Starting phenix.real_space_refine on Fri Feb 6 05:32:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g2h_50976/02_2026/9g2h_50976.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g2h_50976/02_2026/9g2h_50976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g2h_50976/02_2026/9g2h_50976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g2h_50976/02_2026/9g2h_50976.map" model { file = "/net/cci-nas-00/data/ceres_data/9g2h_50976/02_2026/9g2h_50976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g2h_50976/02_2026/9g2h_50976.cif" } resolution = 2.55 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= 0.030 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 14074 2.51 5 N 3795 2.21 5 O 4298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 22239 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 10956 Classifications: {'peptide': 1366} Link IDs: {'PTRANS': 49, 'TRANS': 1316} Chain breaks: 3 Chain: "B" Number of atoms: 10956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 10956 Classifications: {'peptide': 1366} Link IDs: {'PTRANS': 49, 'TRANS': 1316} Chain breaks: 3 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: 22239 At special positions: 0 Unit cell: (171.81, 145.25, 131.14, 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 4298 8.00 N 3795 7.00 C 14074 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 A1766 " " NAG A2802 " - " ASN A1986 " " NAG A2803 " - " ASN A1705 " " NAG A2804 " - " ASN A2641 " " NAG A2805 " - " ASN A1800 " " NAG B2801 " - " ASN B1766 " " NAG B2802 " - " ASN B1986 " " NAG B2803 " - " ASN B2641 " " NAG B2804 " - " ASN B1800 " " NAG C 1 " - " ASN A1609 " " NAG D 1 " - " ASN A2330 " " NAG E 1 " - " ASN A1885 " " NAG F 1 " - " ASN B1609 " " NAG G 1 " - " ASN B2330 " " NAG H 1 " - " ASN B1885 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5052 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 21 sheets defined 10.1% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 1074 through 1076 No H-bonds generated for 'chain 'A' and resid 1074 through 1076' Processing helix chain 'A' and resid 2403 through 2407 Processing helix chain 'A' and resid 2434 through 2440 removed outlier: 3.622A pdb=" N MET A2437 " --> pdb=" O ASP A2434 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A2438 " --> pdb=" O TYR A2435 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A2439 " --> pdb=" O THR A2436 " (cutoff:3.500A) Processing helix chain 'A' and resid 2453 through 2457 Processing helix chain 'A' and resid 2464 through 2468 removed outlier: 3.590A pdb=" N ASN A2467 " --> pdb=" O ASP A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2471 through 2479 Processing helix chain 'A' and resid 2482 through 2487 removed outlier: 4.320A pdb=" N ILE A2486 " --> pdb=" O GLN A2482 " (cutoff:3.500A) Processing helix chain 'A' and resid 2501 through 2509 Processing helix chain 'A' and resid 2517 through 2531 Processing helix chain 'A' and resid 2583 through 2594 Processing helix chain 'A' and resid 2620 through 2628 Processing helix chain 'A' and resid 2679 through 2711 removed outlier: 3.511A pdb=" N LEU A2689 " --> pdb=" O LYS A2685 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A2695 " --> pdb=" O GLN A2691 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A2699 " --> pdb=" O ARG A2695 " (cutoff:3.500A) Processing helix chain 'A' and resid 2719 through 2730 Processing helix chain 'A' and resid 2746 through 2750 Processing helix chain 'A' and resid 2752 through 2754 No H-bonds generated for 'chain 'A' and resid 2752 through 2754' Processing helix chain 'B' and resid 1074 through 1076 No H-bonds generated for 'chain 'B' and resid 1074 through 1076' Processing helix chain 'B' and resid 2403 through 2407 Processing helix chain 'B' and resid 2435 through 2440 removed outlier: 3.821A pdb=" N TRP B2438 " --> pdb=" O TYR B2435 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B2439 " --> pdb=" O THR B2436 " (cutoff:3.500A) Processing helix chain 'B' and resid 2453 through 2457 Processing helix chain 'B' and resid 2464 through 2468 removed outlier: 3.668A pdb=" N ASN B2467 " --> pdb=" O ASP B2464 " (cutoff:3.500A) Processing helix chain 'B' and resid 2471 through 2479 Processing helix chain 'B' and resid 2482 through 2487 removed outlier: 4.042A pdb=" N ILE B2486 " --> pdb=" O GLN B2482 " (cutoff:3.500A) Processing helix chain 'B' and resid 2501 through 2509 Processing helix chain 'B' and resid 2517 through 2531 Processing helix chain 'B' and resid 2583 through 2594 Processing helix chain 'B' and resid 2620 through 2628 Processing helix chain 'B' and resid 2679 through 2711 removed outlier: 3.701A pdb=" N THR B2699 " --> pdb=" O ARG B2695 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B2700 " --> pdb=" O ALA B2696 " (cutoff:3.500A) Processing helix chain 'B' and resid 2719 through 2729 Processing helix chain 'B' and resid 2746 through 2754 removed outlier: 4.543A pdb=" N ASP B2751 " --> pdb=" O GLU B2748 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER B2753 " --> pdb=" O ALA B2750 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER B2754 " --> pdb=" O ASP B2751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1030 through 1033 Processing sheet with id=AA2, first strand: chain 'A' and resid 1049 through 1050 Processing sheet with id=AA3, first strand: chain 'A' and resid 1108 through 1115 removed outlier: 3.560A pdb=" N VAL A1103 " --> pdb=" O PHE A1110 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A1112 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1186 through 1188 Processing sheet with id=AA5, first strand: chain 'A' and resid 1576 through 1580 removed outlier: 3.506A pdb=" N TYR A1597 " --> pdb=" O VAL A1588 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLN A1596 " --> pdb=" O PHE A1610 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER A1600 " --> pdb=" O TYR A1606 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR A1606 " --> pdb=" O SER A1600 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A1607 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP A1623 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN A1609 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A1621 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A1611 " --> pdb=" O THR A1619 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N THR A1619 " --> pdb=" O ILE A1631 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG A1640 " --> pdb=" O LEU A1652 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS A1661 " --> pdb=" O MET A1673 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA A1683 " --> pdb=" O TYR A1695 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A1694 " --> pdb=" O VAL A1706 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A1706 " --> pdb=" O PHE A1694 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A1696 " --> pdb=" O THR A1704 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR A1704 " --> pdb=" O LEU A1716 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR A1768 " --> pdb=" O CYS A1764 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A1798 " --> pdb=" O HIS A1782 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER A1811 " --> pdb=" O VAL A1834 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL A1834 " --> pdb=" O SER A1811 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU A1813 " --> pdb=" O LEU A1832 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A1832 " --> pdb=" O GLU A1813 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG A1815 " --> pdb=" O ARG A1830 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A1830 " --> pdb=" O ARG A1815 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG A1817 " --> pdb=" O PHE A1828 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE A1828 " --> pdb=" O ARG A1817 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU A1819 " --> pdb=" O THR A1826 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1840 " --> pdb=" O LEU A1832 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A1834 " --> pdb=" O ASN A1838 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASN A1838 " --> pdb=" O VAL A1834 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE A1873 " --> pdb=" O VAL A1886 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A1896 " --> pdb=" O SER A1887 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA A1895 " --> pdb=" O THR A1906 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER A1903 " --> pdb=" O PHE A1919 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE A1919 " --> pdb=" O SER A1903 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A1905 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG A1917 " --> pdb=" O ARG A1905 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP A1907 " --> pdb=" O VAL A1915 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL A1915 " --> pdb=" O TYR A1927 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N HIS A1955 " --> pdb=" O MET A1967 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A1990 " --> pdb=" O THR A2002 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR A2002 " --> pdb=" O ILE A1990 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP A1992 " --> pdb=" O LEU A2000 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU A2000 " --> pdb=" O TYR A2013 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER A2022 " --> pdb=" O PHE A2033 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS A2043 " --> pdb=" O TYR A2058 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER A2053 " --> pdb=" O PHE A2072 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A2072 " --> pdb=" O SER A2053 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR A2055 " --> pdb=" O TYR A2070 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR A2070 " --> pdb=" O THR A2055 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG A2057 " --> pdb=" O GLN A2068 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A2068 " --> pdb=" O ARG A2057 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG A2059 " --> pdb=" O ASP A2066 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N LEU A2064 " --> pdb=" O TYR A2086 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N TYR A2086 " --> pdb=" O LEU A2064 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP A2066 " --> pdb=" O TYR A2084 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A2081 " --> pdb=" O PRO A2098 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP A2083 " --> pdb=" O ILE A2096 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE A2096 " --> pdb=" O ASP A2083 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A2085 " --> pdb=" O ALA A2094 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA A2094 " --> pdb=" O TYR A2110 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A2109 " --> pdb=" O PHE A2122 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE A2122 " --> pdb=" O LEU A2109 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG A2111 " --> pdb=" O GLU A2120 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU A2120 " --> pdb=" O VAL A2127 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS A2154 " --> pdb=" O THR A2169 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR A2169 " --> pdb=" O LYS A2154 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A2156 " --> pdb=" O TRP A2167 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRP A2167 " --> pdb=" O VAL A2156 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR A2158 " --> pdb=" O MET A2165 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N MET A2165 " --> pdb=" O LEU A2185 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A2185 " --> pdb=" O MET A2165 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP A2167 " --> pdb=" O LEU A2183 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU A2183 " --> pdb=" O TRP A2167 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR A2169 " --> pdb=" O ARG A2181 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A2181 " --> pdb=" O THR A2169 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN A2171 " --> pdb=" O ILE A2179 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE A2179 " --> pdb=" O TYR A2196 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A2193 " --> pdb=" O VAL A2209 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A2209 " --> pdb=" O LYS A2193 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A2195 " --> pdb=" O VAL A2207 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL A2207 " --> pdb=" O THR A2195 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP A2197 " --> pdb=" O GLN A2205 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A2209 " --> pdb=" O PRO A2213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2218 through 2219 removed outlier: 5.371A pdb=" N HIS A2226 " --> pdb=" O LEU A2239 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU A2250 " --> pdb=" O PRO A2238 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG A2240 " --> pdb=" O THR A2248 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR A2248 " --> pdb=" O TYR A2255 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLN A2254 " --> pdb=" O ARG A2266 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG A2266 " --> pdb=" O GLN A2254 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS A2256 " --> pdb=" O CYS A2264 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N CYS A2264 " --> pdb=" O PHE A2271 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A2281 " --> pdb=" O GLU A2272 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N THR A2280 " --> pdb=" O TYR A2293 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N SER A2290 " --> pdb=" O THR A2306 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR A2306 " --> pdb=" O SER A2290 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN A2292 " --> pdb=" O TYR A2304 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR A2304 " --> pdb=" O GLN A2292 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG A2294 " --> pdb=" O ALA A2302 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA A2302 " --> pdb=" O TYR A2314 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A2348 " --> pdb=" O VAL A2360 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR A2359 " --> pdb=" O VAL A2371 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A2371 " --> pdb=" O TYR A2359 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A2361 " --> pdb=" O LEU A2369 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU A2369 " --> pdb=" O LEU A2382 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN A2381 " --> pdb=" O ASP A2393 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP A2393 " --> pdb=" O GLN A2381 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN A2383 " --> pdb=" O TYR A2391 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2408 through 2410 removed outlier: 3.739A pdb=" N LEU A2415 " --> pdb=" O ASP A2410 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2565 through 2570 removed outlier: 3.622A pdb=" N ALA A2596 " --> pdb=" O VAL A2574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2565 through 2570 removed outlier: 3.622A pdb=" N ALA A2596 " --> pdb=" O VAL A2574 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A2659 " --> pdb=" O TYR A2674 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A2632 " --> pdb=" O VAL A2644 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2735 through 2739 Processing sheet with id=AB2, first strand: chain 'B' and resid 1030 through 1033 Processing sheet with id=AB3, first strand: chain 'B' and resid 1049 through 1050 Processing sheet with id=AB4, first strand: chain 'B' and resid 1108 through 1114 removed outlier: 3.581A pdb=" N VAL B1103 " --> pdb=" O PHE B1110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1186 through 1188 Processing sheet with id=AB6, first strand: chain 'B' and resid 1576 through 1580 removed outlier: 6.292A pdb=" N LEU B1586 " --> pdb=" O THR B1598 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR B1598 " --> pdb=" O LEU B1586 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1588 " --> pdb=" O GLN B1596 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLN B1596 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN B1609 " --> pdb=" O GLN B1596 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR B1598 " --> pdb=" O LEU B1607 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B1607 " --> pdb=" O ASP B1623 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP B1623 " --> pdb=" O LEU B1607 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN B1609 " --> pdb=" O LEU B1621 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B1621 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B1611 " --> pdb=" O THR B1619 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR B1619 " --> pdb=" O ILE B1631 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ARG B1640 " --> pdb=" O LEU B1652 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR B1651 " --> pdb=" O VAL B1663 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL B1663 " --> pdb=" O THR B1651 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR B1653 " --> pdb=" O LYS B1661 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYS B1661 " --> pdb=" O MET B1673 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASP B1676 " --> pdb=" O LEU B1682 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B1682 " --> pdb=" O ASP B1676 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N LEU B1681 " --> pdb=" O TYR B1697 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N TYR B1697 " --> pdb=" O LEU B1681 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA B1683 " --> pdb=" O TYR B1695 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR B1704 " --> pdb=" O LEU B1716 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B1768 " --> pdb=" O CYS B1764 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B1798 " --> pdb=" O HIS B1782 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER B1811 " --> pdb=" O VAL B1834 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B1834 " --> pdb=" O SER B1811 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU B1813 " --> pdb=" O LEU B1832 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU B1832 " --> pdb=" O GLU B1813 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG B1815 " --> pdb=" O ARG B1830 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG B1830 " --> pdb=" O ARG B1815 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG B1817 " --> pdb=" O PHE B1828 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B1828 " --> pdb=" O ARG B1817 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU B1819 " --> pdb=" O THR B1826 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B1840 " --> pdb=" O LEU B1832 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B1834 " --> pdb=" O ASN B1838 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN B1838 " --> pdb=" O VAL B1834 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE B1873 " --> pdb=" O VAL B1886 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA B1895 " --> pdb=" O THR B1906 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER B1903 " --> pdb=" O PHE B1919 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE B1919 " --> pdb=" O SER B1903 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG B1905 " --> pdb=" O ARG B1917 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B1917 " --> pdb=" O ARG B1905 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP B1907 " --> pdb=" O VAL B1915 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL B1915 " --> pdb=" O TYR B1927 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N HIS B1955 " --> pdb=" O MET B1967 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B1990 " --> pdb=" O THR B2002 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR B2002 " --> pdb=" O ILE B1990 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP B1992 " --> pdb=" O LEU B2000 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU B2000 " --> pdb=" O TYR B2013 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN B2010 " --> pdb=" O TYR B2026 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR B2026 " --> pdb=" O GLN B2010 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE B2012 " --> pdb=" O ILE B2024 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B2024 " --> pdb=" O PHE B2012 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS B2014 " --> pdb=" O SER B2022 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER B2022 " --> pdb=" O PHE B2033 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYS B2043 " --> pdb=" O TYR B2058 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER B2053 " --> pdb=" O PHE B2072 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE B2072 " --> pdb=" O SER B2053 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR B2055 " --> pdb=" O TYR B2070 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR B2070 " --> pdb=" O THR B2055 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG B2057 " --> pdb=" O GLN B2068 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN B2068 " --> pdb=" O ARG B2057 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG B2059 " --> pdb=" O ASP B2066 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N LEU B2064 " --> pdb=" O TYR B2086 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N TYR B2086 " --> pdb=" O LEU B2064 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP B2066 " --> pdb=" O TYR B2084 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG B2081 " --> pdb=" O PRO B2098 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP B2083 " --> pdb=" O ILE B2096 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B2096 " --> pdb=" O ASP B2083 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B2085 " --> pdb=" O ALA B2094 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1576 through 1580 removed outlier: 6.292A pdb=" N LEU B1586 " --> pdb=" O THR B1598 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR B1598 " --> pdb=" O LEU B1586 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1588 " --> pdb=" O GLN B1596 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLN B1596 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN B1609 " --> pdb=" O GLN B1596 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR B1598 " --> pdb=" O LEU B1607 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B1607 " --> pdb=" O ASP B1623 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP B1623 " --> pdb=" O LEU B1607 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN B1609 " --> pdb=" O LEU B1621 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B1621 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B1611 " --> pdb=" O THR B1619 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR B1619 " --> pdb=" O ILE B1631 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ARG B1640 " --> pdb=" O LEU B1652 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR B1651 " --> pdb=" O VAL B1663 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL B1663 " --> pdb=" O THR B1651 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR B1653 " --> pdb=" O LYS B1661 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYS B1661 " --> pdb=" O MET B1673 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASP B1676 " --> pdb=" O LEU B1682 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B1682 " --> pdb=" O ASP B1676 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N LEU B1681 " --> pdb=" O TYR B1697 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N TYR B1697 " --> pdb=" O LEU B1681 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA B1683 " --> pdb=" O TYR B1695 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR B1704 " --> pdb=" O LEU B1716 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B1768 " --> pdb=" O CYS B1764 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B1798 " --> pdb=" O HIS B1782 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER B1811 " --> pdb=" O VAL B1834 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B1834 " --> pdb=" O SER B1811 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU B1813 " --> pdb=" O LEU B1832 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU B1832 " --> pdb=" O GLU B1813 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG B1815 " --> pdb=" O ARG B1830 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG B1830 " --> pdb=" O ARG B1815 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG B1817 " --> pdb=" O PHE B1828 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B1828 " --> pdb=" O ARG B1817 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU B1819 " --> pdb=" O THR B1826 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B1840 " --> pdb=" O LEU B1832 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B1834 " --> pdb=" O ASN B1838 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN B1838 " --> pdb=" O VAL B1834 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE B1873 " --> pdb=" O VAL B1886 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA B1895 " --> pdb=" O THR B1906 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER B1903 " --> pdb=" O PHE B1919 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE B1919 " --> pdb=" O SER B1903 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG B1905 " --> pdb=" O ARG B1917 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B1917 " --> pdb=" O ARG B1905 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP B1907 " --> pdb=" O VAL B1915 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL B1915 " --> pdb=" O TYR B1927 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N HIS B1955 " --> pdb=" O MET B1967 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B1990 " --> pdb=" O THR B2002 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR B2002 " --> pdb=" O ILE B1990 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP B1992 " --> pdb=" O LEU B2000 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU B2000 " --> pdb=" O TYR B2013 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN B2010 " --> pdb=" O TYR B2026 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR B2026 " --> pdb=" O GLN B2010 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE B2012 " --> pdb=" O ILE B2024 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B2024 " --> pdb=" O PHE B2012 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS B2014 " --> pdb=" O SER B2022 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER B2022 " --> pdb=" O PHE B2033 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYS B2043 " --> pdb=" O TYR B2058 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER B2053 " --> pdb=" O PHE B2072 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE B2072 " --> pdb=" O SER B2053 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR B2055 " --> pdb=" O TYR B2070 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR B2070 " --> pdb=" O THR B2055 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG B2057 " --> pdb=" O GLN B2068 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN B2068 " --> pdb=" O ARG B2057 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG B2059 " --> pdb=" O ASP B2066 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N LEU B2064 " --> pdb=" O TYR B2086 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N TYR B2086 " --> pdb=" O LEU B2064 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP B2066 " --> pdb=" O TYR B2084 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG B2081 " --> pdb=" O PRO B2098 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP B2083 " --> pdb=" O ILE B2096 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B2096 " --> pdb=" O ASP B2083 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B2085 " --> pdb=" O ALA B2094 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA B2094 " --> pdb=" O TYR B2110 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B2109 " --> pdb=" O PHE B2122 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE B2122 " --> pdb=" O LEU B2109 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B2111 " --> pdb=" O GLU B2120 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU B2120 " --> pdb=" O VAL B2127 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LYS B2154 " --> pdb=" O THR B2169 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B2169 " --> pdb=" O LYS B2154 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B2156 " --> pdb=" O TRP B2167 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TRP B2167 " --> pdb=" O VAL B2156 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR B2158 " --> pdb=" O MET B2165 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N MET B2165 " --> pdb=" O LEU B2185 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU B2185 " --> pdb=" O MET B2165 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP B2167 " --> pdb=" O LEU B2183 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU B2183 " --> pdb=" O TRP B2167 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR B2169 " --> pdb=" O ARG B2181 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG B2181 " --> pdb=" O THR B2169 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN B2171 " --> pdb=" O ILE B2179 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE B2179 " --> pdb=" O TYR B2196 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS B2193 " --> pdb=" O VAL B2209 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL B2209 " --> pdb=" O LYS B2193 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B2195 " --> pdb=" O VAL B2207 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B2207 " --> pdb=" O THR B2195 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP B2197 " --> pdb=" O GLN B2205 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B2209 " --> pdb=" O PRO B2213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 2218 through 2219 removed outlier: 5.491A pdb=" N HIS B2226 " --> pdb=" O LEU B2239 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU B2250 " --> pdb=" O PRO B2238 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG B2240 " --> pdb=" O THR B2248 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B2248 " --> pdb=" O TYR B2255 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N CYS B2264 " --> pdb=" O PHE B2271 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B2281 " --> pdb=" O GLU B2272 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR B2280 " --> pdb=" O TYR B2293 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ALA B2302 " --> pdb=" O TYR B2314 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE B2348 " --> pdb=" O VAL B2360 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR B2359 " --> pdb=" O VAL B2371 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B2371 " --> pdb=" O TYR B2359 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B2361 " --> pdb=" O LEU B2369 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU B2369 " --> pdb=" O LEU B2382 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN B2381 " --> pdb=" O ASP B2393 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP B2393 " --> pdb=" O GLN B2381 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN B2383 " --> pdb=" O TYR B2391 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 2408 through 2410 removed outlier: 3.766A pdb=" N LEU B2415 " --> pdb=" O ASP B2410 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 2565 through 2570 removed outlier: 3.714A pdb=" N ALA B2596 " --> pdb=" O VAL B2574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 2565 through 2570 removed outlier: 3.714A pdb=" N ALA B2596 " --> pdb=" O VAL B2574 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR B2659 " --> pdb=" O TYR B2674 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 2735 through 2739 1077 hydrogen bonds defined for protein. 2859 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: 7.47 Time building geometry restraints manager: 2.29 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: 7175 1.34 - 1.46: 4954 1.46 - 1.58: 10478 1.58 - 1.70: 0 1.70 - 1.81: 134 Bond restraints: 22741 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.91e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C1 NAG A2801 " pdb=" O5 NAG A2801 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.05e+00 ... (remaining 22736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 30146 1.88 - 3.76: 596 3.76 - 5.65: 62 5.65 - 7.53: 16 7.53 - 9.41: 2 Bond angle restraints: 30822 Sorted by residual: angle pdb=" C THR A2419 " pdb=" N GLN A2420 " pdb=" CA GLN A2420 " ideal model delta sigma weight residual 125.66 131.67 -6.01 1.85e+00 2.92e-01 1.06e+01 angle pdb=" CB MET A2437 " pdb=" CG MET A2437 " pdb=" SD MET A2437 " ideal model delta sigma weight residual 112.70 122.11 -9.41 3.00e+00 1.11e-01 9.84e+00 angle pdb=" C PRO B1983 " pdb=" N GLU B1984 " pdb=" CA GLU B1984 " ideal model delta sigma weight residual 122.82 127.26 -4.44 1.42e+00 4.96e-01 9.76e+00 angle pdb=" N ILE A1097 " pdb=" CA ILE A1097 " pdb=" C ILE A1097 " ideal model delta sigma weight residual 113.71 110.75 2.96 9.50e-01 1.11e+00 9.74e+00 angle pdb=" CA MET A2437 " pdb=" CB MET A2437 " pdb=" CG MET A2437 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.40e+00 ... (remaining 30817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.86: 12224 20.86 - 41.71: 1195 41.71 - 62.57: 289 62.57 - 83.42: 59 83.42 - 104.28: 19 Dihedral angle restraints: 13786 sinusoidal: 5838 harmonic: 7948 Sorted by residual: dihedral pdb=" CA TYR B1597 " pdb=" C TYR B1597 " pdb=" N THR B1598 " pdb=" CA THR B1598 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA MET B2141 " pdb=" C MET B2141 " pdb=" N THR B2142 " pdb=" CA THR B2142 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR B2137 " pdb=" C THR B2137 " pdb=" N THR B2138 " pdb=" CA THR B2138 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 13783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2852 0.064 - 0.127: 536 0.127 - 0.191: 34 0.191 - 0.254: 0 0.254 - 0.318: 4 Chirality restraints: 3426 Sorted by residual: chirality pdb=" C1 NAG A2803 " pdb=" ND2 ASN A1705 " pdb=" C2 NAG A2803 " pdb=" O5 NAG A2803 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.53e+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 2.00e+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 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3423 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B2492 " -0.386 9.50e-02 1.11e+02 1.74e-01 2.37e+01 pdb=" NE ARG B2492 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG B2492 " -0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG B2492 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B2492 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B1026 " 0.063 5.00e-02 4.00e+02 9.47e-02 1.44e+01 pdb=" N PRO B1027 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B1027 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B1027 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2439 " -0.232 9.50e-02 1.11e+02 1.05e-01 8.73e+00 pdb=" NE ARG A2439 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A2439 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A2439 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A2439 " -0.000 2.00e-02 2.50e+03 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5317 2.80 - 3.33: 17363 3.33 - 3.85: 37300 3.85 - 4.38: 44071 4.38 - 4.90: 77827 Nonbonded interactions: 181878 Sorted by model distance: nonbonded pdb=" OG1 THR A2007 " pdb=" OD2 ASP A2260 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR B2007 " pdb=" OD2 ASP B2260 " model vdw 2.279 3.040 nonbonded pdb=" O LEU B2225 " pdb=" OH TYR B2241 " model vdw 2.299 3.040 nonbonded pdb=" O SER A1940 " pdb=" OG SER A1940 " model vdw 2.301 3.040 nonbonded pdb=" OE2 GLU A2335 " pdb=" OG SER A2352 " model vdw 2.301 3.040 ... (remaining 181873 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 1024 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: 2.640 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: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.590 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 0.053 22765 Z= 0.178 Angle : 0.641 9.533 30894 Z= 0.331 Chirality : 0.049 0.318 3426 Planarity : 0.006 0.174 3941 Dihedral : 17.776 104.281 8734 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.79 % Allowed : 25.46 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2716 helix: -2.66 (0.23), residues: 224 sheet: 1.68 (0.17), residues: 916 loop : -0.46 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG B2492 TYR 0.023 0.002 TYR B2112 PHE 0.027 0.002 PHE B1781 TRP 0.017 0.002 TRP A1691 HIS 0.018 0.002 HIS B1955 Details of bonding type rmsd covalent geometry : bond 0.00391 (22741) covalent geometry : angle 0.62038 (30822) hydrogen bonds : bond 0.20861 ( 879) hydrogen bonds : angle 8.27674 ( 2859) link_ALPHA1-3 : bond 0.00529 ( 1) link_ALPHA1-3 : angle 1.42809 ( 3) link_BETA1-4 : bond 0.01384 ( 8) link_BETA1-4 : angle 2.78252 ( 24) link_NAG-ASN : bond 0.00468 ( 15) link_NAG-ASN : angle 3.82421 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 709 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1144 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8023 (m) REVERT: A 1160 GLU cc_start: 0.6828 (tp30) cc_final: 0.6325 (tm-30) REVERT: A 1586 LEU cc_start: 0.8758 (tp) cc_final: 0.8512 (tt) REVERT: A 1622 ILE cc_start: 0.8535 (mt) cc_final: 0.8260 (tt) REVERT: A 1640 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7437 (mmm-85) REVERT: A 1704 THR cc_start: 0.8261 (m) cc_final: 0.8010 (p) REVERT: A 1723 SER cc_start: 0.8412 (p) cc_final: 0.8078 (t) REVERT: A 1765 ASN cc_start: 0.7631 (m110) cc_final: 0.7412 (m110) REVERT: A 1805 MET cc_start: 0.8319 (ptt) cc_final: 0.7986 (ptt) REVERT: A 1849 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7259 (mtt90) REVERT: A 1962 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8338 (m) REVERT: A 1975 TYR cc_start: 0.8575 (p90) cc_final: 0.8333 (p90) REVERT: A 2052 PHE cc_start: 0.7663 (m-10) cc_final: 0.7219 (m-80) REVERT: A 2240 ARG cc_start: 0.7362 (mtt90) cc_final: 0.7130 (mtt90) REVERT: A 2249 ARG cc_start: 0.7619 (ttt180) cc_final: 0.7419 (ttm-80) REVERT: A 2350 MET cc_start: 0.8790 (mtm) cc_final: 0.8589 (mtm) REVERT: A 2375 ASN cc_start: 0.7998 (p0) cc_final: 0.7747 (p0) REVERT: A 2482 GLN cc_start: 0.7954 (tp40) cc_final: 0.7739 (mm-40) REVERT: A 2536 GLN cc_start: 0.7878 (tt0) cc_final: 0.7662 (mt0) REVERT: A 2623 ASP cc_start: 0.7258 (m-30) cc_final: 0.6715 (m-30) REVERT: A 2674 TYR cc_start: 0.8488 (m-80) cc_final: 0.7691 (m-80) REVERT: A 2683 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7140 (tt0) REVERT: A 2687 ARG cc_start: 0.8287 (ttt-90) cc_final: 0.7972 (ttt-90) REVERT: B 1202 GLN cc_start: 0.7944 (mt0) cc_final: 0.7667 (mt0) REVERT: B 1646 ASP cc_start: 0.8180 (p0) cc_final: 0.7622 (p0) REVERT: B 1648 GLN cc_start: 0.7611 (tp40) cc_final: 0.6981 (mp10) REVERT: B 1723 SER cc_start: 0.8352 (p) cc_final: 0.7896 (t) REVERT: B 1733 ARG cc_start: 0.7303 (tpp80) cc_final: 0.7066 (mpp80) REVERT: B 1765 ASN cc_start: 0.7579 (m110) cc_final: 0.7106 (m-40) REVERT: B 1807 ASN cc_start: 0.8290 (m-40) cc_final: 0.8088 (m110) REVERT: B 1845 ASP cc_start: 0.8059 (p0) cc_final: 0.7829 (t0) REVERT: B 1975 TYR cc_start: 0.8641 (p90) cc_final: 0.8314 (p90) REVERT: B 2052 PHE cc_start: 0.7564 (m-80) cc_final: 0.7200 (m-80) REVERT: B 2320 HIS cc_start: 0.8158 (m-70) cc_final: 0.7555 (m-70) REVERT: B 2566 MET cc_start: 0.7528 (tmt) cc_final: 0.7234 (tmm) REVERT: B 2591 SER cc_start: 0.8439 (t) cc_final: 0.8110 (p) REVERT: B 2623 ASP cc_start: 0.7452 (m-30) cc_final: 0.6901 (m-30) REVERT: B 2674 TYR cc_start: 0.8413 (m-80) cc_final: 0.7506 (m-80) REVERT: B 2690 ASP cc_start: 0.7793 (t0) cc_final: 0.7527 (t0) outliers start: 19 outliers final: 4 residues processed: 719 average time/residue: 0.6916 time to fit residues: 561.5165 Evaluate side-chains 611 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 605 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 2526 HIS Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1924 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1195 HIS A1596 GLN A1678 ASN A1756 GLN A1807 ASN A1955 HIS A2087 HIS A2171 GLN A2226 HIS A2292 GLN A2440 ASN A2520 GLN A2660 ASN A2725 GLN B1195 HIS B1596 GLN B1657 ASN B1705 ASN B1838 ASN B1939 GLN B2087 HIS B2146 HIS B2226 HIS B2292 GLN B2310 HIS B2457 ASN B2520 GLN B2543 HIS B2660 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102011 restraints weight = 29527.200| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.70 r_work: 0.3231 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 22765 Z= 0.248 Angle : 0.618 8.127 30894 Z= 0.326 Chirality : 0.048 0.271 3426 Planarity : 0.005 0.066 3941 Dihedral : 7.441 74.761 3563 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.58 % Allowed : 23.92 % Favored : 72.50 % 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: 0.64 (0.16), residues: 2716 helix: -0.12 (0.33), residues: 226 sheet: 1.64 (0.17), residues: 898 loop : -0.19 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B2111 TYR 0.018 0.002 TYR B2130 PHE 0.020 0.002 PHE A2122 TRP 0.016 0.002 TRP A1691 HIS 0.009 0.002 HIS B1970 Details of bonding type rmsd covalent geometry : bond 0.00583 (22741) covalent geometry : angle 0.60085 (30822) hydrogen bonds : bond 0.05049 ( 879) hydrogen bonds : angle 5.93103 ( 2859) link_ALPHA1-3 : bond 0.01248 ( 1) link_ALPHA1-3 : angle 0.76646 ( 3) link_BETA1-4 : bond 0.00645 ( 8) link_BETA1-4 : angle 2.53685 ( 24) link_NAG-ASN : bond 0.00416 ( 15) link_NAG-ASN : angle 3.40092 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 607 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7494 (p) REVERT: A 1144 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8060 (m) REVERT: A 1160 GLU cc_start: 0.7086 (tp30) cc_final: 0.6707 (tp30) REVERT: A 1640 ARG cc_start: 0.8118 (mmm-85) cc_final: 0.7838 (mmm-85) REVERT: A 1687 ASP cc_start: 0.7607 (p0) cc_final: 0.7384 (p0) REVERT: A 1704 THR cc_start: 0.8189 (m) cc_final: 0.7853 (p) REVERT: A 1708 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8237 (mtm-85) REVERT: A 1723 SER cc_start: 0.8386 (p) cc_final: 0.8125 (m) REVERT: A 1849 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7566 (mtt90) REVERT: A 1902 MET cc_start: 0.8116 (mtt) cc_final: 0.7836 (mtt) REVERT: A 1975 TYR cc_start: 0.8609 (p90) cc_final: 0.8336 (p90) REVERT: A 2375 ASN cc_start: 0.7966 (p0) cc_final: 0.7753 (p0) REVERT: A 2452 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8677 (ttp) REVERT: A 2530 PHE cc_start: 0.8298 (t80) cc_final: 0.7995 (t80) REVERT: A 2536 GLN cc_start: 0.7967 (tt0) cc_final: 0.7715 (mt0) REVERT: A 2566 MET cc_start: 0.7762 (tmm) cc_final: 0.7275 (tmm) REVERT: A 2623 ASP cc_start: 0.7163 (m-30) cc_final: 0.6520 (m-30) REVERT: A 2674 TYR cc_start: 0.8454 (m-80) cc_final: 0.7504 (m-80) REVERT: A 2687 ARG cc_start: 0.8512 (ttt-90) cc_final: 0.8140 (ttt-90) REVERT: A 2695 ARG cc_start: 0.8607 (mtm-85) cc_final: 0.8238 (mtp180) REVERT: B 1144 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8097 (m) REVERT: B 1202 GLN cc_start: 0.8169 (mt0) cc_final: 0.7963 (mt0) REVERT: B 1646 ASP cc_start: 0.8235 (p0) cc_final: 0.7679 (p0) REVERT: B 1648 GLN cc_start: 0.7920 (tp40) cc_final: 0.7300 (mp10) REVERT: B 1723 SER cc_start: 0.8319 (p) cc_final: 0.7938 (t) REVERT: B 1765 ASN cc_start: 0.7733 (m110) cc_final: 0.7291 (m-40) REVERT: B 2107 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7896 (t) REVERT: B 2623 ASP cc_start: 0.7289 (m-30) cc_final: 0.6956 (m-30) REVERT: B 2674 TYR cc_start: 0.8384 (m-80) cc_final: 0.7630 (m-80) REVERT: B 2694 GLN cc_start: 0.8195 (mp-120) cc_final: 0.7938 (mm110) REVERT: B 2712 ARG cc_start: 0.7882 (mtp-110) cc_final: 0.7404 (mtp-110) REVERT: B 2745 GLN cc_start: 0.7875 (mt0) cc_final: 0.7630 (tt0) outliers start: 86 outliers final: 36 residues processed: 638 average time/residue: 0.7175 time to fit residues: 514.8755 Evaluate side-chains 632 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 590 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1705 ASN Chi-restraints excluded: chain A residue 1708 ARG Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 2044 MET Chi-restraints excluded: chain A residue 2256 LYS Chi-restraints excluded: chain A residue 2452 MET Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2526 HIS Chi-restraints excluded: chain A residue 2557 THR Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain A residue 2607 GLU Chi-restraints excluded: chain A residue 2690 ASP Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1643 LEU Chi-restraints excluded: chain B residue 1686 SER Chi-restraints excluded: chain B residue 1696 ASP Chi-restraints excluded: chain B residue 1739 VAL Chi-restraints excluded: chain B residue 1816 LEU Chi-restraints excluded: chain B residue 1838 ASN Chi-restraints excluded: chain B residue 1950 SER Chi-restraints excluded: chain B residue 1951 SER Chi-restraints excluded: chain B residue 2107 VAL Chi-restraints excluded: chain B residue 2115 ILE Chi-restraints excluded: chain B residue 2160 MET Chi-restraints excluded: chain B residue 2233 SER Chi-restraints excluded: chain B residue 2264 CYS Chi-restraints excluded: chain B residue 2607 GLU Chi-restraints excluded: chain B residue 2753 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 231 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1678 ASN A1756 GLN A1807 ASN A2087 HIS A2226 HIS A2254 GLN A2660 ASN A2694 GLN A2725 GLN B1807 ASN B2046 ASN B2146 HIS B2226 HIS B2292 GLN B2310 HIS B2660 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102385 restraints weight = 30338.794| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.69 r_work: 0.3233 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22765 Z= 0.157 Angle : 0.546 7.380 30894 Z= 0.289 Chirality : 0.046 0.251 3426 Planarity : 0.004 0.055 3941 Dihedral : 6.542 57.263 3561 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.75 % Allowed : 23.21 % Favored : 73.04 % 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: 0.84 (0.16), residues: 2716 helix: 0.76 (0.35), residues: 226 sheet: 1.53 (0.16), residues: 918 loop : -0.04 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B2111 TYR 0.012 0.001 TYR A2130 PHE 0.015 0.002 PHE A2122 TRP 0.011 0.001 TRP A1691 HIS 0.009 0.001 HIS A1955 Details of bonding type rmsd covalent geometry : bond 0.00358 (22741) covalent geometry : angle 0.53077 (30822) hydrogen bonds : bond 0.04205 ( 879) hydrogen bonds : angle 5.56911 ( 2859) link_ALPHA1-3 : bond 0.01220 ( 1) link_ALPHA1-3 : angle 0.92024 ( 3) link_BETA1-4 : bond 0.00824 ( 8) link_BETA1-4 : angle 2.35797 ( 24) link_NAG-ASN : bond 0.00287 ( 15) link_NAG-ASN : angle 3.00576 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 606 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7525 (p) REVERT: A 1144 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8083 (m) REVERT: A 1640 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7847 (mmm-85) REVERT: A 1687 ASP cc_start: 0.7598 (p0) cc_final: 0.7376 (p0) REVERT: A 1704 THR cc_start: 0.8185 (m) cc_final: 0.7851 (p) REVERT: A 1708 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8200 (mtm-85) REVERT: A 1723 SER cc_start: 0.8373 (p) cc_final: 0.8085 (m) REVERT: A 1849 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7651 (mtt90) REVERT: A 1975 TYR cc_start: 0.8591 (p90) cc_final: 0.8342 (p90) REVERT: A 2243 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 2375 ASN cc_start: 0.7906 (p0) cc_final: 0.7626 (p0) REVERT: A 2536 GLN cc_start: 0.7928 (tt0) cc_final: 0.7690 (mt0) REVERT: A 2566 MET cc_start: 0.7772 (tmm) cc_final: 0.7489 (tmm) REVERT: A 2623 ASP cc_start: 0.7180 (m-30) cc_final: 0.6539 (m-30) REVERT: A 2674 TYR cc_start: 0.8432 (m-80) cc_final: 0.7501 (m-80) REVERT: A 2687 ARG cc_start: 0.8483 (ttt-90) cc_final: 0.8062 (ttt-90) REVERT: B 1202 GLN cc_start: 0.8114 (mt0) cc_final: 0.7899 (mt0) REVERT: B 1646 ASP cc_start: 0.8258 (p0) cc_final: 0.7708 (p0) REVERT: B 1648 GLN cc_start: 0.7831 (tp40) cc_final: 0.7205 (mp10) REVERT: B 1723 SER cc_start: 0.8319 (p) cc_final: 0.8024 (m) REVERT: B 1765 ASN cc_start: 0.7717 (m110) cc_final: 0.7276 (m-40) REVERT: B 1802 SER cc_start: 0.8398 (m) cc_final: 0.8161 (p) REVERT: B 1848 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8274 (pt) REVERT: B 2107 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7919 (t) REVERT: B 2216 ARG cc_start: 0.7606 (ttp80) cc_final: 0.7316 (ttp80) REVERT: B 2218 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.8028 (m) REVERT: B 2530 PHE cc_start: 0.8455 (t80) cc_final: 0.8254 (t80) REVERT: B 2623 ASP cc_start: 0.7357 (m-30) cc_final: 0.7004 (m-30) REVERT: B 2674 TYR cc_start: 0.8355 (m-80) cc_final: 0.7564 (m-80) REVERT: B 2709 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7387 (mtp180) REVERT: B 2712 ARG cc_start: 0.7884 (mtp-110) cc_final: 0.7412 (mtp-110) REVERT: B 2745 GLN cc_start: 0.7840 (mt0) cc_final: 0.7587 (tt0) outliers start: 90 outliers final: 42 residues processed: 637 average time/residue: 0.7137 time to fit residues: 513.2003 Evaluate side-chains 635 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 586 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1705 ASN Chi-restraints excluded: chain A residue 1708 ARG Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 2044 MET Chi-restraints excluded: chain A residue 2053 SER Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2471 ASP Chi-restraints excluded: chain A residue 2526 HIS Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 2557 THR Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain A residue 2607 GLU Chi-restraints excluded: chain A residue 2690 ASP Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1643 LEU Chi-restraints excluded: chain B residue 1686 SER Chi-restraints excluded: chain B residue 1696 ASP Chi-restraints excluded: chain B residue 1739 VAL Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1916 SER Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1950 SER Chi-restraints excluded: chain B residue 1984 GLU Chi-restraints excluded: chain B residue 2074 GLU Chi-restraints excluded: chain B residue 2107 VAL Chi-restraints excluded: chain B residue 2218 SER Chi-restraints excluded: chain B residue 2233 SER Chi-restraints excluded: chain B residue 2252 ASP Chi-restraints excluded: chain B residue 2264 CYS Chi-restraints excluded: chain B residue 2557 THR Chi-restraints excluded: chain B residue 2607 GLU Chi-restraints excluded: chain B residue 2723 LYS Chi-restraints excluded: chain B residue 2753 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 207 optimal weight: 1.9990 chunk 231 optimal weight: 0.0980 chunk 161 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 245 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1678 ASN A1756 GLN A1807 ASN A2226 HIS A2254 GLN A2292 GLN A2660 ASN A2694 GLN A2725 GLN B1705 ASN B1807 ASN B1939 GLN ** B2121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2146 HIS B2226 HIS B2292 GLN B2660 ASN B2694 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101667 restraints weight = 30328.998| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.68 r_work: 0.3223 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22765 Z= 0.190 Angle : 0.563 7.665 30894 Z= 0.296 Chirality : 0.046 0.262 3426 Planarity : 0.004 0.056 3941 Dihedral : 6.099 59.360 3561 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.25 % Allowed : 23.08 % Favored : 72.67 % 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: 0.88 (0.16), residues: 2716 helix: 1.08 (0.35), residues: 226 sheet: 1.53 (0.16), residues: 918 loop : -0.04 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1905 TYR 0.013 0.002 TYR A2130 PHE 0.019 0.002 PHE A2122 TRP 0.012 0.001 TRP A1691 HIS 0.010 0.001 HIS A1955 Details of bonding type rmsd covalent geometry : bond 0.00446 (22741) covalent geometry : angle 0.54665 (30822) hydrogen bonds : bond 0.04132 ( 879) hydrogen bonds : angle 5.48328 ( 2859) link_ALPHA1-3 : bond 0.01200 ( 1) link_ALPHA1-3 : angle 1.10983 ( 3) link_BETA1-4 : bond 0.00786 ( 8) link_BETA1-4 : angle 2.32751 ( 24) link_NAG-ASN : bond 0.00334 ( 15) link_NAG-ASN : angle 3.11022 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 598 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7549 (p) REVERT: A 1144 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8067 (m) REVERT: A 1584 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7712 (mm110) REVERT: A 1640 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7898 (mmm-85) REVERT: A 1687 ASP cc_start: 0.7618 (p0) cc_final: 0.7378 (p0) REVERT: A 1704 THR cc_start: 0.8208 (m) cc_final: 0.7861 (p) REVERT: A 1708 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8204 (mtm-85) REVERT: A 1723 SER cc_start: 0.8379 (p) cc_final: 0.8072 (m) REVERT: A 1849 ARG cc_start: 0.8213 (mtt90) cc_final: 0.7509 (mtt90) REVERT: A 1975 TYR cc_start: 0.8614 (p90) cc_final: 0.8194 (p90) REVERT: A 2243 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8431 (tt) REVERT: A 2375 ASN cc_start: 0.7920 (p0) cc_final: 0.7643 (p0) REVERT: A 2437 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7684 (ppp) REVERT: A 2536 GLN cc_start: 0.7927 (tt0) cc_final: 0.7701 (mt0) REVERT: A 2566 MET cc_start: 0.7765 (tmm) cc_final: 0.7529 (tmm) REVERT: A 2623 ASP cc_start: 0.7164 (m-30) cc_final: 0.6584 (m-30) REVERT: A 2674 TYR cc_start: 0.8428 (m-80) cc_final: 0.7476 (m-80) REVERT: A 2687 ARG cc_start: 0.8477 (ttt-90) cc_final: 0.8034 (ttt-90) REVERT: A 2709 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7377 (ttp-170) REVERT: A 2745 GLN cc_start: 0.7846 (mt0) cc_final: 0.7564 (tt0) REVERT: B 1086 THR cc_start: 0.7843 (m) cc_final: 0.7411 (p) REVERT: B 1105 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7545 (p) REVERT: B 1202 GLN cc_start: 0.8122 (mt0) cc_final: 0.7895 (mt0) REVERT: B 1646 ASP cc_start: 0.8260 (p0) cc_final: 0.7726 (p0) REVERT: B 1648 GLN cc_start: 0.7851 (tp40) cc_final: 0.7230 (mp10) REVERT: B 1723 SER cc_start: 0.8339 (p) cc_final: 0.8048 (m) REVERT: B 1765 ASN cc_start: 0.7727 (m110) cc_final: 0.7289 (m-40) REVERT: B 1802 SER cc_start: 0.8418 (m) cc_final: 0.8154 (p) REVERT: B 1848 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8196 (pt) REVERT: B 2107 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7899 (t) REVERT: B 2216 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7369 (ttp80) REVERT: B 2495 MET cc_start: 0.7260 (tmm) cc_final: 0.7005 (tmm) REVERT: B 2530 PHE cc_start: 0.8447 (t80) cc_final: 0.8162 (t80) REVERT: B 2623 ASP cc_start: 0.7342 (m-30) cc_final: 0.6955 (m-30) REVERT: B 2674 TYR cc_start: 0.8383 (m-80) cc_final: 0.7580 (m-80) REVERT: B 2709 ARG cc_start: 0.7622 (mtp180) cc_final: 0.7402 (ttp-170) REVERT: B 2712 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.7315 (mtp-110) REVERT: B 2745 GLN cc_start: 0.7850 (mt0) cc_final: 0.7589 (tt0) outliers start: 102 outliers final: 46 residues processed: 633 average time/residue: 0.6324 time to fit residues: 453.4884 Evaluate side-chains 641 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 586 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1705 ASN Chi-restraints excluded: chain A residue 1708 ARG Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 2044 MET Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2264 CYS Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2379 ILE Chi-restraints excluded: chain A residue 2437 MET Chi-restraints excluded: chain A residue 2471 ASP Chi-restraints excluded: chain A residue 2526 HIS Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 2557 THR Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain A residue 2607 GLU Chi-restraints excluded: chain A residue 2690 ASP Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1643 LEU Chi-restraints excluded: chain B residue 1686 SER Chi-restraints excluded: chain B residue 1696 ASP Chi-restraints excluded: chain B residue 1739 VAL Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1859 LYS Chi-restraints excluded: chain B residue 1861 THR Chi-restraints excluded: chain B residue 1916 SER Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1950 SER Chi-restraints excluded: chain B residue 1951 SER Chi-restraints excluded: chain B residue 1967 MET Chi-restraints excluded: chain B residue 2074 GLU Chi-restraints excluded: chain B residue 2075 GLU Chi-restraints excluded: chain B residue 2107 VAL Chi-restraints excluded: chain B residue 2115 ILE Chi-restraints excluded: chain B residue 2160 MET Chi-restraints excluded: chain B residue 2216 ARG Chi-restraints excluded: chain B residue 2233 SER Chi-restraints excluded: chain B residue 2264 CYS Chi-restraints excluded: chain B residue 2557 THR Chi-restraints excluded: chain B residue 2607 GLU Chi-restraints excluded: chain B residue 2617 ILE Chi-restraints excluded: chain B residue 2723 LYS Chi-restraints excluded: chain B residue 2753 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 124 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1678 ASN A1756 GLN A1807 ASN A1955 HIS A2087 HIS A2226 HIS A2292 GLN A2311 HIS A2543 HIS A2660 ASN A2694 GLN B1705 ASN B1807 ASN B1939 GLN B1955 HIS B2046 ASN ** B2121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2146 HIS B2226 HIS B2292 GLN B2311 HIS B2660 ASN B2694 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100816 restraints weight = 30218.043| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.67 r_work: 0.3207 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 22765 Z= 0.256 Angle : 0.603 8.144 30894 Z= 0.316 Chirality : 0.048 0.282 3426 Planarity : 0.004 0.057 3941 Dihedral : 6.011 59.678 3561 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.25 % Allowed : 23.38 % Favored : 72.38 % 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: 0.87 (0.16), residues: 2716 helix: 1.19 (0.34), residues: 226 sheet: 1.54 (0.16), residues: 916 loop : -0.08 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1905 TYR 0.015 0.002 TYR A2130 PHE 0.023 0.002 PHE A2122 TRP 0.013 0.002 TRP A1691 HIS 0.009 0.002 HIS A1955 Details of bonding type rmsd covalent geometry : bond 0.00606 (22741) covalent geometry : angle 0.58591 (30822) hydrogen bonds : bond 0.04384 ( 879) hydrogen bonds : angle 5.56362 ( 2859) link_ALPHA1-3 : bond 0.01200 ( 1) link_ALPHA1-3 : angle 1.12639 ( 3) link_BETA1-4 : bond 0.00805 ( 8) link_BETA1-4 : angle 2.41287 ( 24) link_NAG-ASN : bond 0.00402 ( 15) link_NAG-ASN : angle 3.39418 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 591 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7575 (p) REVERT: A 1144 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8070 (m) REVERT: A 1584 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7733 (mm110) REVERT: A 1687 ASP cc_start: 0.7662 (p0) cc_final: 0.7429 (p0) REVERT: A 1704 THR cc_start: 0.8225 (m) cc_final: 0.7901 (p) REVERT: A 1723 SER cc_start: 0.8395 (p) cc_final: 0.8090 (m) REVERT: A 1848 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8238 (pt) REVERT: A 1849 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7532 (mtt90) REVERT: A 1902 MET cc_start: 0.8107 (mtt) cc_final: 0.7878 (mtt) REVERT: A 1910 LYS cc_start: 0.8303 (mmtm) cc_final: 0.8076 (mmtm) REVERT: A 1975 TYR cc_start: 0.8596 (p90) cc_final: 0.8293 (p90) REVERT: A 2243 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 2375 ASN cc_start: 0.7942 (p0) cc_final: 0.7707 (p0) REVERT: A 2566 MET cc_start: 0.7728 (tmm) cc_final: 0.7504 (tmm) REVERT: A 2623 ASP cc_start: 0.7191 (m-30) cc_final: 0.6570 (m-30) REVERT: A 2674 TYR cc_start: 0.8458 (m-80) cc_final: 0.7525 (m-80) REVERT: A 2687 ARG cc_start: 0.8441 (ttt-90) cc_final: 0.8033 (ttt-90) REVERT: A 2709 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7373 (ttp-170) REVERT: A 2745 GLN cc_start: 0.7880 (mt0) cc_final: 0.7600 (tt0) REVERT: B 1086 THR cc_start: 0.7873 (m) cc_final: 0.7476 (p) REVERT: B 1105 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7634 (p) REVERT: B 1646 ASP cc_start: 0.8281 (p0) cc_final: 0.7703 (p0) REVERT: B 1648 GLN cc_start: 0.7870 (tp40) cc_final: 0.7232 (mp10) REVERT: B 1723 SER cc_start: 0.8352 (p) cc_final: 0.8081 (m) REVERT: B 1765 ASN cc_start: 0.7727 (m110) cc_final: 0.7299 (m-40) REVERT: B 1802 SER cc_start: 0.8427 (m) cc_final: 0.8188 (p) REVERT: B 1805 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8232 (ptt) REVERT: B 1819 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6875 (mt-10) REVERT: B 1848 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8341 (pt) REVERT: B 2077 MET cc_start: 0.8052 (mmt) cc_final: 0.5513 (mmt) REVERT: B 2107 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7876 (t) REVERT: B 2495 MET cc_start: 0.7309 (tmm) cc_final: 0.7065 (tmm) REVERT: B 2530 PHE cc_start: 0.8441 (t80) cc_final: 0.8167 (t80) REVERT: B 2623 ASP cc_start: 0.7351 (m-30) cc_final: 0.6895 (m-30) REVERT: B 2674 TYR cc_start: 0.8410 (m-80) cc_final: 0.7606 (m-80) REVERT: B 2709 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7436 (ttp-170) REVERT: B 2712 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7312 (mtp-110) REVERT: B 2745 GLN cc_start: 0.7845 (mt0) cc_final: 0.7582 (tt0) outliers start: 102 outliers final: 52 residues processed: 625 average time/residue: 0.6446 time to fit residues: 456.5574 Evaluate side-chains 642 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 582 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1705 ASN Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 1918 MET Chi-restraints excluded: chain A residue 2044 MET Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2239 LEU Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2256 LYS Chi-restraints excluded: chain A residue 2264 CYS Chi-restraints excluded: chain A residue 2379 ILE Chi-restraints excluded: chain A residue 2400 MET Chi-restraints excluded: chain A residue 2471 ASP Chi-restraints excluded: chain A residue 2526 HIS Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 2537 VAL Chi-restraints excluded: chain A residue 2557 THR Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain A residue 2607 GLU Chi-restraints excluded: chain A residue 2690 ASP Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1186 THR Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1643 LEU Chi-restraints excluded: chain B residue 1686 SER Chi-restraints excluded: chain B residue 1696 ASP Chi-restraints excluded: chain B residue 1724 ILE Chi-restraints excluded: chain B residue 1739 VAL Chi-restraints excluded: chain B residue 1805 MET Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1861 THR Chi-restraints excluded: chain B residue 1916 SER Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1926 SER Chi-restraints excluded: chain B residue 1950 SER Chi-restraints excluded: chain B residue 1951 SER Chi-restraints excluded: chain B residue 1958 THR Chi-restraints excluded: chain B residue 1971 THR Chi-restraints excluded: chain B residue 2074 GLU Chi-restraints excluded: chain B residue 2107 VAL Chi-restraints excluded: chain B residue 2115 ILE Chi-restraints excluded: chain B residue 2160 MET Chi-restraints excluded: chain B residue 2233 SER Chi-restraints excluded: chain B residue 2252 ASP Chi-restraints excluded: chain B residue 2264 CYS Chi-restraints excluded: chain B residue 2557 THR Chi-restraints excluded: chain B residue 2607 GLU Chi-restraints excluded: chain B residue 2723 LYS Chi-restraints excluded: chain B residue 2753 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1756 GLN A1807 ASN A1955 HIS A2226 HIS A2254 GLN A2292 GLN A2543 HIS A2660 ASN A2694 GLN B1705 ASN B1807 ASN B1939 GLN B1955 HIS ** B2121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2146 HIS B2226 HIS B2292 GLN B2405 HIS B2660 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.101771 restraints weight = 30381.976| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.68 r_work: 0.3224 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22765 Z= 0.167 Angle : 0.550 7.569 30894 Z= 0.290 Chirality : 0.045 0.262 3426 Planarity : 0.004 0.083 3941 Dihedral : 5.773 59.200 3561 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.58 % Allowed : 24.17 % Favored : 72.25 % 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: 0.92 (0.16), residues: 2716 helix: 1.41 (0.35), residues: 226 sheet: 1.53 (0.16), residues: 916 loop : -0.04 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2731 TYR 0.013 0.001 TYR B1927 PHE 0.016 0.002 PHE A2122 TRP 0.011 0.001 TRP A1691 HIS 0.010 0.001 HIS A1955 Details of bonding type rmsd covalent geometry : bond 0.00387 (22741) covalent geometry : angle 0.53436 (30822) hydrogen bonds : bond 0.03913 ( 879) hydrogen bonds : angle 5.40925 ( 2859) link_ALPHA1-3 : bond 0.01058 ( 1) link_ALPHA1-3 : angle 1.19362 ( 3) link_BETA1-4 : bond 0.00746 ( 8) link_BETA1-4 : angle 2.12379 ( 24) link_NAG-ASN : bond 0.00288 ( 15) link_NAG-ASN : angle 3.04438 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 602 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 PRO cc_start: 0.8573 (Cg_endo) cc_final: 0.8329 (Cg_exo) REVERT: A 1105 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7571 (p) REVERT: A 1144 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8068 (m) REVERT: A 1584 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7724 (mm110) REVERT: A 1640 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7730 (mmm-85) REVERT: A 1687 ASP cc_start: 0.7678 (p0) cc_final: 0.7466 (p0) REVERT: A 1704 THR cc_start: 0.8202 (m) cc_final: 0.7872 (p) REVERT: A 1708 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8218 (mtm-85) REVERT: A 1723 SER cc_start: 0.8373 (p) cc_final: 0.8049 (m) REVERT: A 1848 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8219 (pt) REVERT: A 1849 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7519 (mtt90) REVERT: A 1910 LYS cc_start: 0.8316 (mmtm) cc_final: 0.8087 (mmtm) REVERT: A 1975 TYR cc_start: 0.8572 (p90) cc_final: 0.8270 (p90) REVERT: A 2243 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8436 (tt) REVERT: A 2375 ASN cc_start: 0.7914 (p0) cc_final: 0.7640 (p0) REVERT: A 2566 MET cc_start: 0.7743 (tmm) cc_final: 0.7513 (tmm) REVERT: A 2591 SER cc_start: 0.8501 (p) cc_final: 0.8232 (p) REVERT: A 2623 ASP cc_start: 0.7173 (m-30) cc_final: 0.6579 (m-30) REVERT: A 2674 TYR cc_start: 0.8436 (m-80) cc_final: 0.7540 (m-80) REVERT: A 2687 ARG cc_start: 0.8410 (ttt-90) cc_final: 0.8028 (ttt-90) REVERT: A 2709 ARG cc_start: 0.7599 (mtp180) cc_final: 0.7391 (ttp-170) REVERT: A 2745 GLN cc_start: 0.7871 (mt0) cc_final: 0.7601 (tt0) REVERT: B 1086 THR cc_start: 0.7858 (m) cc_final: 0.7505 (p) REVERT: B 1105 VAL cc_start: 0.7933 (OUTLIER) cc_final: 0.7577 (p) REVERT: B 1646 ASP cc_start: 0.8285 (p0) cc_final: 0.7728 (p0) REVERT: B 1648 GLN cc_start: 0.7865 (tp40) cc_final: 0.7226 (mp10) REVERT: B 1723 SER cc_start: 0.8342 (p) cc_final: 0.8066 (m) REVERT: B 1765 ASN cc_start: 0.7719 (m110) cc_final: 0.7311 (m-40) REVERT: B 1802 SER cc_start: 0.8422 (m) cc_final: 0.8166 (p) REVERT: B 1819 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6885 (mt-10) REVERT: B 1848 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8368 (pt) REVERT: B 2107 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7840 (t) REVERT: B 2495 MET cc_start: 0.7295 (tmm) cc_final: 0.7054 (tmm) REVERT: B 2530 PHE cc_start: 0.8419 (t80) cc_final: 0.8153 (t80) REVERT: B 2623 ASP cc_start: 0.7351 (m-30) cc_final: 0.6874 (m-30) REVERT: B 2674 TYR cc_start: 0.8413 (m-80) cc_final: 0.7612 (m-80) REVERT: B 2709 ARG cc_start: 0.7667 (mtp180) cc_final: 0.7441 (ttp-170) REVERT: B 2712 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7305 (mtp-110) REVERT: B 2745 GLN cc_start: 0.7843 (mt0) cc_final: 0.7575 (tt0) outliers start: 86 outliers final: 51 residues processed: 629 average time/residue: 0.7195 time to fit residues: 511.3021 Evaluate side-chains 645 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 586 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1705 ASN Chi-restraints excluded: chain A residue 1708 ARG Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 2044 MET Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2239 LEU Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2264 CYS Chi-restraints excluded: chain A residue 2379 ILE Chi-restraints excluded: chain A residue 2471 ASP Chi-restraints excluded: chain A residue 2526 HIS Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 2537 VAL Chi-restraints excluded: chain A residue 2557 THR Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain A residue 2607 GLU Chi-restraints excluded: chain A residue 2627 LEU Chi-restraints excluded: chain A residue 2690 ASP Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1643 LEU Chi-restraints excluded: chain B residue 1657 ASN Chi-restraints excluded: chain B residue 1686 SER Chi-restraints excluded: chain B residue 1696 ASP Chi-restraints excluded: chain B residue 1724 ILE Chi-restraints excluded: chain B residue 1739 VAL Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1859 LYS Chi-restraints excluded: chain B residue 1861 THR Chi-restraints excluded: chain B residue 1916 SER Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1950 SER Chi-restraints excluded: chain B residue 1967 MET Chi-restraints excluded: chain B residue 2014 LYS Chi-restraints excluded: chain B residue 2044 MET Chi-restraints excluded: chain B residue 2074 GLU Chi-restraints excluded: chain B residue 2107 VAL Chi-restraints excluded: chain B residue 2115 ILE Chi-restraints excluded: chain B residue 2160 MET Chi-restraints excluded: chain B residue 2233 SER Chi-restraints excluded: chain B residue 2252 ASP Chi-restraints excluded: chain B residue 2264 CYS Chi-restraints excluded: chain B residue 2486 ILE Chi-restraints excluded: chain B residue 2531 LEU Chi-restraints excluded: chain B residue 2557 THR Chi-restraints excluded: chain B residue 2607 GLU Chi-restraints excluded: chain B residue 2723 LYS Chi-restraints excluded: chain B residue 2753 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 175 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 259 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1756 GLN A1807 ASN A1955 HIS A2190 ASN A2226 HIS A2254 GLN A2543 HIS A2660 ASN A2694 GLN B1705 ASN B1807 ASN B1939 GLN B1955 HIS B2121 HIS B2146 HIS B2190 ASN B2226 HIS B2395 ASN B2660 ASN B2694 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102792 restraints weight = 30120.690| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.67 r_work: 0.3242 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22765 Z= 0.122 Angle : 0.519 7.379 30894 Z= 0.274 Chirality : 0.044 0.247 3426 Planarity : 0.004 0.055 3941 Dihedral : 5.555 58.737 3561 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.54 % Allowed : 23.92 % Favored : 72.54 % 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: 0.96 (0.16), residues: 2716 helix: 1.62 (0.35), residues: 226 sheet: 1.61 (0.17), residues: 878 loop : -0.03 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2731 TYR 0.012 0.001 TYR B1927 PHE 0.012 0.001 PHE A2122 TRP 0.010 0.001 TRP A2289 HIS 0.011 0.001 HIS A1955 Details of bonding type rmsd covalent geometry : bond 0.00275 (22741) covalent geometry : angle 0.50619 (30822) hydrogen bonds : bond 0.03541 ( 879) hydrogen bonds : angle 5.19259 ( 2859) link_ALPHA1-3 : bond 0.00992 ( 1) link_ALPHA1-3 : angle 1.18269 ( 3) link_BETA1-4 : bond 0.00709 ( 8) link_BETA1-4 : angle 1.88147 ( 24) link_NAG-ASN : bond 0.00258 ( 15) link_NAG-ASN : angle 2.71945 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 611 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 PRO cc_start: 0.8561 (Cg_endo) cc_final: 0.8338 (Cg_exo) REVERT: A 1105 VAL cc_start: 0.7835 (OUTLIER) cc_final: 0.7517 (p) REVERT: A 1144 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8049 (m) REVERT: A 1576 TYR cc_start: 0.8204 (m-80) cc_final: 0.7965 (m-80) REVERT: A 1584 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7715 (mm110) REVERT: A 1622 ILE cc_start: 0.8728 (mt) cc_final: 0.8465 (tt) REVERT: A 1640 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7846 (mmm-85) REVERT: A 1704 THR cc_start: 0.8149 (m) cc_final: 0.7819 (p) REVERT: A 1708 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8213 (mtm-85) REVERT: A 1723 SER cc_start: 0.8371 (p) cc_final: 0.8023 (m) REVERT: A 1819 GLU cc_start: 0.6919 (mp0) cc_final: 0.6664 (mp0) REVERT: A 1848 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8330 (pt) REVERT: A 1849 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7626 (mtt90) REVERT: A 1910 LYS cc_start: 0.8296 (mmtm) cc_final: 0.8073 (mmtm) REVERT: A 1975 TYR cc_start: 0.8586 (p90) cc_final: 0.8208 (p90) REVERT: A 2243 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8426 (tt) REVERT: A 2375 ASN cc_start: 0.7866 (p0) cc_final: 0.7582 (p0) REVERT: A 2566 MET cc_start: 0.7731 (tmm) cc_final: 0.7437 (tmm) REVERT: A 2591 SER cc_start: 0.8477 (p) cc_final: 0.8184 (p) REVERT: A 2623 ASP cc_start: 0.7149 (m-30) cc_final: 0.6576 (m-30) REVERT: A 2674 TYR cc_start: 0.8444 (m-80) cc_final: 0.7571 (m-80) REVERT: A 2687 ARG cc_start: 0.8387 (ttt-90) cc_final: 0.8022 (ttt-90) REVERT: A 2709 ARG cc_start: 0.7567 (mtp180) cc_final: 0.7364 (ttp-170) REVERT: A 2745 GLN cc_start: 0.7835 (mt0) cc_final: 0.7561 (tt0) REVERT: B 1086 THR cc_start: 0.7854 (m) cc_final: 0.7504 (p) REVERT: B 1622 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8476 (tp) REVERT: B 1646 ASP cc_start: 0.8273 (p0) cc_final: 0.7726 (p0) REVERT: B 1648 GLN cc_start: 0.7837 (tp40) cc_final: 0.7185 (mp10) REVERT: B 1723 SER cc_start: 0.8354 (p) cc_final: 0.8083 (m) REVERT: B 1765 ASN cc_start: 0.7657 (m110) cc_final: 0.7273 (m-40) REVERT: B 1802 SER cc_start: 0.8421 (m) cc_final: 0.8161 (p) REVERT: B 1848 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8306 (pt) REVERT: B 2107 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7804 (t) REVERT: B 2495 MET cc_start: 0.7277 (tmm) cc_final: 0.7033 (tmm) REVERT: B 2623 ASP cc_start: 0.7300 (m-30) cc_final: 0.6836 (m-30) REVERT: B 2674 TYR cc_start: 0.8379 (m-80) cc_final: 0.7556 (m-80) REVERT: B 2709 ARG cc_start: 0.7618 (mtp180) cc_final: 0.7400 (ttp-170) REVERT: B 2712 ARG cc_start: 0.7761 (mtp-110) cc_final: 0.7283 (mtp-110) REVERT: B 2745 GLN cc_start: 0.7814 (mt0) cc_final: 0.7539 (tt0) outliers start: 85 outliers final: 45 residues processed: 640 average time/residue: 0.6602 time to fit residues: 476.6844 Evaluate side-chains 645 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 592 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1705 ASN Chi-restraints excluded: chain A residue 1708 ARG Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2239 LEU Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2256 LYS Chi-restraints excluded: chain A residue 2471 ASP Chi-restraints excluded: chain A residue 2526 HIS Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 2537 VAL Chi-restraints excluded: chain A residue 2557 THR Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain A residue 2607 GLU Chi-restraints excluded: chain A residue 2690 ASP Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1643 LEU Chi-restraints excluded: chain B residue 1657 ASN Chi-restraints excluded: chain B residue 1686 SER Chi-restraints excluded: chain B residue 1696 ASP Chi-restraints excluded: chain B residue 1724 ILE Chi-restraints excluded: chain B residue 1739 VAL Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1861 THR Chi-restraints excluded: chain B residue 1916 SER Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1951 SER Chi-restraints excluded: chain B residue 2074 GLU Chi-restraints excluded: chain B residue 2107 VAL Chi-restraints excluded: chain B residue 2115 ILE Chi-restraints excluded: chain B residue 2233 SER Chi-restraints excluded: chain B residue 2252 ASP Chi-restraints excluded: chain B residue 2264 CYS Chi-restraints excluded: chain B residue 2526 HIS Chi-restraints excluded: chain B residue 2531 LEU Chi-restraints excluded: chain B residue 2557 THR Chi-restraints excluded: chain B residue 2607 GLU Chi-restraints excluded: chain B residue 2723 LYS Chi-restraints excluded: chain B residue 2753 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 252 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 213 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 260 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1756 GLN ** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1807 ASN A1955 HIS A2190 ASN A2226 HIS A2254 GLN A2310 HIS A2543 HIS A2660 ASN B1047 ASN B1705 ASN B1807 ASN B1939 GLN B1955 HIS B2146 HIS B2226 HIS B2660 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102762 restraints weight = 30053.960| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.67 r_work: 0.3243 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22765 Z= 0.127 Angle : 0.526 7.459 30894 Z= 0.278 Chirality : 0.044 0.248 3426 Planarity : 0.004 0.053 3941 Dihedral : 5.498 58.948 3561 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.92 % Allowed : 24.92 % Favored : 72.17 % 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: 1.02 (0.16), residues: 2716 helix: 1.67 (0.35), residues: 226 sheet: 1.54 (0.16), residues: 938 loop : 0.01 (0.17), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1817 TYR 0.013 0.001 TYR B2084 PHE 0.012 0.001 PHE A2122 TRP 0.010 0.001 TRP A1814 HIS 0.012 0.001 HIS A1955 Details of bonding type rmsd covalent geometry : bond 0.00290 (22741) covalent geometry : angle 0.51408 (30822) hydrogen bonds : bond 0.03519 ( 879) hydrogen bonds : angle 5.14604 ( 2859) link_ALPHA1-3 : bond 0.00934 ( 1) link_ALPHA1-3 : angle 1.08494 ( 3) link_BETA1-4 : bond 0.00685 ( 8) link_BETA1-4 : angle 1.83711 ( 24) link_NAG-ASN : bond 0.00258 ( 15) link_NAG-ASN : angle 2.68072 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 600 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 PRO cc_start: 0.8571 (Cg_endo) cc_final: 0.8348 (Cg_exo) REVERT: A 1105 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7510 (p) REVERT: A 1144 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8049 (m) REVERT: A 1576 TYR cc_start: 0.8213 (m-80) cc_final: 0.7978 (m-80) REVERT: A 1584 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7716 (mm110) REVERT: A 1622 ILE cc_start: 0.8742 (mt) cc_final: 0.8466 (tt) REVERT: A 1704 THR cc_start: 0.8122 (m) cc_final: 0.7804 (p) REVERT: A 1708 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8204 (mtm-85) REVERT: A 1723 SER cc_start: 0.8366 (p) cc_final: 0.8008 (m) REVERT: A 1819 GLU cc_start: 0.6899 (mp0) cc_final: 0.6645 (mp0) REVERT: A 1848 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8307 (pt) REVERT: A 1849 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7668 (mtt90) REVERT: A 1910 LYS cc_start: 0.8298 (mmtm) cc_final: 0.8084 (mmtm) REVERT: A 1975 TYR cc_start: 0.8550 (p90) cc_final: 0.8238 (p90) REVERT: A 2243 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8423 (tt) REVERT: A 2375 ASN cc_start: 0.7875 (p0) cc_final: 0.7597 (p0) REVERT: A 2566 MET cc_start: 0.7722 (tmm) cc_final: 0.7442 (tmm) REVERT: A 2591 SER cc_start: 0.8502 (p) cc_final: 0.8211 (p) REVERT: A 2623 ASP cc_start: 0.7175 (m-30) cc_final: 0.6652 (m-30) REVERT: A 2674 TYR cc_start: 0.8426 (m-80) cc_final: 0.7543 (m-80) REVERT: A 2687 ARG cc_start: 0.8380 (ttt-90) cc_final: 0.8050 (ttt-90) REVERT: A 2709 ARG cc_start: 0.7550 (mtp180) cc_final: 0.7349 (ttp-170) REVERT: A 2745 GLN cc_start: 0.7845 (mt0) cc_final: 0.7569 (tt0) REVERT: B 1086 THR cc_start: 0.7844 (m) cc_final: 0.7511 (p) REVERT: B 1622 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8476 (tp) REVERT: B 1646 ASP cc_start: 0.8264 (p0) cc_final: 0.7724 (p0) REVERT: B 1648 GLN cc_start: 0.7843 (tp40) cc_final: 0.7157 (mp10) REVERT: B 1765 ASN cc_start: 0.7666 (m110) cc_final: 0.7273 (m-40) REVERT: B 1802 SER cc_start: 0.8420 (m) cc_final: 0.8157 (p) REVERT: B 1848 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8299 (pt) REVERT: B 2107 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7845 (t) REVERT: B 2141 MET cc_start: 0.8597 (ptm) cc_final: 0.8381 (ppp) REVERT: B 2272 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8112 (mt-10) REVERT: B 2495 MET cc_start: 0.7303 (tmm) cc_final: 0.7042 (tmm) REVERT: B 2597 TYR cc_start: 0.8530 (m-80) cc_final: 0.8142 (m-80) REVERT: B 2623 ASP cc_start: 0.7329 (m-30) cc_final: 0.6872 (m-30) REVERT: B 2674 TYR cc_start: 0.8364 (m-80) cc_final: 0.7548 (m-80) REVERT: B 2687 ARG cc_start: 0.8494 (ttt-90) cc_final: 0.8238 (ttt-90) REVERT: B 2709 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7406 (ttp-170) REVERT: B 2712 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.7257 (mtp-110) REVERT: B 2745 GLN cc_start: 0.7799 (mt0) cc_final: 0.7527 (tt0) outliers start: 70 outliers final: 47 residues processed: 628 average time/residue: 0.5999 time to fit residues: 427.5486 Evaluate side-chains 639 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 584 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1705 ASN Chi-restraints excluded: chain A residue 1708 ARG Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 2115 ILE Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2239 LEU Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2256 LYS Chi-restraints excluded: chain A residue 2264 CYS Chi-restraints excluded: chain A residue 2471 ASP Chi-restraints excluded: chain A residue 2526 HIS Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 2534 GLU Chi-restraints excluded: chain A residue 2537 VAL Chi-restraints excluded: chain A residue 2557 THR Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain A residue 2607 GLU Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1643 LEU Chi-restraints excluded: chain B residue 1686 SER Chi-restraints excluded: chain B residue 1696 ASP Chi-restraints excluded: chain B residue 1739 VAL Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1950 SER Chi-restraints excluded: chain B residue 1951 SER Chi-restraints excluded: chain B residue 1958 THR Chi-restraints excluded: chain B residue 2044 MET Chi-restraints excluded: chain B residue 2074 GLU Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2107 VAL Chi-restraints excluded: chain B residue 2108 ASP Chi-restraints excluded: chain B residue 2115 ILE Chi-restraints excluded: chain B residue 2264 CYS Chi-restraints excluded: chain B residue 2526 HIS Chi-restraints excluded: chain B residue 2531 LEU Chi-restraints excluded: chain B residue 2557 THR Chi-restraints excluded: chain B residue 2607 GLU Chi-restraints excluded: chain B residue 2631 ILE Chi-restraints excluded: chain B residue 2723 LYS Chi-restraints excluded: chain B residue 2753 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 2 optimal weight: 0.0770 chunk 267 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 228 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1756 GLN ** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1807 ASN A1820 GLN A1955 HIS A2226 HIS A2254 GLN A2543 HIS A2660 ASN A2694 GLN B1047 ASN B1705 ASN B1807 ASN B1939 GLN B1955 HIS B2146 HIS B2190 ASN B2226 HIS B2660 ASN B2694 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102585 restraints weight = 30279.884| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.68 r_work: 0.3240 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22765 Z= 0.139 Angle : 0.539 7.774 30894 Z= 0.283 Chirality : 0.045 0.250 3426 Planarity : 0.004 0.053 3941 Dihedral : 5.490 57.286 3561 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.83 % Allowed : 25.21 % Favored : 71.96 % 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: 0.99 (0.16), residues: 2716 helix: 1.67 (0.35), residues: 226 sheet: 1.57 (0.16), residues: 912 loop : -0.02 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1817 TYR 0.013 0.001 TYR B1927 PHE 0.013 0.001 PHE A2122 TRP 0.009 0.001 TRP A2289 HIS 0.012 0.001 HIS A1955 Details of bonding type rmsd covalent geometry : bond 0.00321 (22741) covalent geometry : angle 0.52649 (30822) hydrogen bonds : bond 0.03558 ( 879) hydrogen bonds : angle 5.14821 ( 2859) link_ALPHA1-3 : bond 0.00811 ( 1) link_ALPHA1-3 : angle 1.02456 ( 3) link_BETA1-4 : bond 0.00682 ( 8) link_BETA1-4 : angle 1.85911 ( 24) link_NAG-ASN : bond 0.00260 ( 15) link_NAG-ASN : angle 2.71145 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 586 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 PRO cc_start: 0.8580 (Cg_endo) cc_final: 0.8355 (Cg_exo) REVERT: A 1105 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7516 (p) REVERT: A 1144 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8042 (m) REVERT: A 1584 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7714 (mm110) REVERT: A 1622 ILE cc_start: 0.8747 (mt) cc_final: 0.8472 (tt) REVERT: A 1704 THR cc_start: 0.8119 (m) cc_final: 0.7810 (p) REVERT: A 1708 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8209 (mtm-85) REVERT: A 1723 SER cc_start: 0.8367 (p) cc_final: 0.8015 (m) REVERT: A 1819 GLU cc_start: 0.6891 (mp0) cc_final: 0.6598 (mp0) REVERT: A 1848 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8312 (pt) REVERT: A 1849 ARG cc_start: 0.8215 (mtt90) cc_final: 0.7488 (mtt90) REVERT: A 1910 LYS cc_start: 0.8301 (mmtm) cc_final: 0.8084 (mmtm) REVERT: A 1975 TYR cc_start: 0.8534 (p90) cc_final: 0.8227 (p90) REVERT: A 2243 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8422 (tt) REVERT: A 2375 ASN cc_start: 0.7886 (p0) cc_final: 0.7609 (p0) REVERT: A 2566 MET cc_start: 0.7727 (tmm) cc_final: 0.7409 (tmm) REVERT: A 2591 SER cc_start: 0.8497 (p) cc_final: 0.8203 (p) REVERT: A 2623 ASP cc_start: 0.7161 (m-30) cc_final: 0.6634 (m-30) REVERT: A 2674 TYR cc_start: 0.8428 (m-80) cc_final: 0.7534 (m-80) REVERT: A 2687 ARG cc_start: 0.8368 (ttt-90) cc_final: 0.8042 (ttt-90) REVERT: A 2709 ARG cc_start: 0.7542 (mtp180) cc_final: 0.7335 (ttp-170) REVERT: A 2745 GLN cc_start: 0.7845 (mt0) cc_final: 0.7573 (tt0) REVERT: B 1086 THR cc_start: 0.7836 (m) cc_final: 0.7484 (p) REVERT: B 1622 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8485 (tp) REVERT: B 1646 ASP cc_start: 0.8266 (p0) cc_final: 0.7725 (p0) REVERT: B 1648 GLN cc_start: 0.7830 (tp40) cc_final: 0.7155 (mp10) REVERT: B 1765 ASN cc_start: 0.7674 (m110) cc_final: 0.7267 (m-40) REVERT: B 1802 SER cc_start: 0.8438 (m) cc_final: 0.8184 (p) REVERT: B 1813 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: B 1817 ARG cc_start: 0.8143 (ptm-80) cc_final: 0.7889 (ptm-80) REVERT: B 1819 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6819 (mt-10) REVERT: B 1848 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8295 (pt) REVERT: B 2107 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7784 (t) REVERT: B 2272 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8120 (mt-10) REVERT: B 2495 MET cc_start: 0.7314 (tmm) cc_final: 0.7068 (tmm) REVERT: B 2597 TYR cc_start: 0.8484 (m-80) cc_final: 0.8134 (m-80) REVERT: B 2623 ASP cc_start: 0.7334 (m-30) cc_final: 0.6877 (m-30) REVERT: B 2674 TYR cc_start: 0.8369 (m-80) cc_final: 0.7550 (m-80) REVERT: B 2687 ARG cc_start: 0.8482 (ttt-90) cc_final: 0.8237 (ttt-90) REVERT: B 2709 ARG cc_start: 0.7618 (mtp180) cc_final: 0.7390 (ttp-170) REVERT: B 2712 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7274 (mtp-110) REVERT: B 2745 GLN cc_start: 0.7798 (mt0) cc_final: 0.7526 (tt0) outliers start: 68 outliers final: 49 residues processed: 613 average time/residue: 0.6631 time to fit residues: 459.2383 Evaluate side-chains 642 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 584 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1705 ASN Chi-restraints excluded: chain A residue 1708 ARG Chi-restraints excluded: chain A residue 1722 LYS Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1848 ILE Chi-restraints excluded: chain A residue 2053 SER Chi-restraints excluded: chain A residue 2115 ILE Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2239 LEU Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2256 LYS Chi-restraints excluded: chain A residue 2471 ASP Chi-restraints excluded: chain A residue 2526 HIS Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 2534 GLU Chi-restraints excluded: chain A residue 2537 VAL Chi-restraints excluded: chain A residue 2557 THR Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain A residue 2607 GLU Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1643 LEU Chi-restraints excluded: chain B residue 1657 ASN Chi-restraints excluded: chain B residue 1686 SER Chi-restraints excluded: chain B residue 1696 ASP Chi-restraints excluded: chain B residue 1739 VAL Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1950 SER Chi-restraints excluded: chain B residue 1951 SER Chi-restraints excluded: chain B residue 1958 THR Chi-restraints excluded: chain B residue 1967 MET Chi-restraints excluded: chain B residue 2014 LYS Chi-restraints excluded: chain B residue 2044 MET Chi-restraints excluded: chain B residue 2074 GLU Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2107 VAL Chi-restraints excluded: chain B residue 2108 ASP Chi-restraints excluded: chain B residue 2115 ILE Chi-restraints excluded: chain B residue 2237 MET Chi-restraints excluded: chain B residue 2264 CYS Chi-restraints excluded: chain B residue 2526 HIS Chi-restraints excluded: chain B residue 2531 LEU Chi-restraints excluded: chain B residue 2557 THR Chi-restraints excluded: chain B residue 2607 GLU Chi-restraints excluded: chain B residue 2723 LYS Chi-restraints excluded: chain B residue 2753 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 117 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1641 HIS A1756 GLN ** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1807 ASN A1955 HIS A2087 HIS A2226 HIS A2254 GLN A2292 GLN A2543 HIS A2660 ASN A2694 GLN B1047 ASN B1807 ASN B1939 GLN B1955 HIS B2087 HIS B2146 HIS B2190 ASN B2226 HIS B2660 ASN B2694 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100610 restraints weight = 30316.899| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.67 r_work: 0.3207 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 22765 Z= 0.281 Angle : 0.634 7.962 30894 Z= 0.330 Chirality : 0.049 0.284 3426 Planarity : 0.004 0.055 3941 Dihedral : 5.793 56.354 3561 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.96 % Allowed : 25.29 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2716 helix: 1.41 (0.34), residues: 228 sheet: 1.51 (0.16), residues: 914 loop : -0.07 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1817 TYR 0.019 0.002 TYR A2283 PHE 0.024 0.002 PHE B2122 TRP 0.015 0.002 TRP B2430 HIS 0.011 0.002 HIS A1955 Details of bonding type rmsd covalent geometry : bond 0.00670 (22741) covalent geometry : angle 0.61855 (30822) hydrogen bonds : bond 0.04349 ( 879) hydrogen bonds : angle 5.44895 ( 2859) link_ALPHA1-3 : bond 0.00882 ( 1) link_ALPHA1-3 : angle 0.96406 ( 3) link_BETA1-4 : bond 0.00726 ( 8) link_BETA1-4 : angle 2.23146 ( 24) link_NAG-ASN : bond 0.00435 ( 15) link_NAG-ASN : angle 3.35294 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5432 Ramachandran restraints generated. 2716 Oldfield, 0 Emsley, 2716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 584 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.7868 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 1144 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8058 (m) REVERT: A 1584 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7704 (mm110) REVERT: A 1622 ILE cc_start: 0.8736 (mt) cc_final: 0.8446 (tt) REVERT: A 1640 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7861 (mmm-85) REVERT: A 1704 THR cc_start: 0.8173 (m) cc_final: 0.7880 (p) REVERT: A 1723 SER cc_start: 0.8397 (p) cc_final: 0.8091 (m) REVERT: A 1819 GLU cc_start: 0.6910 (mp0) cc_final: 0.6638 (mp0) REVERT: A 1910 LYS cc_start: 0.8315 (mmtm) cc_final: 0.8101 (mmtm) REVERT: A 1975 TYR cc_start: 0.8532 (p90) cc_final: 0.8228 (p90) REVERT: A 2168 MET cc_start: 0.8983 (ttp) cc_final: 0.8693 (ttm) REVERT: A 2243 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8463 (tt) REVERT: A 2375 ASN cc_start: 0.7925 (p0) cc_final: 0.7662 (p0) REVERT: A 2566 MET cc_start: 0.7748 (tmm) cc_final: 0.7410 (tmm) REVERT: A 2623 ASP cc_start: 0.7222 (m-30) cc_final: 0.6665 (m-30) REVERT: A 2674 TYR cc_start: 0.8469 (m-80) cc_final: 0.7612 (m-80) REVERT: A 2687 ARG cc_start: 0.8418 (ttt-90) cc_final: 0.8036 (ttt-90) REVERT: A 2709 ARG cc_start: 0.7550 (mtp180) cc_final: 0.7347 (ttp-170) REVERT: A 2745 GLN cc_start: 0.7912 (mt0) cc_final: 0.7632 (tt0) REVERT: B 1086 THR cc_start: 0.7844 (m) cc_final: 0.7479 (p) REVERT: B 1105 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7645 (p) REVERT: B 1646 ASP cc_start: 0.8282 (p0) cc_final: 0.7678 (p0) REVERT: B 1648 GLN cc_start: 0.7871 (tp40) cc_final: 0.7210 (mp10) REVERT: B 1723 SER cc_start: 0.8388 (p) cc_final: 0.8118 (m) REVERT: B 1765 ASN cc_start: 0.7710 (m110) cc_final: 0.7306 (m-40) REVERT: B 1802 SER cc_start: 0.8434 (m) cc_final: 0.8189 (p) REVERT: B 1813 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: B 1819 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6897 (mt-10) REVERT: B 1848 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8442 (pt) REVERT: B 2077 MET cc_start: 0.8155 (mmt) cc_final: 0.5724 (mmt) REVERT: B 2107 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7826 (t) REVERT: B 2495 MET cc_start: 0.7348 (tmm) cc_final: 0.7073 (tmm) REVERT: B 2623 ASP cc_start: 0.7321 (m-30) cc_final: 0.6818 (m-30) REVERT: B 2674 TYR cc_start: 0.8425 (m-80) cc_final: 0.7635 (m-80) REVERT: B 2709 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7453 (ttp-170) REVERT: B 2712 ARG cc_start: 0.7786 (mtp-110) cc_final: 0.7312 (mtp-110) REVERT: B 2745 GLN cc_start: 0.7841 (mt0) cc_final: 0.7574 (tt0) outliers start: 71 outliers final: 47 residues processed: 608 average time/residue: 0.7302 time to fit residues: 502.8532 Evaluate side-chains 632 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 578 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1705 ASN Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 2115 ILE Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2239 LEU Chi-restraints excluded: chain A residue 2243 LEU Chi-restraints excluded: chain A residue 2264 CYS Chi-restraints excluded: chain A residue 2471 ASP Chi-restraints excluded: chain A residue 2526 HIS Chi-restraints excluded: chain A residue 2531 LEU Chi-restraints excluded: chain A residue 2534 GLU Chi-restraints excluded: chain A residue 2537 VAL Chi-restraints excluded: chain A residue 2557 THR Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain A residue 2607 GLU Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1038 THR Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1112 LYS Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1643 LEU Chi-restraints excluded: chain B residue 1686 SER Chi-restraints excluded: chain B residue 1696 ASP Chi-restraints excluded: chain B residue 1739 VAL Chi-restraints excluded: chain B residue 1813 GLU Chi-restraints excluded: chain B residue 1848 ILE Chi-restraints excluded: chain B residue 1859 LYS Chi-restraints excluded: chain B residue 1924 VAL Chi-restraints excluded: chain B residue 1950 SER Chi-restraints excluded: chain B residue 1951 SER Chi-restraints excluded: chain B residue 1958 THR Chi-restraints excluded: chain B residue 2014 LYS Chi-restraints excluded: chain B residue 2074 GLU Chi-restraints excluded: chain B residue 2107 VAL Chi-restraints excluded: chain B residue 2115 ILE Chi-restraints excluded: chain B residue 2233 SER Chi-restraints excluded: chain B residue 2237 MET Chi-restraints excluded: chain B residue 2252 ASP Chi-restraints excluded: chain B residue 2264 CYS Chi-restraints excluded: chain B residue 2526 HIS Chi-restraints excluded: chain B residue 2531 LEU Chi-restraints excluded: chain B residue 2557 THR Chi-restraints excluded: chain B residue 2580 SER Chi-restraints excluded: chain B residue 2607 GLU Chi-restraints excluded: chain B residue 2631 ILE Chi-restraints excluded: chain B residue 2723 LYS Chi-restraints excluded: chain B residue 2753 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 106 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1756 GLN ** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1807 ASN A1955 HIS A2226 HIS A2254 GLN A2543 HIS A2660 ASN A2694 GLN B1047 ASN B1705 ASN B1807 ASN B1939 GLN B1955 HIS B2146 HIS B2226 HIS B2292 GLN B2660 ASN B2694 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.118995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102726 restraints weight = 30128.337| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.67 r_work: 0.3242 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22765 Z= 0.126 Angle : 0.540 8.004 30894 Z= 0.285 Chirality : 0.045 0.249 3426 Planarity : 0.004 0.054 3941 Dihedral : 5.524 57.554 3561 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.46 % Allowed : 26.08 % Favored : 71.46 % 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: 0.92 (0.16), residues: 2716 helix: 1.62 (0.35), residues: 226 sheet: 1.55 (0.16), residues: 878 loop : -0.05 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1817 TYR 0.018 0.001 TYR B2084 PHE 0.012 0.001 PHE A2122 TRP 0.011 0.001 TRP A2289 HIS 0.012 0.001 HIS A1955 Details of bonding type rmsd covalent geometry : bond 0.00290 (22741) covalent geometry : angle 0.52781 (30822) hydrogen bonds : bond 0.03533 ( 879) hydrogen bonds : angle 5.21660 ( 2859) link_ALPHA1-3 : bond 0.00910 ( 1) link_ALPHA1-3 : angle 1.17535 ( 3) link_BETA1-4 : bond 0.00669 ( 8) link_BETA1-4 : angle 1.83210 ( 24) link_NAG-ASN : bond 0.00258 ( 15) link_NAG-ASN : angle 2.72112 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11044.16 seconds wall clock time: 188 minutes 15.78 seconds (11295.78 seconds total)