801 (mp) REVERT: A 1618 GLU cc_start: 0.7704 (tt0) cc_final: 0.7394 (tt0) REVERT: A 1693 TYR cc_start: 0.8280 (m-80) cc_final: 0.7854 (m-80) REVERT: A 1700 ARG cc_start: 0.8240 (mmt90) cc_final: 0.7729 (mmt-90) REVERT: A 1710 VAL cc_start: 0.8854 (t) cc_final: 0.8465 (m) REVERT: A 1713 SER cc_start: 0.8262 (m) cc_final: 0.7730 (t) REVERT: A 1720 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7449 (ptpp) REVERT: A 1723 THR cc_start: 0.8763 (m) cc_final: 0.8307 (p) REVERT: A 1731 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7601 (mtt90) REVERT: A 1738 ILE cc_start: 0.8608 (mt) cc_final: 0.8203 (mm) REVERT: A 1745 GLU cc_start: 0.6446 (mp0) cc_final: 0.6063 (mp0) REVERT: A 1842 TYR cc_start: 0.8132 (t80) cc_final: 0.7561 (t80) REVERT: A 1865 ASP cc_start: 0.7865 (t0) cc_final: 0.7635 (t70) REVERT: A 1887 PHE cc_start: 0.8292 (m-80) cc_final: 0.7949 (m-80) REVERT: A 1900 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7808 (mtp) REVERT: A 1903 ARG cc_start: 0.7677 (mtt90) cc_final: 0.7170 (mtt-85) REVERT: A 1905 ASP cc_start: 0.7783 (m-30) cc_final: 0.7442 (m-30) REVERT: A 1932 MET cc_start: 0.7885 (tmm) cc_final: 0.7120 (ttm) REVERT: A 1975 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7769 (ttm110) REVERT: A 1994 ASP cc_start: 0.8116 (p0) cc_final: 0.7603 (p0) REVERT: A 1996 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7035 (mtm110) REVERT: A 2000 THR cc_start: 0.8255 (m) cc_final: 0.7957 (t) REVERT: A 2057 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7621 (ttp-170) REVERT: A 2065 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7697 (ttmm) REVERT: A 2079 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7685 (ttm110) REVERT: A 2109 ARG cc_start: 0.7715 (ttt90) cc_final: 0.7444 (ttm-80) REVERT: A 2116 LYS cc_start: 0.8517 (mttt) cc_final: 0.8300 (mttm) REVERT: A 2138 VAL cc_start: 0.8297 (t) cc_final: 0.7857 (p) REVERT: A 2190 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7511 (p) REVERT: A 2213 TRP cc_start: 0.8024 (m-90) cc_final: 0.7663 (m-10) REVERT: A 2273 SER cc_start: 0.8205 (m) cc_final: 0.7945 (t) REVERT: A 2292 ARG cc_start: 0.8396 (tpp80) cc_final: 0.8100 (ttm-80) REVERT: A 2303 LYS cc_start: 0.8417 (tttt) cc_final: 0.7999 (mtpt) REVERT: A 2322 ARG cc_start: 0.8390 (ttm170) cc_final: 0.8177 (ttp-170) REVERT: A 2337 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7880 (mt) REVERT: A 2348 MET cc_start: 0.8363 (mtp) cc_final: 0.8099 (mtt) REVERT: A 2349 GLU cc_start: 0.7989 (tt0) cc_final: 0.7663 (tt0) REVERT: A 2427 ARG cc_start: 0.8417 (ptp-110) cc_final: 0.7932 (mtp-110) REVERT: A 2453 ASN cc_start: 0.8302 (m-40) cc_final: 0.8078 (m110) REVERT: A 2484 ILE cc_start: 0.8805 (pt) cc_final: 0.8464 (mt) REVERT: A 2508 SER cc_start: 0.8495 (p) cc_final: 0.8189 (t) REVERT: A 2526 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7587 (tp40) REVERT: A 2554 THR cc_start: 0.8570 (m) cc_final: 0.8327 (m) REVERT: A 2571 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7234 (mtp180) REVERT: A 2574 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8091 (p) REVERT: A 2589 SER cc_start: 0.8472 (p) cc_final: 0.8262 (p) REVERT: A 2599 LYS cc_start: 0.8502 (mtmm) cc_final: 0.8036 (mmmt) REVERT: A 2604 ILE cc_start: 0.8220 (mt) cc_final: 0.7899 (tt) REVERT: A 2682 GLU cc_start: 0.7735 (tp30) cc_final: 0.7322 (tp30) REVERT: A 2699 TRP cc_start: 0.8049 (m100) cc_final: 0.7739 (m100) REVERT: A 2711 GLU cc_start: 0.7713 (tt0) cc_final: 0.7273 (tp30) REVERT: A 2722 GLN cc_start: 0.8031 (tp40) cc_final: 0.7810 (tp40) REVERT: B 1032 SER cc_start: 0.8226 (t) cc_final: 0.7824 (m) REVERT: B 1043 GLU cc_start: 0.8128 (mp0) cc_final: 0.7876 (mp0) REVERT: B 1049 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7929 (tp30) REVERT: B 1101 PHE cc_start: 0.7272 (t80) cc_final: 0.6901 (t80) REVERT: B 1121 ASP cc_start: 0.7872 (p0) cc_final: 0.7530 (p0) REVERT: B 1125 GLN cc_start: 0.7819 (mp10) cc_final: 0.7386 (mp10) REVERT: B 1173 ASP cc_start: 0.7887 (t0) cc_final: 0.7537 (m-30) REVERT: B 1174 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7826 (mmtp) REVERT: B 1184 ILE cc_start: 0.8109 (mm) cc_final: 0.7560 (mt) REVERT: B 1599 LEU cc_start: 0.8171 (mt) cc_final: 0.7955 (mp) REVERT: B 1614 ASN cc_start: 0.8045 (m-40) cc_final: 0.7803 (m-40) REVERT: B 1638 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7482 (mmm-85) REVERT: B 1693 TYR cc_start: 0.8389 (m-80) cc_final: 0.8156 (m-80) REVERT: B 1710 VAL cc_start: 0.8713 (t) cc_final: 0.8349 (m) REVERT: B 1723 THR cc_start: 0.8726 (m) cc_final: 0.8323 (p) REVERT: B 1731 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7690 (mtt-85) REVERT: B 1770 MET cc_start: 0.7971 (tpt) cc_final: 0.7770 (tpp) REVERT: B 1784 HIS cc_start: 0.7769 (t70) cc_final: 0.7464 (t70) REVERT: B 1796 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7594 (mtm-85) REVERT: B 1799 ILE cc_start: 0.8513 (mp) cc_final: 0.8232 (mt) REVERT: B 1808 ASN cc_start: 0.7551 (m-40) cc_final: 0.7238 (m-40) REVERT: B 1900 MET cc_start: 0.7969 (mtp) cc_final: 0.7709 (mtp) REVERT: B 1903 ARG cc_start: 0.7891 (mtt180) cc_final: 0.7446 (mtt-85) REVERT: B 1919 ASP cc_start: 0.7818 (p0) cc_final: 0.7513 (p0) REVERT: B 1922 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8081 (m) REVERT: B 1950 ASP cc_start: 0.8174 (m-30) cc_final: 0.7849 (t0) REVERT: B 1990 ASP cc_start: 0.7748 (m-30) cc_final: 0.7429 (m-30) REVERT: B 1996 ARG cc_start: 0.7931 (mmt90) cc_final: 0.6774 (mtm180) REVERT: B 1999 LYS cc_start: 0.8379 (tttt) cc_final: 0.8138 (tttp) REVERT: B 2013 TYR cc_start: 0.8419 (m-80) cc_final: 0.8210 (m-80) REVERT: B 2057 ARG cc_start: 0.7939 (ttp-170) cc_final: 0.7592 (ttp80) REVERT: B 2112 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7674 (tp30) REVERT: B 2163 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6608 (mtp) REVERT: B 2190 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7489 (p) REVERT: B 2193 THR cc_start: 0.8420 (m) cc_final: 0.7893 (p) REVERT: B 2273 SER cc_start: 0.7958 (m) cc_final: 0.7737 (t) REVERT: B 2337 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7721 (mt) REVERT: B 2403 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7794 (m90) REVERT: B 2418 GLN cc_start: 0.7707 (mt0) cc_final: 0.7138 (mt0) REVERT: B 2427 ARG cc_start: 0.8494 (ptp-170) cc_final: 0.8015 (mtp-110) REVERT: B 2467 VAL cc_start: 0.8476 (t) cc_final: 0.8236 (m) REVERT: B 2508 SER cc_start: 0.8459 (p) cc_final: 0.8243 (t) REVERT: B 2550 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7845 (m90) REVERT: B 2554 THR cc_start: 0.8530 (m) cc_final: 0.8295 (m) REVERT: B 2561 LYS cc_start: 0.7832 (mtpp) cc_final: 0.7488 (mtpp) REVERT: B 2582 GLU cc_start: 0.6915 (tt0) cc_final: 0.6625 (tt0) REVERT: B 2589 SER cc_start: 0.8415 (t) cc_final: 0.7993 (p) REVERT: B 2604 ILE cc_start: 0.8026 (mt) cc_final: 0.7559 (tt) REVERT: B 2605 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: B 2671 ARG cc_start: 0.6930 (ttt180) cc_final: 0.6503 (ttt-90) outliers start: 101 outliers final: 65 residues processed: 692 average time/residue: 0.1797 time to fit residues: 183.0624 Evaluate side-chains 693 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 616 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1654 THR Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1846 ILE Chi-restraints excluded: chain A residue 1851 ILE Chi-restraints excluded: chain A residue 1892 LEU Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1909 GLN Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2019 LEU Chi-restraints excluded: chain A residue 2020 SER Chi-restraints excluded: chain A residue 2035 GLU Chi-restraints excluded: chain A residue 2042 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2204 SER Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2258 ASP Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain A residue 2398 MET Chi-restraints excluded: chain A residue 2430 SER Chi-restraints excluded: chain A residue 2441 LYS Chi-restraints excluded: chain A residue 2471 LYS Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2503 SER Chi-restraints excluded: chain A residue 2532 GLU Chi-restraints excluded: chain A residue 2550 HIS Chi-restraints excluded: chain A residue 2556 THR Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2593 ASN Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain B residue 1181 LYS Chi-restraints excluded: chain B residue 1567 VAL Chi-restraints excluded: chain B residue 1571 PHE Chi-restraints excluded: chain B residue 1647 ILE Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1738 ILE Chi-restraints excluded: chain B residue 1739 THR Chi-restraints excluded: chain B residue 1768 ARG Chi-restraints excluded: chain B residue 1851 ILE Chi-restraints excluded: chain B residue 1892 LEU Chi-restraints excluded: chain B residue 1909 GLN Chi-restraints excluded: chain B residue 1922 VAL Chi-restraints excluded: chain B residue 1932 MET Chi-restraints excluded: chain B residue 1982 GLU Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2019 LEU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2163 MET Chi-restraints excluded: chain B residue 2190 THR Chi-restraints excluded: chain B residue 2224 HIS Chi-restraints excluded: chain B residue 2240 ASP Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2375 LEU Chi-restraints excluded: chain B residue 2403 HIS Chi-restraints excluded: chain B residue 2430 SER Chi-restraints excluded: chain B residue 2437 ARG Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 2550 HIS Chi-restraints excluded: chain B residue 2574 THR Chi-restraints excluded: chain B residue 2593 ASN Chi-restraints excluded: chain B residue 2605 GLU Chi-restraints excluded: chain B residue 2657 THR Chi-restraints excluded: chain B residue 2752 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 171 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 245 optimal weight: 0.0770 chunk 267 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 chunk 139 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2379 GLN B1582 GLN B2085 HIS B2524 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108571 restraints weight = 32855.396| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.42 r_work: 0.3126 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22801 Z= 0.128 Angle : 0.553 13.730 30954 Z= 0.286 Chirality : 0.046 0.532 3444 Planarity : 0.004 0.068 3945 Dihedral : 5.697 57.190 3566 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.41 % Allowed : 26.41 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2728 helix: 1.33 (0.36), residues: 224 sheet: 1.08 (0.17), residues: 882 loop : -0.65 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B2490 TYR 0.018 0.002 TYR A2663 PHE 0.018 0.001 PHE A1826 TRP 0.014 0.001 TRP A2436 HIS 0.010 0.001 HIS A1593 Details of bonding type rmsd covalent geometry : bond 0.00285 (22777) covalent geometry : angle 0.53562 (30882) hydrogen bonds : bond 0.03550 ( 874) hydrogen bonds : angle 4.91505 ( 3174) link_ALPHA1-3 : bond 0.01167 ( 1) link_ALPHA1-3 : angle 1.23613 ( 3) link_BETA1-4 : bond 0.00524 ( 8) link_BETA1-4 : angle 1.77443 ( 24) link_NAG-ASN : bond 0.00457 ( 15) link_NAG-ASN : angle 3.43532 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 630 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1032 SER cc_start: 0.8304 (t) cc_final: 0.7804 (m) REVERT: A 1101 PHE cc_start: 0.7220 (t80) cc_final: 0.6464 (t80) REVERT: A 1103 LYS cc_start: 0.7683 (mmmm) cc_final: 0.6853 (mmmm) REVERT: A 1125 GLN cc_start: 0.7392 (mp10) cc_final: 0.6807 (mp10) REVERT: A 1153 ARG cc_start: 0.7764 (tpp80) cc_final: 0.6972 (tpp80) REVERT: A 1173 ASP cc_start: 0.7779 (t0) cc_final: 0.7429 (t0) REVERT: A 1174 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7888 (mmtm) REVERT: A 1575 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7158 (mm-30) REVERT: A 1599 LEU cc_start: 0.7983 (mt) cc_final: 0.7724 (mp) REVERT: A 1618 GLU cc_start: 0.7765 (tt0) cc_final: 0.7458 (tt0) REVERT: A 1693 TYR cc_start: 0.8233 (m-80) cc_final: 0.7796 (m-10) REVERT: A 1700 ARG cc_start: 0.8124 (mmt90) cc_final: 0.7650 (mmt-90) REVERT: A 1710 VAL cc_start: 0.8854 (t) cc_final: 0.8482 (m) REVERT: A 1713 SER cc_start: 0.8240 (m) cc_final: 0.7740 (t) REVERT: A 1720 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7426 (ptpp) REVERT: A 1723 THR cc_start: 0.8759 (m) cc_final: 0.8305 (p) REVERT: A 1731 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7549 (mtt90) REVERT: A 1738 ILE cc_start: 0.8567 (mt) cc_final: 0.8165 (mm) REVERT: A 1745 GLU cc_start: 0.6563 (mp0) cc_final: 0.6109 (mp0) REVERT: A 1816 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6944 (tmmt) REVERT: A 1835 ARG cc_start: 0.7625 (mtm180) cc_final: 0.7010 (mtm180) REVERT: A 1842 TYR cc_start: 0.8082 (t80) cc_final: 0.7565 (t80) REVERT: A 1850 LYS cc_start: 0.8101 (tttt) cc_final: 0.7816 (ttmm) REVERT: A 1865 ASP cc_start: 0.7735 (t0) cc_final: 0.7455 (t70) REVERT: A 1887 PHE cc_start: 0.8237 (m-80) cc_final: 0.7889 (m-80) REVERT: A 1900 MET cc_start: 0.8061 (mtt) cc_final: 0.7731 (mtp) REVERT: A 1903 ARG cc_start: 0.7652 (mtt90) cc_final: 0.7186 (mtp85) REVERT: A 1905 ASP cc_start: 0.7767 (m-30) cc_final: 0.7423 (m-30) REVERT: A 1932 MET cc_start: 0.7874 (tmm) cc_final: 0.7101 (ttm) REVERT: A 1965 MET cc_start: 0.8646 (mpp) cc_final: 0.7837 (mpp) REVERT: A 1994 ASP cc_start: 0.8007 (p0) cc_final: 0.7426 (p0) REVERT: A 1996 ARG cc_start: 0.8068 (mmt90) cc_final: 0.6909 (mtm110) REVERT: A 2000 THR cc_start: 0.8221 (m) cc_final: 0.7906 (t) REVERT: A 2013 TYR cc_start: 0.8328 (m-80) cc_final: 0.8103 (m-80) REVERT: A 2057 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7623 (ttp-170) REVERT: A 2065 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7658 (ttmm) REVERT: A 2079 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7644 (ttm110) REVERT: A 2109 ARG cc_start: 0.7656 (ttt90) cc_final: 0.7389 (ttm-80) REVERT: A 2113 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8357 (mp) REVERT: A 2116 LYS cc_start: 0.8513 (mttt) cc_final: 0.8268 (mttm) REVERT: A 2138 VAL cc_start: 0.8267 (t) cc_final: 0.7823 (p) REVERT: A 2190 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7484 (p) REVERT: A 2194 TYR cc_start: 0.8296 (m-80) cc_final: 0.8089 (m-80) REVERT: A 2213 TRP cc_start: 0.8014 (m-90) cc_final: 0.7698 (m-10) REVERT: A 2292 ARG cc_start: 0.8398 (tpp80) cc_final: 0.8146 (ttm-80) REVERT: A 2303 LYS cc_start: 0.8403 (tttt) cc_final: 0.7984 (mtpt) REVERT: A 2337 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7867 (mt) REVERT: A 2348 MET cc_start: 0.8341 (mtp) cc_final: 0.8114 (mtt) REVERT: A 2349 GLU cc_start: 0.7986 (tt0) cc_final: 0.7648 (tt0) REVERT: A 2418 GLN cc_start: 0.7565 (tt0) cc_final: 0.7309 (tt0) REVERT: A 2427 ARG cc_start: 0.8371 (ptp-110) cc_final: 0.7888 (mtp-110) REVERT: A 2484 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8457 (mt) REVERT: A 2508 SER cc_start: 0.8497 (p) cc_final: 0.8192 (t) REVERT: A 2526 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7522 (tp40) REVERT: A 2554 THR cc_start: 0.8574 (m) cc_final: 0.8304 (m) REVERT: A 2589 SER cc_start: 0.8427 (p) cc_final: 0.8221 (p) REVERT: A 2599 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8035 (mmmt) REVERT: A 2604 ILE cc_start: 0.8182 (mt) cc_final: 0.7933 (tt) REVERT: A 2607 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7334 (mtpp) REVERT: A 2682 GLU cc_start: 0.7685 (tp30) cc_final: 0.7275 (tp30) REVERT: A 2699 TRP cc_start: 0.8029 (m100) cc_final: 0.7734 (m100) REVERT: A 2711 GLU cc_start: 0.7735 (tt0) cc_final: 0.7281 (tp30) REVERT: A 2714 ARG cc_start: 0.8109 (mtm180) cc_final: 0.7825 (mtm180) REVERT: A 2722 GLN cc_start: 0.8037 (tp40) cc_final: 0.7820 (tp40) REVERT: B 1032 SER cc_start: 0.8213 (t) cc_final: 0.7825 (m) REVERT: B 1043 GLU cc_start: 0.8135 (mp0) cc_final: 0.7895 (mp0) REVERT: B 1049 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7894 (tp30) REVERT: B 1101 PHE cc_start: 0.7298 (t80) cc_final: 0.6909 (t80) REVERT: B 1125 GLN cc_start: 0.7709 (mp10) cc_final: 0.6899 (mp10) REVERT: B 1153 ARG cc_start: 0.8068 (tpp-160) cc_final: 0.7770 (mmt180) REVERT: B 1173 ASP cc_start: 0.7890 (t0) cc_final: 0.7532 (m-30) REVERT: B 1174 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7835 (mmtp) REVERT: B 1599 LEU cc_start: 0.8152 (mt) cc_final: 0.7941 (mp) REVERT: B 1614 ASN cc_start: 0.8060 (m-40) cc_final: 0.7825 (m-40) REVERT: B 1638 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7439 (mmm-85) REVERT: B 1693 TYR cc_start: 0.8373 (m-80) cc_final: 0.8127 (m-80) REVERT: B 1710 VAL cc_start: 0.8695 (t) cc_final: 0.8334 (m) REVERT: B 1723 THR cc_start: 0.8722 (m) cc_final: 0.8317 (p) REVERT: B 1731 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7710 (mtt-85) REVERT: B 1770 MET cc_start: 0.7955 (tpt) cc_final: 0.7740 (tpp) REVERT: B 1784 HIS cc_start: 0.7641 (t70) cc_final: 0.7417 (t70) REVERT: B 1796 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7584 (mtm-85) REVERT: B 1799 ILE cc_start: 0.8499 (mp) cc_final: 0.8237 (mt) REVERT: B 1808 ASN cc_start: 0.7423 (m-40) cc_final: 0.7215 (m-40) REVERT: B 1813 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7354 (mtt90) REVERT: B 1889 ASN cc_start: 0.8231 (p0) cc_final: 0.7766 (m-40) REVERT: B 1900 MET cc_start: 0.7916 (mtp) cc_final: 0.7649 (mtp) REVERT: B 1903 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7427 (mtt-85) REVERT: B 1919 ASP cc_start: 0.7794 (p0) cc_final: 0.7503 (p0) REVERT: B 1922 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8043 (m) REVERT: B 1950 ASP cc_start: 0.8148 (m-30) cc_final: 0.7821 (t0) REVERT: B 1965 MET cc_start: 0.8616 (mpp) cc_final: 0.7835 (mpp) REVERT: B 1990 ASP cc_start: 0.7731 (m-30) cc_final: 0.7407 (m-30) REVERT: B 1996 ARG cc_start: 0.7887 (mmt90) cc_final: 0.6671 (mtm110) REVERT: B 1999 LYS cc_start: 0.8342 (tttt) cc_final: 0.8115 (tttp) REVERT: B 2013 TYR cc_start: 0.8384 (m-80) cc_final: 0.8084 (m-80) REVERT: B 2057 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7645 (ttp80) REVERT: B 2190 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7477 (p) REVERT: B 2193 THR cc_start: 0.8377 (m) cc_final: 0.8149 (t) REVERT: B 2213 TRP cc_start: 0.8056 (m-10) cc_final: 0.7799 (m-10) REVERT: B 2251 VAL cc_start: 0.8052 (p) cc_final: 0.7733 (m) REVERT: B 2273 SER cc_start: 0.7930 (m) cc_final: 0.7703 (t) REVERT: B 2337 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7721 (mt) REVERT: B 2403 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7716 (m90) REVERT: B 2418 GLN cc_start: 0.7699 (mt0) cc_final: 0.7126 (mt0) REVERT: B 2427 ARG cc_start: 0.8453 (ptp-170) cc_final: 0.7880 (mtp-110) REVERT: B 2467 VAL cc_start: 0.8476 (t) cc_final: 0.8247 (m) REVERT: B 2508 SER cc_start: 0.8441 (p) cc_final: 0.8233 (t) REVERT: B 2550 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.8050 (m90) REVERT: B 2554 THR cc_start: 0.8525 (m) cc_final: 0.8292 (m) REVERT: B 2561 LYS cc_start: 0.7813 (mtpp) cc_final: 0.7465 (mtpp) REVERT: B 2582 GLU cc_start: 0.6889 (tt0) cc_final: 0.6598 (tt0) REVERT: B 2589 SER cc_start: 0.8371 (t) cc_final: 0.7942 (p) REVERT: B 2604 ILE cc_start: 0.8029 (mt) cc_final: 0.7573 (tt) REVERT: B 2605 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7681 (pm20) REVERT: B 2671 ARG cc_start: 0.6814 (ttt180) cc_final: 0.6307 (ttt-90) outliers start: 82 outliers final: 57 residues processed: 671 average time/residue: 0.1715 time to fit residues: 170.5222 Evaluate side-chains 683 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 613 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1647 ILE Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1816 LYS Chi-restraints excluded: chain A residue 1851 ILE Chi-restraints excluded: chain A residue 1892 LEU Chi-restraints excluded: chain A residue 1909 GLN Chi-restraints excluded: chain A residue 1926 SER Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2019 LEU Chi-restraints excluded: chain A residue 2020 SER Chi-restraints excluded: chain A residue 2035 GLU Chi-restraints excluded: chain A residue 2042 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2113 ILE Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2201 GLN Chi-restraints excluded: chain A residue 2204 SER Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2258 ASP Chi-restraints excluded: chain A residue 2301 SER Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain A residue 2398 MET Chi-restraints excluded: chain A residue 2430 SER Chi-restraints excluded: chain A residue 2441 LYS Chi-restraints excluded: chain A residue 2471 LYS Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2550 HIS Chi-restraints excluded: chain A residue 2556 THR Chi-restraints excluded: chain A residue 2717 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain B residue 1181 LYS Chi-restraints excluded: chain B residue 1647 ILE Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1731 ARG Chi-restraints excluded: chain B residue 1739 THR Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1851 ILE Chi-restraints excluded: chain B residue 1909 GLN Chi-restraints excluded: chain B residue 1922 VAL Chi-restraints excluded: chain B residue 1932 MET Chi-restraints excluded: chain B residue 2001 SER Chi-restraints excluded: chain B residue 2019 LEU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2093 SER Chi-restraints excluded: chain B residue 2177 ILE Chi-restraints excluded: chain B residue 2190 THR Chi-restraints excluded: chain B residue 2224 HIS Chi-restraints excluded: chain B residue 2240 ASP Chi-restraints excluded: chain B residue 2337 LEU Chi-restraints excluded: chain B residue 2375 LEU Chi-restraints excluded: chain B residue 2403 HIS Chi-restraints excluded: chain B residue 2430 SER Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 2503 SER Chi-restraints excluded: chain B residue 2550 HIS Chi-restraints excluded: chain B residue 2574 THR Chi-restraints excluded: chain B residue 2605 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 114 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 132 optimal weight: 0.0020 chunk 61 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 0.0070 chunk 172 optimal weight: 3.9990 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2453 ASN A2524 HIS A2593 ASN B1582 GLN B1760 GLN B1836 ASN B1855 HIS B2085 HIS B2224 HIS B2524 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106143 restraints weight = 33141.230| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.46 r_work: 0.3131 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22801 Z= 0.108 Angle : 0.535 12.325 30954 Z= 0.277 Chirality : 0.045 0.456 3444 Planarity : 0.003 0.045 3945 Dihedral : 5.535 55.917 3566 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.16 % Allowed : 26.79 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.16), residues: 2728 helix: 1.45 (0.36), residues: 224 sheet: 1.11 (0.17), residues: 906 loop : -0.59 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2490 TYR 0.019 0.001 TYR A2056 PHE 0.040 0.001 PHE A2402 TRP 0.015 0.001 TRP A2436 HIS 0.008 0.001 HIS A2403 Details of bonding type rmsd covalent geometry : bond 0.00238 (22777) covalent geometry : angle 0.51959 (30882) hydrogen bonds : bond 0.03306 ( 874) hydrogen bonds : angle 4.74705 ( 3174) link_ALPHA1-3 : bond 0.01134 ( 1) link_ALPHA1-3 : angle 1.18130 ( 3) link_BETA1-4 : bond 0.00504 ( 8) link_BETA1-4 : angle 1.65089 ( 24) link_NAG-ASN : bond 0.00405 ( 15) link_NAG-ASN : angle 3.16549 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 624 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1032 SER cc_start: 0.8267 (t) cc_final: 0.7764 (m) REVERT: A 1103 LYS cc_start: 0.7700 (mmmm) cc_final: 0.7197 (mmmm) REVERT: A 1125 GLN cc_start: 0.7411 (mp10) cc_final: 0.6840 (mp10) REVERT: A 1153 ARG cc_start: 0.7721 (tpp80) cc_final: 0.6936 (tpp80) REVERT: A 1173 ASP cc_start: 0.7756 (t0) cc_final: 0.7407 (t0) REVERT: A 1618 GLU cc_start: 0.7787 (tt0) cc_final: 0.7470 (tt0) REVERT: A 1693 TYR cc_start: 0.8186 (m-80) cc_final: 0.7769 (m-10) REVERT: A 1700 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7506 (mmt-90) REVERT: A 1710 VAL cc_start: 0.8868 (t) cc_final: 0.8496 (m) REVERT: A 1720 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7400 (ptpp) REVERT: A 1723 THR cc_start: 0.8699 (m) cc_final: 0.8326 (p) REVERT: A 1731 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7571 (mtt90) REVERT: A 1738 ILE cc_start: 0.8566 (mt) cc_final: 0.8349 (mt) REVERT: A 1745 GLU cc_start: 0.6616 (mp0) cc_final: 0.6067 (mp0) REVERT: A 1796 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7665 (mtm-85) REVERT: A 1813 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7316 (mmm-85) REVERT: A 1816 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6917 (tmmt) REVERT: A 1842 TYR cc_start: 0.8034 (t80) cc_final: 0.7611 (t80) REVERT: A 1850 LYS cc_start: 0.8070 (tttt) cc_final: 0.7775 (ttmm) REVERT: A 1865 ASP cc_start: 0.7715 (t0) cc_final: 0.7400 (t70) REVERT: A 1887 PHE cc_start: 0.8194 (m-80) cc_final: 0.7874 (m-80) REVERT: A 1900 MET cc_start: 0.8018 (mtt) cc_final: 0.7724 (mtp) REVERT: A 1903 ARG cc_start: 0.7678 (mtt90) cc_final: 0.7205 (mtp85) REVERT: A 1905 ASP cc_start: 0.7739 (m-30) cc_final: 0.7396 (m-30) REVERT: A 1932 MET cc_start: 0.7881 (tmm) cc_final: 0.7074 (ttm) REVERT: A 1994 ASP cc_start: 0.7921 (p0) cc_final: 0.7305 (p0) REVERT: A 1996 ARG cc_start: 0.8023 (mmt90) cc_final: 0.6898 (mtm110) REVERT: A 2013 TYR cc_start: 0.8330 (m-80) cc_final: 0.7963 (m-80) REVERT: A 2065 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7675 (ttmm) REVERT: A 2079 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7715 (ttm110) REVERT: A 2109 ARG cc_start: 0.7617 (ttt90) cc_final: 0.7382 (ttm-80) REVERT: A 2116 LYS cc_start: 0.8458 (mttt) cc_final: 0.8257 (mttm) REVERT: A 2138 VAL cc_start: 0.8193 (t) cc_final: 0.7749 (p) REVERT: A 2190 THR cc_start: 0.7867 (m) cc_final: 0.7478 (p) REVERT: A 2213 TRP cc_start: 0.8037 (m-90) cc_final: 0.7774 (m-10) REVERT: A 2292 ARG cc_start: 0.8374 (tpp80) cc_final: 0.8120 (ttm-80) REVERT: A 2303 LYS cc_start: 0.8383 (tttt) cc_final: 0.7975 (mtpt) REVERT: A 2337 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7705 (mp) REVERT: A 2348 MET cc_start: 0.8330 (mtp) cc_final: 0.8091 (mtt) REVERT: A 2349 GLU cc_start: 0.7972 (tt0) cc_final: 0.7660 (tt0) REVERT: A 2427 ARG cc_start: 0.8327 (ptp-110) cc_final: 0.7765 (mtp-110) REVERT: A 2484 ILE cc_start: 0.8763 (pt) cc_final: 0.8460 (mt) REVERT: A 2508 SER cc_start: 0.8518 (p) cc_final: 0.8198 (t) REVERT: A 2526 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7474 (tp40) REVERT: A 2554 THR cc_start: 0.8618 (m) cc_final: 0.8324 (m) REVERT: A 2571 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7160 (mtp180) REVERT: A 2599 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8029 (mmmt) REVERT: A 2604 ILE cc_start: 0.8178 (mt) cc_final: 0.7940 (tt) REVERT: A 2607 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7334 (mtpp) REVERT: A 2682 GLU cc_start: 0.7651 (tp30) cc_final: 0.7232 (tp30) REVERT: A 2699 TRP cc_start: 0.8058 (m100) cc_final: 0.7709 (m100) REVERT: A 2711 GLU cc_start: 0.7745 (tt0) cc_final: 0.7293 (tp30) REVERT: A 2714 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7645 (mtm180) REVERT: A 2722 GLN cc_start: 0.8018 (tp40) cc_final: 0.7810 (tp40) REVERT: B 1032 SER cc_start: 0.8209 (t) cc_final: 0.7810 (m) REVERT: B 1043 GLU cc_start: 0.8159 (mp0) cc_final: 0.7924 (mp0) REVERT: B 1101 PHE cc_start: 0.7297 (t80) cc_final: 0.6909 (t80) REVERT: B 1125 GLN cc_start: 0.7674 (mp10) cc_final: 0.6851 (mp10) REVERT: B 1153 ARG cc_start: 0.8032 (tpp-160) cc_final: 0.7738 (mmt180) REVERT: B 1173 ASP cc_start: 0.7905 (t0) cc_final: 0.7533 (m-30) REVERT: B 1174 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7814 (mmtp) REVERT: B 1184 ILE cc_start: 0.7865 (mm) cc_final: 0.7324 (mt) REVERT: B 1575 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7421 (tt0) REVERT: B 1599 LEU cc_start: 0.8157 (mt) cc_final: 0.7953 (mp) REVERT: B 1614 ASN cc_start: 0.8070 (m-40) cc_final: 0.7841 (m-40) REVERT: B 1638 ARG cc_start: 0.7716 (mmm-85) cc_final: 0.7421 (mmm-85) REVERT: B 1710 VAL cc_start: 0.8697 (t) cc_final: 0.8387 (m) REVERT: B 1723 THR cc_start: 0.8699 (m) cc_final: 0.8295 (p) REVERT: B 1731 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7712 (mtt-85) REVERT: B 1760 GLN cc_start: 0.7964 (mm110) cc_final: 0.7626 (mm110) REVERT: B 1796 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7659 (mtm-85) REVERT: B 1799 ILE cc_start: 0.8545 (mp) cc_final: 0.8255 (mt) REVERT: B 1812 TRP cc_start: 0.8299 (m100) cc_final: 0.7950 (m100) REVERT: B 1842 TYR cc_start: 0.8129 (t80) cc_final: 0.7913 (t80) REVERT: B 1903 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7396 (mtt-85) REVERT: B 1919 ASP cc_start: 0.7774 (p0) cc_final: 0.7484 (p0) REVERT: B 1922 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8040 (m) REVERT: B 1950 ASP cc_start: 0.8148 (m-30) cc_final: 0.7813 (t0) REVERT: B 1990 ASP cc_start: 0.7674 (m-30) cc_final: 0.7350 (m-30) REVERT: B 1996 ARG cc_start: 0.7886 (mmt90) cc_final: 0.6714 (mtm110) REVERT: B 1999 LYS cc_start: 0.8340 (tttt) cc_final: 0.8109 (tttp) REVERT: B 2013 TYR cc_start: 0.8367 (m-80) cc_final: 0.8027 (m-80) REVERT: B 2057 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7618 (ttp80) REVERT: B 2190 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7501 (p) REVERT: B 2193 THR cc_start: 0.8380 (m) cc_final: 0.8164 (t) REVERT: B 2213 TRP cc_start: 0.8064 (m-10) cc_final: 0.7856 (m-10) REVERT: B 2224 HIS cc_start: 0.5978 (OUTLIER) cc_final: 0.5557 (t-170) REVERT: B 2251 VAL cc_start: 0.8011 (p) cc_final: 0.7672 (m) REVERT: B 2273 SER cc_start: 0.7919 (m) cc_final: 0.7701 (t) REVERT: B 2398 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6936 (tpp) REVERT: B 2403 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7638 (m90) REVERT: B 2418 GLN cc_start: 0.7706 (mt0) cc_final: 0.7125 (mt0) REVERT: B 2427 ARG cc_start: 0.8441 (ptp-170) cc_final: 0.7897 (mtp-110) REVERT: B 2467 VAL cc_start: 0.8477 (t) cc_final: 0.8253 (m) REVERT: B 2484 ILE cc_start: 0.8777 (pt) cc_final: 0.8347 (mt) REVERT: B 2493 MET cc_start: 0.6683 (mmm) cc_final: 0.6334 (mmm) REVERT: B 2508 SER cc_start: 0.8454 (p) cc_final: 0.8249 (t) REVERT: B 2554 THR cc_start: 0.8518 (m) cc_final: 0.8288 (m) REVERT: B 2561 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7467 (mtpp) REVERT: B 2582 GLU cc_start: 0.6823 (tt0) cc_final: 0.6528 (tt0) REVERT: B 2589 SER cc_start: 0.8367 (t) cc_final: 0.7936 (p) REVERT: B 2604 ILE cc_start: 0.8056 (mt) cc_final: 0.7596 (tt) REVERT: B 2605 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: B 2671 ARG cc_start: 0.6774 (ttt180) cc_final: 0.6278 (ttt-90) outliers start: 76 outliers final: 53 residues processed: 664 average time/residue: 0.1784 time to fit residues: 174.2693 Evaluate side-chains 672 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 609 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1816 LYS Chi-restraints excluded: chain A residue 1851 ILE Chi-restraints excluded: chain A residue 1869 ARG Chi-restraints excluded: chain A residue 1909 GLN Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2019 LEU Chi-restraints excluded: chain A residue 2020 SER Chi-restraints excluded: chain A residue 2042 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2144 HIS Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2201 GLN Chi-restraints excluded: chain A residue 2204 SER Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2301 SER Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain A residue 2398 MET Chi-restraints excluded: chain A residue 2430 SER Chi-restraints excluded: chain A residue 2441 LYS Chi-restraints excluded: chain A residue 2471 LYS Chi-restraints excluded: chain A residue 2550 HIS Chi-restraints excluded: chain A residue 2717 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain B residue 1181 LYS Chi-restraints excluded: chain B residue 1647 ILE Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1731 ARG Chi-restraints excluded: chain B residue 1739 THR Chi-restraints excluded: chain B residue 1811 GLU Chi-restraints excluded: chain B residue 1851 ILE Chi-restraints excluded: chain B residue 1866 GLN Chi-restraints excluded: chain B residue 1892 LEU Chi-restraints excluded: chain B residue 1909 GLN Chi-restraints excluded: chain B residue 1922 VAL Chi-restraints excluded: chain B residue 1932 MET Chi-restraints excluded: chain B residue 2019 LEU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2085 HIS Chi-restraints excluded: chain B residue 2093 SER Chi-restraints excluded: chain B residue 2177 ILE Chi-restraints excluded: chain B residue 2190 THR Chi-restraints excluded: chain B residue 2224 HIS Chi-restraints excluded: chain B residue 2398 MET Chi-restraints excluded: chain B residue 2403 HIS Chi-restraints excluded: chain B residue 2430 SER Chi-restraints excluded: chain B residue 2437 ARG Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 2503 SER Chi-restraints excluded: chain B residue 2574 THR Chi-restraints excluded: chain B residue 2605 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 86 optimal weight: 0.5980 chunk 229 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 179 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 13 optimal weight: 0.0010 chunk 37 optimal weight: 2.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1582 GLN B1740 ASN B1808 ASN B1855 HIS B2085 HIS B2524 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108272 restraints weight = 32873.495| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.43 r_work: 0.3196 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22801 Z= 0.113 Angle : 0.547 11.770 30954 Z= 0.282 Chirality : 0.046 0.425 3444 Planarity : 0.003 0.055 3945 Dihedral : 5.447 56.867 3564 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.00 % Allowed : 27.20 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.16), residues: 2728 helix: 1.48 (0.36), residues: 224 sheet: 1.10 (0.17), residues: 906 loop : -0.58 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B2490 TYR 0.018 0.001 TYR B2056 PHE 0.029 0.001 PHE A2402 TRP 0.016 0.001 TRP A2436 HIS 0.010 0.001 HIS B2085 Details of bonding type rmsd covalent geometry : bond 0.00252 (22777) covalent geometry : angle 0.52959 (30882) hydrogen bonds : bond 0.03294 ( 874) hydrogen bonds : angle 4.66157 ( 3174) link_ALPHA1-3 : bond 0.01115 ( 1) link_ALPHA1-3 : angle 1.17133 ( 3) link_BETA1-4 : bond 0.00508 ( 8) link_BETA1-4 : angle 1.68397 ( 24) link_NAG-ASN : bond 0.00399 ( 15) link_NAG-ASN : angle 3.46892 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 608 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1032 SER cc_start: 0.8224 (t) cc_final: 0.7699 (m) REVERT: A 1103 LYS cc_start: 0.7744 (mmmm) cc_final: 0.7257 (mmmm) REVERT: A 1125 GLN cc_start: 0.7467 (mp10) cc_final: 0.6911 (mp10) REVERT: A 1153 ARG cc_start: 0.7733 (tpp80) cc_final: 0.6948 (tpp80) REVERT: A 1173 ASP cc_start: 0.7724 (t0) cc_final: 0.7404 (t0) REVERT: A 1575 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7017 (mm-30) REVERT: A 1618 GLU cc_start: 0.7738 (tt0) cc_final: 0.7468 (tt0) REVERT: A 1693 TYR cc_start: 0.8168 (m-80) cc_final: 0.7840 (m-80) REVERT: A 1700 ARG cc_start: 0.8098 (mmt90) cc_final: 0.7549 (mpt180) REVERT: A 1710 VAL cc_start: 0.8883 (t) cc_final: 0.8536 (m) REVERT: A 1720 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7357 (ptpp) REVERT: A 1723 THR cc_start: 0.8690 (m) cc_final: 0.8249 (p) REVERT: A 1731 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7630 (mtt90) REVERT: A 1738 ILE cc_start: 0.8580 (mt) cc_final: 0.8184 (mm) REVERT: A 1745 GLU cc_start: 0.6613 (mp0) cc_final: 0.6226 (mp0) REVERT: A 1813 ARG cc_start: 0.7891 (tpp-160) cc_final: 0.7364 (mmm-85) REVERT: A 1816 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7063 (tmmt) REVERT: A 1835 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7213 (mtm180) REVERT: A 1842 TYR cc_start: 0.8082 (t80) cc_final: 0.7733 (t80) REVERT: A 1850 LYS cc_start: 0.8117 (tttt) cc_final: 0.7855 (ttmm) REVERT: A 1865 ASP cc_start: 0.7775 (t0) cc_final: 0.7460 (t70) REVERT: A 1887 PHE cc_start: 0.8221 (m-80) cc_final: 0.7905 (m-80) REVERT: A 1900 MET cc_start: 0.8101 (mtt) cc_final: 0.7831 (mtp) REVERT: A 1903 ARG cc_start: 0.7703 (mtt90) cc_final: 0.7273 (mtp85) REVERT: A 1905 ASP cc_start: 0.7744 (m-30) cc_final: 0.7448 (m-30) REVERT: A 1932 MET cc_start: 0.7885 (tmm) cc_final: 0.7038 (ttm) REVERT: A 1965 MET cc_start: 0.8604 (mpp) cc_final: 0.7954 (mpp) REVERT: A 1996 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7155 (mtm-85) REVERT: A 2000 THR cc_start: 0.8170 (m) cc_final: 0.7833 (t) REVERT: A 2013 TYR cc_start: 0.8357 (m-80) cc_final: 0.8052 (m-80) REVERT: A 2065 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7736 (ttmm) REVERT: A 2079 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7719 (ttm110) REVERT: A 2109 ARG cc_start: 0.7662 (ttt90) cc_final: 0.7462 (ttm-80) REVERT: A 2112 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7717 (mp0) REVERT: A 2113 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8418 (mp) REVERT: A 2138 VAL cc_start: 0.8222 (t) cc_final: 0.7771 (p) REVERT: A 2139 MET cc_start: 0.7944 (ppp) cc_final: 0.7526 (ptm) REVERT: A 2190 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7551 (p) REVERT: A 2213 TRP cc_start: 0.8076 (m-90) cc_final: 0.7848 (m-10) REVERT: A 2292 ARG cc_start: 0.8372 (tpp80) cc_final: 0.8135 (ttm-80) REVERT: A 2303 LYS cc_start: 0.8411 (tttt) cc_final: 0.8022 (mtpt) REVERT: A 2337 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7784 (mp) REVERT: A 2348 MET cc_start: 0.8395 (mtp) cc_final: 0.8171 (mtt) REVERT: A 2349 GLU cc_start: 0.8039 (tt0) cc_final: 0.7743 (tt0) REVERT: A 2484 ILE cc_start: 0.8739 (pt) cc_final: 0.8469 (mt) REVERT: A 2508 SER cc_start: 0.8514 (p) cc_final: 0.8175 (t) REVERT: A 2526 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7508 (tp40) REVERT: A 2554 THR cc_start: 0.8633 (m) cc_final: 0.8334 (m) REVERT: A 2599 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8071 (mmmt) REVERT: A 2604 ILE cc_start: 0.8264 (mt) cc_final: 0.8002 (tt) REVERT: A 2607 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7452 (mtpp) REVERT: A 2682 GLU cc_start: 0.7618 (tp30) cc_final: 0.7212 (tp30) REVERT: A 2699 TRP cc_start: 0.8113 (m100) cc_final: 0.7777 (m100) REVERT: A 2711 GLU cc_start: 0.7710 (tt0) cc_final: 0.7286 (tp30) REVERT: A 2714 ARG cc_start: 0.8243 (mtm180) cc_final: 0.7902 (mtm180) REVERT: A 2722 GLN cc_start: 0.8021 (tp40) cc_final: 0.7811 (tp40) REVERT: B 1032 SER cc_start: 0.8158 (t) cc_final: 0.7752 (m) REVERT: B 1043 GLU cc_start: 0.8141 (mp0) cc_final: 0.7922 (mp0) REVERT: B 1101 PHE cc_start: 0.7186 (t80) cc_final: 0.6875 (t80) REVERT: B 1125 GLN cc_start: 0.7703 (mp10) cc_final: 0.6883 (mp10) REVERT: B 1153 ARG cc_start: 0.8072 (tpp-160) cc_final: 0.7740 (mmt180) REVERT: B 1173 ASP cc_start: 0.7880 (t0) cc_final: 0.7548 (m-30) REVERT: B 1174 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7877 (mmtp) REVERT: B 1184 ILE cc_start: 0.7927 (mm) cc_final: 0.7476 (mt) REVERT: B 1575 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7396 (tt0) REVERT: B 1638 ARG cc_start: 0.7773 (mmm-85) cc_final: 0.7509 (mmm-85) REVERT: B 1710 VAL cc_start: 0.8759 (t) cc_final: 0.8436 (m) REVERT: B 1723 THR cc_start: 0.8682 (m) cc_final: 0.8299 (p) REVERT: B 1731 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7705 (mtt-85) REVERT: B 1799 ILE cc_start: 0.8612 (mp) cc_final: 0.8312 (mt) REVERT: B 1812 TRP cc_start: 0.8307 (m100) cc_final: 0.8000 (m100) REVERT: B 1842 TYR cc_start: 0.8216 (t80) cc_final: 0.7983 (t80) REVERT: B 1903 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7512 (mtt-85) REVERT: B 1919 ASP cc_start: 0.7801 (p0) cc_final: 0.7503 (p0) REVERT: B 1922 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8092 (m) REVERT: B 1950 ASP cc_start: 0.8113 (m-30) cc_final: 0.7803 (t0) REVERT: B 1965 MET cc_start: 0.8590 (mpp) cc_final: 0.8127 (mpp) REVERT: B 1990 ASP cc_start: 0.7638 (m-30) cc_final: 0.7336 (m-30) REVERT: B 1996 ARG cc_start: 0.7896 (mmt90) cc_final: 0.6836 (mtm110) REVERT: B 1999 LYS cc_start: 0.8347 (tttt) cc_final: 0.8141 (tttp) REVERT: B 2000 THR cc_start: 0.8465 (m) cc_final: 0.8057 (t) REVERT: B 2013 TYR cc_start: 0.8394 (m-80) cc_final: 0.8082 (m-80) REVERT: B 2057 ARG cc_start: 0.7991 (ttp-170) cc_final: 0.7713 (ttp80) REVERT: B 2139 MET cc_start: 0.8157 (ppp) cc_final: 0.7723 (ptm) REVERT: B 2190 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7597 (p) REVERT: B 2273 SER cc_start: 0.7993 (m) cc_final: 0.7748 (t) REVERT: B 2398 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6981 (tpp) REVERT: B 2403 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7663 (m90) REVERT: B 2418 GLN cc_start: 0.7687 (mt0) cc_final: 0.7175 (mt0) REVERT: B 2427 ARG cc_start: 0.8469 (ptp-170) cc_final: 0.7932 (mtp-110) REVERT: B 2455 ASN cc_start: 0.8164 (t0) cc_final: 0.7692 (t0) REVERT: B 2467 VAL cc_start: 0.8482 (t) cc_final: 0.8245 (m) REVERT: B 2484 ILE cc_start: 0.8756 (pt) cc_final: 0.8355 (mt) REVERT: B 2493 MET cc_start: 0.6642 (mmm) cc_final: 0.6310 (mmm) REVERT: B 2508 SER cc_start: 0.8471 (p) cc_final: 0.8232 (t) REVERT: B 2554 THR cc_start: 0.8558 (m) cc_final: 0.8309 (m) REVERT: B 2561 LYS cc_start: 0.7834 (mtpp) cc_final: 0.7533 (mtpp) REVERT: B 2582 GLU cc_start: 0.6784 (tt0) cc_final: 0.6512 (tt0) REVERT: B 2589 SER cc_start: 0.8408 (t) cc_final: 0.7978 (p) REVERT: B 2604 ILE cc_start: 0.8149 (mt) cc_final: 0.7660 (tt) REVERT: B 2605 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7728 (pm20) REVERT: B 2671 ARG cc_start: 0.6771 (ttt180) cc_final: 0.6317 (ttt-90) outliers start: 72 outliers final: 53 residues processed: 648 average time/residue: 0.1742 time to fit residues: 166.1071 Evaluate side-chains 667 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 603 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1816 LYS Chi-restraints excluded: chain A residue 1851 ILE Chi-restraints excluded: chain A residue 1869 ARG Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2019 LEU Chi-restraints excluded: chain A residue 2020 SER Chi-restraints excluded: chain A residue 2042 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2113 ILE Chi-restraints excluded: chain A residue 2129 ASP Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2201 GLN Chi-restraints excluded: chain A residue 2204 SER Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2301 SER Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2375 LEU Chi-restraints excluded: chain A residue 2398 MET Chi-restraints excluded: chain A residue 2430 SER Chi-restraints excluded: chain A residue 2441 LYS Chi-restraints excluded: chain A residue 2471 LYS Chi-restraints excluded: chain A residue 2532 GLU Chi-restraints excluded: chain A residue 2550 HIS Chi-restraints excluded: chain A residue 2717 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain B residue 1647 ILE Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1731 ARG Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1739 THR Chi-restraints excluded: chain B residue 1851 ILE Chi-restraints excluded: chain B residue 1866 GLN Chi-restraints excluded: chain B residue 1892 LEU Chi-restraints excluded: chain B residue 1909 GLN Chi-restraints excluded: chain B residue 1922 VAL Chi-restraints excluded: chain B residue 1932 MET Chi-restraints excluded: chain B residue 2019 LEU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2093 SER Chi-restraints excluded: chain B residue 2190 THR Chi-restraints excluded: chain B residue 2240 ASP Chi-restraints excluded: chain B residue 2398 MET Chi-restraints excluded: chain B residue 2403 HIS Chi-restraints excluded: chain B residue 2430 SER Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 2550 HIS Chi-restraints excluded: chain B residue 2574 THR Chi-restraints excluded: chain B residue 2605 GLU Chi-restraints excluded: chain B residue 2721 LYS Chi-restraints excluded: chain B residue 2731 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 32 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 chunk 109 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2418 GLN B1582 GLN B1614 ASN ** B1780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1941 GLN B2085 HIS B2393 ASN B2524 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108304 restraints weight = 32734.950| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.41 r_work: 0.3151 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22801 Z= 0.162 Angle : 0.578 11.602 30954 Z= 0.298 Chirality : 0.046 0.403 3444 Planarity : 0.004 0.048 3945 Dihedral : 5.580 59.119 3564 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.91 % Allowed : 27.25 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2728 helix: 1.42 (0.36), residues: 224 sheet: 1.03 (0.17), residues: 906 loop : -0.62 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B2490 TYR 0.019 0.002 TYR A2056 PHE 0.032 0.002 PHE A2402 TRP 0.018 0.001 TRP A2436 HIS 0.009 0.001 HIS A1639 Details of bonding type rmsd covalent geometry : bond 0.00364 (22777) covalent geometry : angle 0.56108 (30882) hydrogen bonds : bond 0.03621 ( 874) hydrogen bonds : angle 4.72851 ( 3174) link_ALPHA1-3 : bond 0.01018 ( 1) link_ALPHA1-3 : angle 1.10614 ( 3) link_BETA1-4 : bond 0.00543 ( 8) link_BETA1-4 : angle 1.80877 ( 24) link_NAG-ASN : bond 0.00502 ( 15) link_NAG-ASN : angle 3.45235 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 605 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1032 SER cc_start: 0.8271 (t) cc_final: 0.7729 (m) REVERT: A 1050 GLU cc_start: 0.8154 (tt0) cc_final: 0.7812 (tp30) REVERT: A 1101 PHE cc_start: 0.7261 (t80) cc_final: 0.6857 (t80) REVERT: A 1125 GLN cc_start: 0.7435 (mp10) cc_final: 0.6870 (mp10) REVERT: A 1153 ARG cc_start: 0.7781 (tpp80) cc_final: 0.6989 (tpp80) REVERT: A 1173 ASP cc_start: 0.7699 (t0) cc_final: 0.7415 (t0) REVERT: A 1575 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 1618 GLU cc_start: 0.7716 (tt0) cc_final: 0.7420 (tt0) REVERT: A 1693 TYR cc_start: 0.8238 (m-80) cc_final: 0.7780 (m-10) REVERT: A 1700 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7622 (mpt180) REVERT: A 1710 VAL cc_start: 0.8901 (t) cc_final: 0.8538 (m) REVERT: A 1720 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7388 (ptpp) REVERT: A 1723 THR cc_start: 0.8708 (m) cc_final: 0.8331 (p) REVERT: A 1731 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7607 (mtt90) REVERT: A 1738 ILE cc_start: 0.8553 (mt) cc_final: 0.8328 (mt) REVERT: A 1745 GLU cc_start: 0.6661 (mp0) cc_final: 0.6252 (mp0) REVERT: A 1784 HIS cc_start: 0.7444 (t70) cc_final: 0.7055 (t70) REVERT: A 1816 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6994 (tmmt) REVERT: A 1835 ARG cc_start: 0.7548 (mtm180) cc_final: 0.7135 (mtm180) REVERT: A 1842 TYR cc_start: 0.8132 (t80) cc_final: 0.7825 (t80) REVERT: A 1850 LYS cc_start: 0.8148 (tttt) cc_final: 0.7887 (ttmm) REVERT: A 1865 ASP cc_start: 0.7895 (t0) cc_final: 0.7612 (t70) REVERT: A 1887 PHE cc_start: 0.8269 (m-80) cc_final: 0.8022 (m-80) REVERT: A 1900 MET cc_start: 0.8107 (mtt) cc_final: 0.7852 (mtp) REVERT: A 1903 ARG cc_start: 0.7709 (mtt90) cc_final: 0.7256 (mtp85) REVERT: A 1905 ASP cc_start: 0.7778 (m-30) cc_final: 0.7473 (m-30) REVERT: A 1932 MET cc_start: 0.7882 (tmm) cc_final: 0.7080 (ttm) REVERT: A 1965 MET cc_start: 0.8621 (mpp) cc_final: 0.7901 (mpp) REVERT: A 1996 ARG cc_start: 0.8053 (mmt90) cc_final: 0.7219 (mtm110) REVERT: A 2000 THR cc_start: 0.8199 (m) cc_final: 0.7932 (t) REVERT: A 2013 TYR cc_start: 0.8383 (m-80) cc_final: 0.8088 (m-80) REVERT: A 2065 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7715 (ttmm) REVERT: A 2079 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7665 (ttm110) REVERT: A 2109 ARG cc_start: 0.7678 (ttt90) cc_final: 0.7473 (ttm-80) REVERT: A 2112 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7654 (mp0) REVERT: A 2116 LYS cc_start: 0.8507 (mttm) cc_final: 0.8170 (mttt) REVERT: A 2138 VAL cc_start: 0.8196 (t) cc_final: 0.7725 (p) REVERT: A 2139 MET cc_start: 0.7896 (ppp) cc_final: 0.7520 (ptm) REVERT: A 2190 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7519 (p) REVERT: A 2213 TRP cc_start: 0.8072 (m-90) cc_final: 0.7863 (m-10) REVERT: A 2224 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.5988 (t-170) REVERT: A 2292 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8156 (ttm-80) REVERT: A 2303 LYS cc_start: 0.8451 (tttt) cc_final: 0.8081 (mttm) REVERT: A 2337 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7761 (mp) REVERT: A 2348 MET cc_start: 0.8408 (mtp) cc_final: 0.8152 (mtt) REVERT: A 2349 GLU cc_start: 0.8038 (tt0) cc_final: 0.7740 (tt0) REVERT: A 2427 ARG cc_start: 0.8259 (ptp-110) cc_final: 0.7819 (mtp-110) REVERT: A 2484 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8599 (mt) REVERT: A 2526 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7532 (tp40) REVERT: A 2554 THR cc_start: 0.8628 (m) cc_final: 0.8336 (m) REVERT: A 2571 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7214 (mtp180) REVERT: A 2599 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8059 (mmmt) REVERT: A 2604 ILE cc_start: 0.8233 (mt) cc_final: 0.7985 (tt) REVERT: A 2607 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7420 (mtpp) REVERT: A 2682 GLU cc_start: 0.7632 (tp30) cc_final: 0.7204 (tp30) REVERT: A 2699 TRP cc_start: 0.8082 (m100) cc_final: 0.7735 (m100) REVERT: A 2711 GLU cc_start: 0.7723 (tt0) cc_final: 0.7304 (tp30) REVERT: A 2722 GLN cc_start: 0.8028 (tp40) cc_final: 0.7817 (tp40) REVERT: B 1032 SER cc_start: 0.8228 (t) cc_final: 0.7775 (m) REVERT: B 1043 GLU cc_start: 0.8135 (mp0) cc_final: 0.7888 (mp0) REVERT: B 1101 PHE cc_start: 0.7246 (t80) cc_final: 0.6908 (t80) REVERT: B 1125 GLN cc_start: 0.7656 (mp10) cc_final: 0.6818 (mp10) REVERT: B 1153 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7805 (mmt180) REVERT: B 1173 ASP cc_start: 0.7910 (t0) cc_final: 0.7556 (m-30) REVERT: B 1174 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7886 (mmtp) REVERT: B 1184 ILE cc_start: 0.7967 (mm) cc_final: 0.7436 (mt) REVERT: B 1638 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7507 (mmm-85) REVERT: B 1710 VAL cc_start: 0.8773 (t) cc_final: 0.8434 (m) REVERT: B 1723 THR cc_start: 0.8706 (m) cc_final: 0.8301 (p) REVERT: B 1731 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7724 (mtt-85) REVERT: B 1745 GLU cc_start: 0.5945 (mp0) cc_final: 0.5450 (mp0) REVERT: B 1799 ILE cc_start: 0.8570 (mp) cc_final: 0.8249 (mt) REVERT: B 1812 TRP cc_start: 0.8315 (m100) cc_final: 0.7989 (m100) REVERT: B 1842 TYR cc_start: 0.8175 (t80) cc_final: 0.7874 (t80) REVERT: B 1889 ASN cc_start: 0.8216 (p0) cc_final: 0.7804 (m-40) REVERT: B 1903 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7454 (mtt-85) REVERT: B 1922 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8093 (m) REVERT: B 1950 ASP cc_start: 0.8165 (m-30) cc_final: 0.7869 (t0) REVERT: B 1965 MET cc_start: 0.8609 (mpp) cc_final: 0.8100 (mpp) REVERT: B 1990 ASP cc_start: 0.7659 (m-30) cc_final: 0.7342 (m-30) REVERT: B 1996 ARG cc_start: 0.7961 (mmt90) cc_final: 0.6838 (mtm110) REVERT: B 1999 LYS cc_start: 0.8322 (tttt) cc_final: 0.8094 (tttp) REVERT: B 2013 TYR cc_start: 0.8428 (m-80) cc_final: 0.8166 (m-80) REVERT: B 2035 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7817 (mm-30) REVERT: B 2057 ARG cc_start: 0.7976 (ttp-170) cc_final: 0.7685 (ttp80) REVERT: B 2139 MET cc_start: 0.8091 (ppp) cc_final: 0.7741 (ptm) REVERT: B 2190 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7560 (p) REVERT: B 2273 SER cc_start: 0.8091 (m) cc_final: 0.7823 (t) REVERT: B 2403 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7750 (m90) REVERT: B 2418 GLN cc_start: 0.7674 (mt0) cc_final: 0.7117 (mt0) REVERT: B 2455 ASN cc_start: 0.8155 (t0) cc_final: 0.7656 (t0) REVERT: B 2467 VAL cc_start: 0.8487 (t) cc_final: 0.8245 (m) REVERT: B 2508 SER cc_start: 0.8455 (p) cc_final: 0.8224 (t) REVERT: B 2554 THR cc_start: 0.8551 (m) cc_final: 0.8305 (m) REVERT: B 2582 GLU cc_start: 0.6867 (tt0) cc_final: 0.6582 (tt0) REVERT: B 2589 SER cc_start: 0.8406 (t) cc_final: 0.7977 (p) REVERT: B 2604 ILE cc_start: 0.8137 (mt) cc_final: 0.7646 (tt) REVERT: B 2605 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7683 (pm20) outliers start: 70 outliers final: 54 residues processed: 645 average time/residue: 0.1730 time to fit residues: 165.0477 Evaluate side-chains 667 residues out of total 2404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 602 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1099 HIS Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1682 THR Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1816 LYS Chi-restraints excluded: chain A residue 1851 ILE Chi-restraints excluded: chain A residue 1909 GLN Chi-restraints excluded: chain A residue 1993 ASP Chi-restraints excluded: chain A residue 1997 ILE Chi-restraints excluded: chain A residue 2019 LEU Chi-restraints excluded: chain A residue 2020 SER Chi-restraints excluded: chain A residue 2035 GLU Chi-restraints excluded: chain A residue 2042 MET Chi-restraints excluded: chain A residue 2053 THR Chi-restraints excluded: chain A residue 2129 ASP Chi-restraints excluded: chain A residue 2157 GLU Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2201 GLN Chi-restraints excluded: chain A residue 2204 SER Chi-restraints excluded: chain A residue 2224 HIS Chi-restraints excluded: chain A residue 2301 SER Chi-restraints excluded: chain A residue 2337 LEU Chi-restraints excluded: chain A residue 2398 MET Chi-restraints excluded: chain A residue 2430 SER Chi-restraints excluded: chain A residue 2441 LYS Chi-restraints excluded: chain A residue 2471 LYS Chi-restraints excluded: chain A residue 2484 ILE Chi-restraints excluded: chain A residue 2532 GLU Chi-restraints excluded: chain A residue 2550 HIS Chi-restraints excluded: chain A residue 2717 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain B residue 1647 ILE Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1731 ARG Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1739 THR Chi-restraints excluded: chain B residue 1851 ILE Chi-restraints excluded: chain B residue 1892 LEU Chi-restraints excluded: chain B residue 1909 GLN Chi-restraints excluded: chain B residue 1922 VAL Chi-restraints excluded: chain B residue 1932 MET Chi-restraints excluded: chain B residue 1997 ILE Chi-restraints excluded: chain B residue 2019 LEU Chi-restraints excluded: chain B residue 2053 THR Chi-restraints excluded: chain B residue 2066 GLN Chi-restraints excluded: chain B residue 2085 HIS Chi-restraints excluded: chain B residue 2093 SER Chi-restraints excluded: chain B residue 2190 THR Chi-restraints excluded: chain B residue 2240 ASP Chi-restraints excluded: chain B residue 2403 HIS Chi-restraints excluded: chain B residue 2430 SER Chi-restraints excluded: chain B residue 2496 VAL Chi-restraints excluded: chain B residue 2574 THR Chi-restraints excluded: chain B residue 2593 ASN Chi-restraints excluded: chain B residue 2605 GLU Chi-restraints excluded: chain B residue 2721 LYS Chi-restraints excluded: chain B residue 2731 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 209 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 150 optimal weight: 0.4980 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 262 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1582 GLN ** B1780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1855 HIS B1941 GLN B2085 HIS B2524 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108752 restraints weight = 32772.798| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.42 r_work: 0.3169 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22801 Z= 0.129 Angle : 0.565 11.222 30954 Z= 0.291 Chirality : 0.046 0.389 3444 Planarity : 0.004 0.043 3945 Dihedral : 5.510 58.500 3564 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.83 % Allowed : 27.37 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.16), residues: 2728 helix: 1.44 (0.36), residues: 224 sheet: 1.04 (0.17), residues: 906 loop : -0.61 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B2490 TYR 0.019 0.002 TYR A2056 PHE 0.032 0.002 PHE A2402 TRP 0.020 0.001 TRP A2436 HIS 0.014 0.001 HIS B2085 Details of bonding type rmsd covalent geometry : bond 0.00289 (22777) covalent geometry : angle 0.54900 (30882) hydrogen bonds : bond 0.03421 ( 874) hydrogen bonds : angle 4.68725 ( 3174) link_ALPHA1-3 : bond 0.00970 ( 1) link_ALPHA1-3 : angle 1.11129 ( 3) link_BETA1-4 : bond 0.00494 ( 8) link_BETA1-4 : angle 1.73008 ( 24) link_NAG-ASN : bond 0.00425 ( 15) link_NAG-ASN : angle 3.30609 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5905.36 seconds wall clock time: 101 minutes 44.38 seconds (6104.38 seconds total)