Starting phenix.real_space_refine on Fri May 23 20:30:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oxo_17266/05_2025/8oxo_17266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxo_17266/05_2025/8oxo_17266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oxo_17266/05_2025/8oxo_17266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxo_17266/05_2025/8oxo_17266.map" model { file = "/net/cci-nas-00/data/ceres_data/8oxo_17266/05_2025/8oxo_17266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxo_17266/05_2025/8oxo_17266.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 168 5.16 5 C 15224 2.51 5 N 4098 2.21 5 O 4486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23986 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "A" Number of atoms: 11907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1476, 11907 Classifications: {'peptide': 1476} Link IDs: {'PTRANS': 43, 'TRANS': 1432} Chain breaks: 7 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "B" Number of atoms: 11907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1476, 11907 Classifications: {'peptide': 1476} Link IDs: {'PTRANS': 43, 'TRANS': 1432} Chain breaks: 7 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3199 SG CYS A1899 69.579 116.260 101.961 1.00257.79 S ATOM 3205 SG CYS A1900 65.715 115.004 100.028 1.00246.38 S ATOM 15159 SG CYS B1899 27.391 58.820 101.350 1.00246.96 S ATOM 15165 SG CYS B1900 31.644 60.092 100.636 1.00243.40 S Time building chain proxies: 13.96, per 1000 atoms: 0.58 Number of scatterers: 23986 At special positions: 0 Unit cell: (98.294, 175.938, 120.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 168 16.00 P 6 15.00 Mg 2 11.99 O 4486 8.00 N 4098 7.00 C 15224 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 Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3103 " pdb="ZN ZN A3103 " - pdb=" NE2 HIS A1876 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1899 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1900 " pdb=" ZN B3103 " pdb="ZN ZN B3103 " - pdb=" NE2 HIS B1876 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1899 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1900 " 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5660 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 6 sheets defined 74.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 1463 through 1478 Processing helix chain 'A' and resid 1491 through 1509 Processing helix chain 'A' and resid 1517 through 1524 removed outlier: 3.618A pdb=" N LEU A1524 " --> pdb=" O ILE A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1529 removed outlier: 3.957A pdb=" N TYR A1529 " --> pdb=" O PRO A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1548 Processing helix chain 'A' and resid 1552 through 1561 removed outlier: 4.537A pdb=" N ILE A1557 " --> pdb=" O GLU A1553 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR A1558 " --> pdb=" O ASN A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1570 No H-bonds generated for 'chain 'A' and resid 1568 through 1570' Processing helix chain 'A' and resid 1571 through 1583 removed outlier: 3.579A pdb=" N LYS A1580 " --> pdb=" O ILE A1576 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A1581 " --> pdb=" O THR A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1604 Processing helix chain 'A' and resid 1607 through 1609 No H-bonds generated for 'chain 'A' and resid 1607 through 1609' Processing helix chain 'A' and resid 1610 through 1624 Processing helix chain 'A' and resid 1627 through 1635 removed outlier: 3.730A pdb=" N ILE A1631 " --> pdb=" O GLN A1627 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET A1632 " --> pdb=" O MET A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1641 Processing helix chain 'A' and resid 1642 through 1658 Processing helix chain 'A' and resid 1659 through 1661 No H-bonds generated for 'chain 'A' and resid 1659 through 1661' Processing helix chain 'A' and resid 1663 through 1677 removed outlier: 3.669A pdb=" N VAL A1667 " --> pdb=" O GLY A1663 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A1669 " --> pdb=" O LYS A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1703 removed outlier: 3.524A pdb=" N THR A1697 " --> pdb=" O ASP A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1722 Processing helix chain 'A' and resid 1726 through 1742 removed outlier: 3.680A pdb=" N ARG A1730 " --> pdb=" O CYS A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1754 Processing helix chain 'A' and resid 1759 through 1765 Processing helix chain 'A' and resid 1766 through 1768 No H-bonds generated for 'chain 'A' and resid 1766 through 1768' Processing helix chain 'A' and resid 1785 through 1789 removed outlier: 3.683A pdb=" N GLY A1788 " --> pdb=" O PRO A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1796 removed outlier: 3.608A pdb=" N TRP A1795 " --> pdb=" O ASP A1791 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A1796 " --> pdb=" O ILE A1792 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1791 through 1796' Processing helix chain 'A' and resid 1801 through 1816 removed outlier: 3.707A pdb=" N SER A1816 " --> pdb=" O ALA A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1827 through 1832 Processing helix chain 'A' and resid 1834 through 1852 removed outlier: 3.795A pdb=" N CYS A1838 " --> pdb=" O LYS A1834 " (cutoff:3.500A) Proline residue: A1843 - end of helix removed outlier: 3.734A pdb=" N GLN A1852 " --> pdb=" O ASP A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1874 removed outlier: 3.720A pdb=" N LEU A1861 " --> pdb=" O SER A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1902 through 1918 removed outlier: 3.880A pdb=" N GLN A1906 " --> pdb=" O ASP A1902 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1926 through 1931 Processing helix chain 'A' and resid 1937 through 1948 removed outlier: 4.049A pdb=" N VAL A1941 " --> pdb=" O ASN A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1974 Processing helix chain 'A' and resid 1985 through 1997 Processing helix chain 'A' and resid 2000 through 2012 Processing helix chain 'A' and resid 2028 through 2039 Processing helix chain 'A' and resid 2041 through 2052 removed outlier: 3.546A pdb=" N VAL A2047 " --> pdb=" O GLY A2043 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2071 removed outlier: 3.533A pdb=" N GLN A2061 " --> pdb=" O SER A2057 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA A2062 " --> pdb=" O SER A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2074 through 2088 Processing helix chain 'A' and resid 2092 through 2106 Processing helix chain 'A' and resid 2123 through 2137 Processing helix chain 'A' and resid 2140 through 2161 removed outlier: 4.058A pdb=" N ARG A2161 " --> pdb=" O GLU A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2189 removed outlier: 4.268A pdb=" N THR A2172 " --> pdb=" O SER A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2212 Processing helix chain 'A' and resid 2216 through 2237 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2241 through 2264 removed outlier: 3.952A pdb=" N GLU A2245 " --> pdb=" O ASN A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2282 removed outlier: 3.501A pdb=" N GLU A2272 " --> pdb=" O THR A2268 " (cutoff:3.500A) Processing helix chain 'A' and resid 2289 through 2302 removed outlier: 4.281A pdb=" N LEU A2293 " --> pdb=" O SER A2289 " (cutoff:3.500A) Processing helix chain 'A' and resid 2304 through 2322 removed outlier: 3.522A pdb=" N ALA A2321 " --> pdb=" O LYS A2317 " (cutoff:3.500A) Processing helix chain 'A' and resid 2327 through 2349 Processing helix chain 'A' and resid 2352 through 2371 removed outlier: 3.710A pdb=" N ILE A2356 " --> pdb=" O ASN A2352 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU A2362 " --> pdb=" O GLN A2358 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYS A2363 " --> pdb=" O THR A2359 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A2371 " --> pdb=" O VAL A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2407 removed outlier: 4.141A pdb=" N GLY A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2430 Processing helix chain 'A' and resid 2435 through 2476 removed outlier: 4.229A pdb=" N SER A2476 " --> pdb=" O ASN A2472 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2482 No H-bonds generated for 'chain 'A' and resid 2480 through 2482' Processing helix chain 'A' and resid 2483 through 2494 Processing helix chain 'A' and resid 2497 through 2507 removed outlier: 3.581A pdb=" N ASN A2501 " --> pdb=" O VAL A2497 " (cutoff:3.500A) Processing helix chain 'A' and resid 2508 through 2511 Processing helix chain 'A' and resid 2512 through 2516 removed outlier: 3.749A pdb=" N LYS A2515 " --> pdb=" O PRO A2512 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A2516 " --> pdb=" O THR A2513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2512 through 2516' Processing helix chain 'A' and resid 2519 through 2525 Processing helix chain 'A' and resid 2534 through 2552 removed outlier: 3.878A pdb=" N HIS A2538 " --> pdb=" O GLY A2534 " (cutoff:3.500A) Processing helix chain 'A' and resid 2553 through 2555 No H-bonds generated for 'chain 'A' and resid 2553 through 2555' Processing helix chain 'A' and resid 2556 through 2565 Processing helix chain 'A' and resid 2567 through 2573 Processing helix chain 'A' and resid 2592 through 2613 removed outlier: 3.799A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2613 through 2633 Processing helix chain 'A' and resid 2635 through 2639 removed outlier: 3.830A pdb=" N LYS A2639 " --> pdb=" O THR A2636 " (cutoff:3.500A) Processing helix chain 'A' and resid 2651 through 2656 removed outlier: 4.062A pdb=" N LYS A2655 " --> pdb=" O GLN A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2722 through 2742 Processing helix chain 'A' and resid 2742 through 2749 removed outlier: 3.535A pdb=" N LYS A2747 " --> pdb=" O THR A2743 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A2748 " --> pdb=" O GLU A2744 " (cutoff:3.500A) Processing helix chain 'A' and resid 2776 through 2781 Processing helix chain 'A' and resid 2786 through 2792 Processing helix chain 'A' and resid 2797 through 2809 Processing helix chain 'A' and resid 2812 through 2826 Processing helix chain 'A' and resid 2830 through 2832 No H-bonds generated for 'chain 'A' and resid 2830 through 2832' Processing helix chain 'A' and resid 2833 through 2839 Processing helix chain 'A' and resid 2841 through 2867 Processing helix chain 'A' and resid 2911 through 2918 Processing helix chain 'A' and resid 2925 through 2940 Processing helix chain 'A' and resid 2941 through 2950 Processing helix chain 'A' and resid 3003 through 3019 Processing helix chain 'A' and resid 3027 through 3041 Processing helix chain 'A' and resid 3041 through 3047 removed outlier: 3.870A pdb=" N ARG A3047 " --> pdb=" O LYS A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3049 through 3053 Processing helix chain 'B' and resid 1463 through 1478 Processing helix chain 'B' and resid 1491 through 1509 Processing helix chain 'B' and resid 1517 through 1525 removed outlier: 3.590A pdb=" N LEU B1524 " --> pdb=" O ILE B1520 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B1525 " --> pdb=" O VAL B1521 " (cutoff:3.500A) Processing helix chain 'B' and resid 1526 through 1529 removed outlier: 3.984A pdb=" N TYR B1529 " --> pdb=" O PRO B1526 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1526 through 1529' Processing helix chain 'B' and resid 1531 through 1548 Processing helix chain 'B' and resid 1552 through 1561 removed outlier: 4.486A pdb=" N ILE B1557 " --> pdb=" O GLU B1553 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B1558 " --> pdb=" O ASN B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1568 through 1570 No H-bonds generated for 'chain 'B' and resid 1568 through 1570' Processing helix chain 'B' and resid 1571 through 1583 removed outlier: 3.842A pdb=" N ILE B1581 " --> pdb=" O THR B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1589 through 1604 Processing helix chain 'B' and resid 1606 through 1609 removed outlier: 3.544A pdb=" N THR B1609 " --> pdb=" O LEU B1606 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1606 through 1609' Processing helix chain 'B' and resid 1610 through 1624 Processing helix chain 'B' and resid 1627 through 1635 removed outlier: 3.771A pdb=" N ILE B1631 " --> pdb=" O GLN B1627 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET B1632 " --> pdb=" O MET B1628 " (cutoff:3.500A) Processing helix chain 'B' and resid 1638 through 1641 Processing helix chain 'B' and resid 1642 through 1658 Processing helix chain 'B' and resid 1659 through 1661 No H-bonds generated for 'chain 'B' and resid 1659 through 1661' Processing helix chain 'B' and resid 1663 through 1677 removed outlier: 3.679A pdb=" N VAL B1667 " --> pdb=" O GLY B1663 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B1669 " --> pdb=" O LYS B1665 " (cutoff:3.500A) Processing helix chain 'B' and resid 1693 through 1703 removed outlier: 3.522A pdb=" N THR B1697 " --> pdb=" O ASP B1693 " (cutoff:3.500A) Processing helix chain 'B' and resid 1705 through 1721 Processing helix chain 'B' and resid 1726 through 1742 removed outlier: 3.695A pdb=" N ARG B1730 " --> pdb=" O CYS B1726 " (cutoff:3.500A) Processing helix chain 'B' and resid 1743 through 1754 Processing helix chain 'B' and resid 1759 through 1765 Processing helix chain 'B' and resid 1766 through 1768 No H-bonds generated for 'chain 'B' and resid 1766 through 1768' Processing helix chain 'B' and resid 1785 through 1789 removed outlier: 3.669A pdb=" N GLY B1788 " --> pdb=" O PRO B1785 " (cutoff:3.500A) Processing helix chain 'B' and resid 1791 through 1796 removed outlier: 3.513A pdb=" N TRP B1795 " --> pdb=" O ASP B1791 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B1796 " --> pdb=" O ILE B1792 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1791 through 1796' Processing helix chain 'B' and resid 1801 through 1816 removed outlier: 3.661A pdb=" N SER B1816 " --> pdb=" O ALA B1812 " (cutoff:3.500A) Processing helix chain 'B' and resid 1827 through 1832 Processing helix chain 'B' and resid 1834 through 1852 removed outlier: 3.759A pdb=" N CYS B1838 " --> pdb=" O LYS B1834 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B1839 " --> pdb=" O THR B1835 " (cutoff:3.500A) Proline residue: B1843 - end of helix removed outlier: 3.782A pdb=" N GLN B1852 " --> pdb=" O ASP B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1856 through 1875 removed outlier: 3.706A pdb=" N LEU B1861 " --> pdb=" O SER B1857 " (cutoff:3.500A) Processing helix chain 'B' and resid 1902 through 1918 removed outlier: 3.747A pdb=" N GLN B1906 " --> pdb=" O ASP B1902 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B1918 " --> pdb=" O ASP B1914 " (cutoff:3.500A) Processing helix chain 'B' and resid 1926 through 1931 Processing helix chain 'B' and resid 1937 through 1948 removed outlier: 4.332A pdb=" N VAL B1941 " --> pdb=" O ASN B1937 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1974 Processing helix chain 'B' and resid 1985 through 1997 Processing helix chain 'B' and resid 2000 through 2012 Processing helix chain 'B' and resid 2028 through 2039 Processing helix chain 'B' and resid 2041 through 2052 removed outlier: 3.618A pdb=" N VAL B2047 " --> pdb=" O GLY B2043 " (cutoff:3.500A) Processing helix chain 'B' and resid 2056 through 2071 removed outlier: 3.556A pdb=" N GLN B2061 " --> pdb=" O SER B2057 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA B2062 " --> pdb=" O SER B2058 " (cutoff:3.500A) Processing helix chain 'B' and resid 2074 through 2088 Processing helix chain 'B' and resid 2092 through 2106 Processing helix chain 'B' and resid 2123 through 2137 Processing helix chain 'B' and resid 2139 through 2161 removed outlier: 4.061A pdb=" N ARG B2161 " --> pdb=" O GLU B2157 " (cutoff:3.500A) Processing helix chain 'B' and resid 2168 through 2189 removed outlier: 4.272A pdb=" N THR B2172 " --> pdb=" O SER B2168 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2212 Processing helix chain 'B' and resid 2216 through 2237 Proline residue: B2222 - end of helix Processing helix chain 'B' and resid 2241 through 2264 removed outlier: 3.937A pdb=" N GLU B2245 " --> pdb=" O ASN B2241 " (cutoff:3.500A) Processing helix chain 'B' and resid 2268 through 2282 removed outlier: 3.502A pdb=" N GLU B2272 " --> pdb=" O THR B2268 " (cutoff:3.500A) Processing helix chain 'B' and resid 2290 through 2302 removed outlier: 3.540A pdb=" N GLU B2294 " --> pdb=" O GLU B2290 " (cutoff:3.500A) Processing helix chain 'B' and resid 2304 through 2322 removed outlier: 3.549A pdb=" N ALA B2321 " --> pdb=" O LYS B2317 " (cutoff:3.500A) Processing helix chain 'B' and resid 2327 through 2349 Processing helix chain 'B' and resid 2352 through 2371 removed outlier: 3.705A pdb=" N ILE B2356 " --> pdb=" O ASN B2352 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B2358 " --> pdb=" O ALA B2354 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU B2362 " --> pdb=" O GLN B2358 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS B2363 " --> pdb=" O THR B2359 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B2371 " --> pdb=" O VAL B2367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2376 through 2406 removed outlier: 4.146A pdb=" N GLY B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) Processing helix chain 'B' and resid 2407 through 2430 Processing helix chain 'B' and resid 2435 through 2476 removed outlier: 4.213A pdb=" N SER B2476 " --> pdb=" O ASN B2472 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2482 No H-bonds generated for 'chain 'B' and resid 2480 through 2482' Processing helix chain 'B' and resid 2483 through 2494 Processing helix chain 'B' and resid 2497 through 2507 removed outlier: 3.584A pdb=" N ASN B2501 " --> pdb=" O VAL B2497 " (cutoff:3.500A) Processing helix chain 'B' and resid 2508 through 2511 Processing helix chain 'B' and resid 2512 through 2516 removed outlier: 3.729A pdb=" N LYS B2515 " --> pdb=" O PRO B2512 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B2516 " --> pdb=" O THR B2513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2512 through 2516' Processing helix chain 'B' and resid 2519 through 2525 Processing helix chain 'B' and resid 2534 through 2552 removed outlier: 3.922A pdb=" N HIS B2538 " --> pdb=" O GLY B2534 " (cutoff:3.500A) Processing helix chain 'B' and resid 2553 through 2555 No H-bonds generated for 'chain 'B' and resid 2553 through 2555' Processing helix chain 'B' and resid 2556 through 2565 Processing helix chain 'B' and resid 2567 through 2573 Processing helix chain 'B' and resid 2592 through 2613 removed outlier: 3.822A pdb=" N ARG B2612 " --> pdb=" O THR B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2613 through 2633 Processing helix chain 'B' and resid 2635 through 2639 removed outlier: 3.830A pdb=" N LYS B2639 " --> pdb=" O THR B2636 " (cutoff:3.500A) Processing helix chain 'B' and resid 2651 through 2656 removed outlier: 4.065A pdb=" N LYS B2655 " --> pdb=" O GLN B2651 " (cutoff:3.500A) Processing helix chain 'B' and resid 2722 through 2742 Processing helix chain 'B' and resid 2742 through 2749 removed outlier: 3.619A pdb=" N LYS B2747 " --> pdb=" O THR B2743 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B2748 " --> pdb=" O GLU B2744 " (cutoff:3.500A) Processing helix chain 'B' and resid 2776 through 2781 Processing helix chain 'B' and resid 2786 through 2792 Processing helix chain 'B' and resid 2797 through 2809 Processing helix chain 'B' and resid 2812 through 2826 Processing helix chain 'B' and resid 2830 through 2832 No H-bonds generated for 'chain 'B' and resid 2830 through 2832' Processing helix chain 'B' and resid 2833 through 2839 Processing helix chain 'B' and resid 2841 through 2867 Processing helix chain 'B' and resid 2911 through 2917 Processing helix chain 'B' and resid 2921 through 2924 removed outlier: 3.643A pdb=" N GLU B2924 " --> pdb=" O THR B2921 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2921 through 2924' Processing helix chain 'B' and resid 2925 through 2940 removed outlier: 3.686A pdb=" N ARG B2929 " --> pdb=" O GLY B2925 " (cutoff:3.500A) Processing helix chain 'B' and resid 2941 through 2950 Processing helix chain 'B' and resid 3003 through 3019 Processing helix chain 'B' and resid 3027 through 3041 Processing helix chain 'B' and resid 3041 through 3047 removed outlier: 3.893A pdb=" N ARG B3047 " --> pdb=" O LYS B3043 " (cutoff:3.500A) Processing helix chain 'B' and resid 3049 through 3053 Processing sheet with id=AA1, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 7.023A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2645 through 2646 removed outlier: 7.023A pdb=" N GLU A2689 " --> pdb=" O ASP A2703 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP A2703 " --> pdb=" O GLU A2689 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A2765 " --> pdb=" O LYS A2717 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id=AA4, first strand: chain 'B' and resid 2645 through 2646 removed outlier: 7.012A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP B2703 " --> pdb=" O GLU B2689 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2645 through 2646 removed outlier: 7.012A pdb=" N GLU B2689 " --> pdb=" O ASP B2703 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP B2703 " --> pdb=" O GLU B2689 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B2765 " --> pdb=" O LYS B2717 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2773 through 2775 1506 hydrogen bonds defined for protein. 4461 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: 9.27 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7845 1.34 - 1.46: 4837 1.46 - 1.58: 11472 1.58 - 1.69: 10 1.69 - 1.81: 256 Bond restraints: 24420 Sorted by residual: bond pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O3A ANP B3101 " pdb=" PB ANP B3101 " ideal model delta sigma weight residual 1.700 1.624 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O5' ANP A3101 " pdb=" PA ANP A3101 " ideal model delta sigma weight residual 1.655 1.595 0.060 2.00e-02 2.50e+03 8.92e+00 ... (remaining 24415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 32797 2.55 - 5.10: 164 5.10 - 7.65: 15 7.65 - 10.20: 3 10.20 - 12.75: 3 Bond angle restraints: 32982 Sorted by residual: angle pdb=" PA ANP B3101 " pdb=" O3A ANP B3101 " pdb=" PB ANP B3101 " ideal model delta sigma weight residual 125.41 138.16 -12.75 3.00e+00 1.11e-01 1.81e+01 angle pdb=" O1B ANP A3101 " pdb=" PB ANP A3101 " pdb=" O3A ANP A3101 " ideal model delta sigma weight residual 103.40 114.53 -11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" O1B ANP B3101 " pdb=" PB ANP B3101 " pdb=" O3A ANP B3101 " ideal model delta sigma weight residual 103.40 114.44 -11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C ILE B1752 " pdb=" N TYR B1753 " pdb=" CA TYR B1753 " ideal model delta sigma weight residual 121.18 127.82 -6.64 1.98e+00 2.55e-01 1.12e+01 angle pdb=" C ILE A1752 " pdb=" N TYR A1753 " pdb=" CA TYR A1753 " ideal model delta sigma weight residual 121.18 127.60 -6.42 1.98e+00 2.55e-01 1.05e+01 ... (remaining 32977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 14024 24.39 - 48.78: 787 48.78 - 73.17: 89 73.17 - 97.57: 26 97.57 - 121.96: 2 Dihedral angle restraints: 14928 sinusoidal: 6220 harmonic: 8708 Sorted by residual: dihedral pdb=" O1A ANP B3101 " pdb=" O3A ANP B3101 " pdb=" PA ANP B3101 " pdb=" PB ANP B3101 " ideal model delta sinusoidal sigma weight residual 83.11 -38.85 121.96 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" O1A ANP A3101 " pdb=" O3A ANP A3101 " pdb=" PA ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sinusoidal sigma weight residual 83.11 -38.66 121.77 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CA ASP A2003 " pdb=" CB ASP A2003 " pdb=" CG ASP A2003 " pdb=" OD1 ASP A2003 " ideal model delta sinusoidal sigma weight residual -30.00 -87.56 57.56 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 14925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3278 0.055 - 0.110: 428 0.110 - 0.166: 28 0.166 - 0.221: 0 0.221 - 0.276: 2 Chirality restraints: 3736 Sorted by residual: chirality pdb=" C3' ANP A3101 " pdb=" C2' ANP A3101 " pdb=" C4' ANP A3101 " pdb=" O3' ANP A3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ANP B3101 " pdb=" C2' ANP B3101 " pdb=" C4' ANP B3101 " pdb=" O3' ANP B3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ILE A1999 " pdb=" N ILE A1999 " pdb=" C ILE A1999 " pdb=" CB ILE A1999 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 3733 not shown) Planarity restraints: 4176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B1565 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO B1566 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B1566 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B1566 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B3006 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C ALA B3006 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA B3006 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU B3007 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B2200 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C GLU B2200 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU B2200 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B2201 " 0.012 2.00e-02 2.50e+03 ... (remaining 4173 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 231 2.64 - 3.21: 22698 3.21 - 3.77: 38330 3.77 - 4.34: 49651 4.34 - 4.90: 82280 Nonbonded interactions: 193190 Sorted by model distance: nonbonded pdb=" O1A ANP B3101 " pdb="MG MG B3102 " model vdw 2.081 2.170 nonbonded pdb=" O2G ANP A3101 " pdb="MG MG A3102 " model vdw 2.088 2.170 nonbonded pdb=" O1A ANP A3101 " pdb="MG MG A3102 " model vdw 2.108 2.170 nonbonded pdb=" OD2 ASP B2889 " pdb="MG MG B3102 " model vdw 2.145 2.170 nonbonded pdb=" OD2 ASP A2889 " pdb="MG MG A3102 " model vdw 2.155 2.170 ... (remaining 193185 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 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: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 57.660 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.110 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:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.003 0.164 24426 Z= 0.144 Angle : 0.508 12.746 32982 Z= 0.261 Chirality : 0.036 0.276 3736 Planarity : 0.004 0.057 4176 Dihedral : 14.348 121.957 9268 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.16), residues: 2930 helix: 1.77 (0.12), residues: 1990 sheet: 0.48 (0.61), residues: 64 loop : -0.06 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2104 HIS 0.004 0.000 HIS B2099 PHE 0.016 0.001 PHE B2462 TYR 0.025 0.001 TYR B1717 ARG 0.002 0.000 ARG A2380 Details of bonding type rmsd hydrogen bonds : bond 0.08146 ( 1498) hydrogen bonds : angle 4.28976 ( 4461) metal coordination : bond 0.00559 ( 6) covalent geometry : bond 0.00277 (24420) covalent geometry : angle 0.50833 (32982) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1475 TYR cc_start: 0.8658 (m-80) cc_final: 0.8421 (m-10) REVERT: A 1575 ARG cc_start: 0.8835 (mtt180) cc_final: 0.8130 (mmm160) REVERT: A 1682 ASP cc_start: 0.8780 (t70) cc_final: 0.8398 (t0) REVERT: A 1720 ASN cc_start: 0.8589 (m110) cc_final: 0.8173 (m110) REVERT: A 1763 TYR cc_start: 0.7807 (m-80) cc_final: 0.7149 (m-80) REVERT: A 1830 MET cc_start: 0.8763 (tmm) cc_final: 0.8489 (pmm) REVERT: A 1935 ASP cc_start: 0.8938 (t0) cc_final: 0.8662 (m-30) REVERT: A 2014 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8308 (tm-30) REVERT: A 2407 SER cc_start: 0.8489 (p) cc_final: 0.8204 (p) REVERT: A 2411 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8914 (mm-30) REVERT: A 2446 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 2448 ASP cc_start: 0.8887 (m-30) cc_final: 0.8578 (m-30) REVERT: A 2450 LEU cc_start: 0.9155 (tt) cc_final: 0.8570 (mm) REVERT: A 2507 ASP cc_start: 0.8264 (t0) cc_final: 0.7768 (m-30) REVERT: A 2519 LEU cc_start: 0.8814 (pp) cc_final: 0.8536 (pp) REVERT: A 2596 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8623 (tm-30) REVERT: A 2597 ASP cc_start: 0.8954 (t0) cc_final: 0.8636 (m-30) REVERT: A 2670 LYS cc_start: 0.9220 (tppp) cc_final: 0.8781 (tmtt) REVERT: A 2736 ASN cc_start: 0.8845 (t0) cc_final: 0.8635 (t0) REVERT: A 2751 THR cc_start: 0.9109 (p) cc_final: 0.8786 (t) REVERT: A 3018 LYS cc_start: 0.9352 (mttt) cc_final: 0.9119 (mttp) REVERT: B 1475 TYR cc_start: 0.8628 (m-80) cc_final: 0.8357 (m-10) REVERT: B 1575 ARG cc_start: 0.8777 (mtt180) cc_final: 0.7980 (mtp85) REVERT: B 1580 LYS cc_start: 0.8960 (mmpt) cc_final: 0.8740 (mmmt) REVERT: B 1682 ASP cc_start: 0.8781 (t70) cc_final: 0.8388 (t0) REVERT: B 1907 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8251 (mtm-85) REVERT: B 1935 ASP cc_start: 0.8866 (t0) cc_final: 0.8478 (m-30) REVERT: B 2014 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8295 (tm-30) REVERT: B 2407 SER cc_start: 0.8494 (p) cc_final: 0.8251 (p) REVERT: B 2411 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8924 (mm-30) REVERT: B 2446 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8045 (tm-30) REVERT: B 2448 ASP cc_start: 0.8876 (m-30) cc_final: 0.8618 (m-30) REVERT: B 2450 LEU cc_start: 0.9181 (tt) cc_final: 0.8595 (mm) REVERT: B 2507 ASP cc_start: 0.8293 (t0) cc_final: 0.7793 (m-30) REVERT: B 2596 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8645 (tm-30) REVERT: B 2597 ASP cc_start: 0.8934 (t0) cc_final: 0.8646 (m-30) REVERT: B 2670 LYS cc_start: 0.9237 (tppp) cc_final: 0.8804 (tmtt) REVERT: B 2723 ARG cc_start: 0.9186 (ttp-110) cc_final: 0.8919 (ttp-110) REVERT: B 2736 ASN cc_start: 0.8839 (t0) cc_final: 0.8609 (t0) REVERT: B 2751 THR cc_start: 0.9130 (p) cc_final: 0.8779 (t) REVERT: B 3018 LYS cc_start: 0.9368 (mttt) cc_final: 0.9129 (mttp) outliers start: 0 outliers final: 1 residues processed: 583 average time/residue: 1.3059 time to fit residues: 876.3110 Evaluate side-chains 305 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 304 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1656 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 231 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 267 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1847 HIS ** A1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2070 ASN A2101 GLN A2106 ASN A2282 ASN A2658 ASN A3038 GLN B1650 ASN B1802 HIS B1847 HIS B1867 GLN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2070 ASN B2101 GLN ** B2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2282 ASN B2658 ASN B3038 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072792 restraints weight = 55177.952| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.76 r_work: 0.3001 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24426 Z= 0.126 Angle : 0.598 9.134 32982 Z= 0.289 Chirality : 0.040 0.270 3736 Planarity : 0.004 0.047 4176 Dihedral : 6.113 114.306 3274 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.02 % Allowed : 12.27 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.16), residues: 2930 helix: 2.36 (0.12), residues: 1998 sheet: 0.75 (0.72), residues: 36 loop : -0.02 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B2638 HIS 0.014 0.001 HIS B2208 PHE 0.020 0.001 PHE A1712 TYR 0.025 0.001 TYR B1844 ARG 0.008 0.000 ARG A2723 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 1498) hydrogen bonds : angle 3.61487 ( 4461) metal coordination : bond 0.00786 ( 6) covalent geometry : bond 0.00293 (24420) covalent geometry : angle 0.59815 (32982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 344 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1556 TYR cc_start: 0.7248 (m-80) cc_final: 0.7003 (m-80) REVERT: A 1575 ARG cc_start: 0.8880 (mtt180) cc_final: 0.7962 (mmm160) REVERT: A 1630 ASP cc_start: 0.8997 (p0) cc_final: 0.8464 (m-30) REVERT: A 1793 ASN cc_start: 0.8844 (m-40) cc_final: 0.8537 (p0) REVERT: A 1844 TYR cc_start: 0.8928 (m-80) cc_final: 0.8634 (m-80) REVERT: A 1935 ASP cc_start: 0.9061 (t0) cc_final: 0.8770 (m-30) REVERT: A 1999 ILE cc_start: 0.9056 (mp) cc_final: 0.8795 (mp) REVERT: A 2049 TYR cc_start: 0.9042 (m-80) cc_final: 0.8839 (m-80) REVERT: A 2196 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8589 (ppp80) REVERT: A 2407 SER cc_start: 0.7927 (p) cc_final: 0.7444 (p) REVERT: A 2411 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8876 (mm-30) REVERT: A 2446 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8389 (tm-30) REVERT: A 2450 LEU cc_start: 0.9084 (tt) cc_final: 0.8584 (mm) REVERT: A 2475 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8981 (mm) REVERT: A 2503 MET cc_start: 0.8748 (ttm) cc_final: 0.8295 (ttm) REVERT: A 2507 ASP cc_start: 0.8595 (t0) cc_final: 0.7902 (m-30) REVERT: A 2596 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8582 (tm-30) REVERT: A 2597 ASP cc_start: 0.8943 (t0) cc_final: 0.8686 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9266 (tppp) cc_final: 0.8733 (tmtt) REVERT: A 2751 THR cc_start: 0.9220 (p) cc_final: 0.8902 (t) REVERT: A 2896 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: A 3018 LYS cc_start: 0.9372 (mttt) cc_final: 0.9115 (mttp) REVERT: B 1556 TYR cc_start: 0.7272 (m-80) cc_final: 0.7068 (m-80) REVERT: B 1575 ARG cc_start: 0.8647 (mtt180) cc_final: 0.8145 (mtp85) REVERT: B 1580 LYS cc_start: 0.8989 (mmpt) cc_final: 0.8782 (mmmt) REVERT: B 1630 ASP cc_start: 0.9008 (p0) cc_final: 0.8395 (m-30) REVERT: B 1714 MET cc_start: 0.9582 (tpp) cc_final: 0.9375 (tpp) REVERT: B 1793 ASN cc_start: 0.8845 (m-40) cc_final: 0.8423 (p0) REVERT: B 1844 TYR cc_start: 0.8919 (m-80) cc_final: 0.8553 (m-80) REVERT: B 1907 ARG cc_start: 0.8512 (ptp-170) cc_final: 0.8215 (mtt90) REVERT: B 2156 GLU cc_start: 0.8233 (pp20) cc_final: 0.7455 (pp20) REVERT: B 2411 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8889 (mm-30) REVERT: B 2428 ARG cc_start: 0.9071 (tpm170) cc_final: 0.8808 (tpm170) REVERT: B 2446 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8411 (tm-30) REVERT: B 2450 LEU cc_start: 0.9089 (tt) cc_final: 0.8578 (mm) REVERT: B 2475 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8880 (mm) REVERT: B 2503 MET cc_start: 0.8743 (ttm) cc_final: 0.8533 (ttm) REVERT: B 2507 ASP cc_start: 0.8604 (t0) cc_final: 0.7953 (m-30) REVERT: B 2597 ASP cc_start: 0.8947 (t0) cc_final: 0.8686 (m-30) REVERT: B 2670 LYS cc_start: 0.9271 (tppp) cc_final: 0.8741 (tmtt) REVERT: B 2751 THR cc_start: 0.9244 (p) cc_final: 0.8908 (t) REVERT: B 2962 MET cc_start: 0.8015 (mtm) cc_final: 0.7664 (mmm) REVERT: B 3018 LYS cc_start: 0.9382 (mttt) cc_final: 0.9104 (mttp) outliers start: 54 outliers final: 17 residues processed: 377 average time/residue: 1.1886 time to fit residues: 523.9366 Evaluate side-chains 324 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 304 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 2003 ASP Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2196 ARG Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2475 LEU Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain B residue 1516 HIS Chi-restraints excluded: chain B residue 1559 ILE Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 2003 ASP Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2606 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 177 optimal weight: 0.0060 chunk 118 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 291 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1720 ASN A1802 HIS ** A1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2002 GLN A2632 ASN A2736 ASN A2809 GLN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2002 GLN B2106 ASN B2197 GLN B2632 ASN B2736 ASN B2896 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.097100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.071245 restraints weight = 54917.180| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.81 r_work: 0.2965 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24426 Z= 0.118 Angle : 0.598 10.086 32982 Z= 0.286 Chirality : 0.039 0.348 3736 Planarity : 0.003 0.046 4176 Dihedral : 4.751 102.907 3270 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.02 % Allowed : 13.76 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.16), residues: 2930 helix: 2.50 (0.12), residues: 1994 sheet: 0.38 (0.77), residues: 38 loop : 0.06 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1805 HIS 0.016 0.001 HIS B1802 PHE 0.019 0.001 PHE A1712 TYR 0.017 0.001 TYR B1696 ARG 0.004 0.000 ARG A2723 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 1498) hydrogen bonds : angle 3.47275 ( 4461) metal coordination : bond 0.00872 ( 6) covalent geometry : bond 0.00275 (24420) covalent geometry : angle 0.59847 (32982) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1556 TYR cc_start: 0.7420 (m-80) cc_final: 0.7216 (m-80) REVERT: A 1565 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: A 1575 ARG cc_start: 0.8812 (mtt180) cc_final: 0.8136 (mmm160) REVERT: A 1619 ARG cc_start: 0.8445 (mpp80) cc_final: 0.8159 (mpp80) REVERT: A 1630 ASP cc_start: 0.8992 (p0) cc_final: 0.8483 (m-30) REVERT: A 1714 MET cc_start: 0.9557 (tpp) cc_final: 0.9335 (tpp) REVERT: A 1720 ASN cc_start: 0.8572 (m-40) cc_final: 0.8202 (m110) REVERT: A 1793 ASN cc_start: 0.8864 (m-40) cc_final: 0.8552 (p0) REVERT: A 1935 ASP cc_start: 0.9022 (t0) cc_final: 0.8808 (m-30) REVERT: A 2049 TYR cc_start: 0.9087 (m-80) cc_final: 0.8849 (m-80) REVERT: A 2051 LEU cc_start: 0.8836 (tm) cc_final: 0.8555 (tm) REVERT: A 2126 GLU cc_start: 0.9427 (tt0) cc_final: 0.9160 (tt0) REVERT: A 2235 MET cc_start: 0.8908 (tpt) cc_final: 0.8637 (tpt) REVERT: A 2239 MET cc_start: 0.7199 (ppp) cc_final: 0.6753 (mmp) REVERT: A 2304 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: A 2407 SER cc_start: 0.7738 (p) cc_final: 0.7201 (p) REVERT: A 2411 GLU cc_start: 0.9360 (mm-30) cc_final: 0.8888 (mm-30) REVERT: A 2446 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8470 (tm-30) REVERT: A 2450 LEU cc_start: 0.9088 (tt) cc_final: 0.8586 (mm) REVERT: A 2475 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8902 (mm) REVERT: A 2507 ASP cc_start: 0.8668 (t0) cc_final: 0.7955 (m-30) REVERT: A 2596 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8563 (tm-30) REVERT: A 2597 ASP cc_start: 0.9024 (t0) cc_final: 0.8717 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9258 (tppp) cc_final: 0.8717 (tmtt) REVERT: A 2736 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8584 (m-40) REVERT: A 2896 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6700 (tm-30) REVERT: A 2915 VAL cc_start: 0.9078 (t) cc_final: 0.8851 (m) REVERT: A 2938 MET cc_start: 0.9305 (mmm) cc_final: 0.8956 (mtm) REVERT: A 3018 LYS cc_start: 0.9381 (mttt) cc_final: 0.9120 (mttp) REVERT: B 1470 TYR cc_start: 0.9322 (m-80) cc_final: 0.8533 (t80) REVERT: B 1475 TYR cc_start: 0.8769 (m-80) cc_final: 0.8473 (m-80) REVERT: B 1556 TYR cc_start: 0.7391 (m-80) cc_final: 0.7116 (m-80) REVERT: B 1575 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8191 (mtp85) REVERT: B 1580 LYS cc_start: 0.9025 (mmpt) cc_final: 0.8794 (mmmt) REVERT: B 1630 ASP cc_start: 0.9048 (p0) cc_final: 0.8511 (m-30) REVERT: B 1793 ASN cc_start: 0.8858 (m-40) cc_final: 0.8452 (p0) REVERT: B 1844 TYR cc_start: 0.8948 (m-80) cc_final: 0.8603 (m-80) REVERT: B 1907 ARG cc_start: 0.8558 (ptp-170) cc_final: 0.8234 (mtt90) REVERT: B 1999 ILE cc_start: 0.8689 (mm) cc_final: 0.8475 (mp) REVERT: B 2008 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8862 (mp) REVERT: B 2156 GLU cc_start: 0.7923 (pp20) cc_final: 0.7526 (pp20) REVERT: B 2158 MET cc_start: 0.9133 (tmm) cc_final: 0.8813 (tmm) REVERT: B 2160 LYS cc_start: 0.8312 (mtmt) cc_final: 0.8028 (mtpt) REVERT: B 2239 MET cc_start: 0.7137 (ppp) cc_final: 0.6718 (mmp) REVERT: B 2411 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8944 (mm-30) REVERT: B 2428 ARG cc_start: 0.9079 (tpm170) cc_final: 0.8879 (tpm170) REVERT: B 2446 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8465 (tm-30) REVERT: B 2450 LEU cc_start: 0.9071 (tt) cc_final: 0.8560 (mm) REVERT: B 2475 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8893 (mm) REVERT: B 2503 MET cc_start: 0.8763 (ttm) cc_final: 0.8524 (ttm) REVERT: B 2507 ASP cc_start: 0.8674 (t0) cc_final: 0.7999 (m-30) REVERT: B 2670 LYS cc_start: 0.9264 (tppp) cc_final: 0.8731 (tmtt) REVERT: B 2736 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8544 (m-40) REVERT: B 2751 THR cc_start: 0.9340 (p) cc_final: 0.9128 (t) REVERT: B 2962 MET cc_start: 0.8030 (mtm) cc_final: 0.7753 (mmm) REVERT: B 3018 LYS cc_start: 0.9391 (mttt) cc_final: 0.9106 (mttm) outliers start: 54 outliers final: 19 residues processed: 345 average time/residue: 1.2010 time to fit residues: 484.5984 Evaluate side-chains 303 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2475 LEU Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2736 ASN Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain B residue 1516 HIS Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1823 ILE Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1932 PHE Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2008 ILE Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2736 ASN Chi-restraints excluded: chain B residue 2896 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 247 optimal weight: 0.4980 chunk 291 optimal weight: 3.9990 chunk 221 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 229 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1518 HIS A1847 HIS ** A1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1946 GLN A2632 ASN B1847 HIS ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2809 GLN B2896 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.096580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070638 restraints weight = 54900.058| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.80 r_work: 0.2955 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24426 Z= 0.113 Angle : 0.580 12.223 32982 Z= 0.276 Chirality : 0.038 0.326 3736 Planarity : 0.003 0.045 4176 Dihedral : 4.374 93.792 3270 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.47 % Allowed : 14.88 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.16), residues: 2930 helix: 2.50 (0.12), residues: 2000 sheet: 0.91 (0.65), residues: 58 loop : -0.02 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1805 HIS 0.012 0.001 HIS B1802 PHE 0.021 0.001 PHE A1712 TYR 0.017 0.001 TYR A1529 ARG 0.004 0.000 ARG A2428 Details of bonding type rmsd hydrogen bonds : bond 0.02850 ( 1498) hydrogen bonds : angle 3.41459 ( 4461) metal coordination : bond 0.00539 ( 6) covalent geometry : bond 0.00267 (24420) covalent geometry : angle 0.58033 (32982) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 298 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1475 TYR cc_start: 0.8784 (m-80) cc_final: 0.8497 (m-80) REVERT: A 1556 TYR cc_start: 0.7446 (m-80) cc_final: 0.7138 (m-80) REVERT: A 1565 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: A 1575 ARG cc_start: 0.8750 (mtt180) cc_final: 0.8042 (mmm160) REVERT: A 1612 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8881 (tp30) REVERT: A 1630 ASP cc_start: 0.9031 (p0) cc_final: 0.8564 (m-30) REVERT: A 1720 ASN cc_start: 0.8709 (m-40) cc_final: 0.8248 (m110) REVERT: A 1793 ASN cc_start: 0.8881 (m-40) cc_final: 0.8567 (p0) REVERT: A 1935 ASP cc_start: 0.9044 (t0) cc_final: 0.8827 (m-30) REVERT: A 2126 GLU cc_start: 0.9428 (tt0) cc_final: 0.9127 (tt0) REVERT: A 2156 GLU cc_start: 0.8387 (pp20) cc_final: 0.7533 (pp20) REVERT: A 2235 MET cc_start: 0.8980 (tpt) cc_final: 0.8737 (tpt) REVERT: A 2304 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: A 2407 SER cc_start: 0.7631 (p) cc_final: 0.7144 (p) REVERT: A 2411 GLU cc_start: 0.9359 (mm-30) cc_final: 0.8806 (mm-30) REVERT: A 2507 ASP cc_start: 0.8645 (t0) cc_final: 0.7950 (m-30) REVERT: A 2596 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8566 (tm-30) REVERT: A 2597 ASP cc_start: 0.9041 (t0) cc_final: 0.8754 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9238 (tppp) cc_final: 0.8667 (tmtt) REVERT: A 2896 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6793 (tm-30) REVERT: A 2924 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8736 (mp0) REVERT: A 3018 LYS cc_start: 0.9371 (mttt) cc_final: 0.9120 (mttp) REVERT: B 1475 TYR cc_start: 0.8752 (m-80) cc_final: 0.8467 (m-80) REVERT: B 1565 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: B 1575 ARG cc_start: 0.8657 (mtt180) cc_final: 0.8214 (mtp85) REVERT: B 1630 ASP cc_start: 0.9085 (p0) cc_final: 0.8563 (m-30) REVERT: B 1793 ASN cc_start: 0.8865 (m-40) cc_final: 0.8472 (p0) REVERT: B 1844 TYR cc_start: 0.8981 (m-80) cc_final: 0.8674 (m-80) REVERT: B 1907 ARG cc_start: 0.8575 (ptp-170) cc_final: 0.8229 (mtt90) REVERT: B 1999 ILE cc_start: 0.8678 (mm) cc_final: 0.8466 (mp) REVERT: B 2008 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8865 (mp) REVERT: B 2051 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8585 (tm) REVERT: B 2156 GLU cc_start: 0.7899 (pp20) cc_final: 0.7482 (pp20) REVERT: B 2157 GLU cc_start: 0.8305 (tp30) cc_final: 0.7854 (tp30) REVERT: B 2160 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8126 (mtpt) REVERT: B 2235 MET cc_start: 0.8867 (tpt) cc_final: 0.8627 (tpt) REVERT: B 2304 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: B 2411 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8923 (mm-30) REVERT: B 2503 MET cc_start: 0.8825 (ttm) cc_final: 0.8624 (ttm) REVERT: B 2507 ASP cc_start: 0.8688 (t0) cc_final: 0.8015 (m-30) REVERT: B 2670 LYS cc_start: 0.9265 (tppp) cc_final: 0.8736 (tmtt) REVERT: B 2751 THR cc_start: 0.9330 (p) cc_final: 0.9117 (t) REVERT: B 2752 ILE cc_start: 0.8692 (mm) cc_final: 0.8454 (mm) REVERT: B 2938 MET cc_start: 0.9317 (mmm) cc_final: 0.8937 (mmm) REVERT: B 2962 MET cc_start: 0.8015 (mtm) cc_final: 0.7763 (mmm) REVERT: B 3018 LYS cc_start: 0.9385 (mttt) cc_final: 0.9126 (mttp) outliers start: 66 outliers final: 21 residues processed: 341 average time/residue: 1.1316 time to fit residues: 455.6111 Evaluate side-chains 297 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1581 ILE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2493 GLU Chi-restraints excluded: chain A residue 2550 MET Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain B residue 1516 HIS Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1823 ILE Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 2008 ILE Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 LEU Chi-restraints excluded: chain B residue 2051 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2304 GLU Chi-restraints excluded: chain B residue 2550 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1690 HIS A2210 GLN A2632 ASN A2736 ASN A2788 HIS ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.092051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065773 restraints weight = 54678.619| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.63 r_work: 0.2860 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24426 Z= 0.201 Angle : 0.643 11.220 32982 Z= 0.311 Chirality : 0.041 0.288 3736 Planarity : 0.003 0.041 4176 Dihedral : 4.416 85.473 3270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.62 % Allowed : 15.78 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.16), residues: 2930 helix: 2.36 (0.12), residues: 2010 sheet: 1.05 (0.64), residues: 58 loop : 0.08 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1933 HIS 0.013 0.001 HIS B2208 PHE 0.019 0.001 PHE A1712 TYR 0.017 0.001 TYR B1470 ARG 0.003 0.000 ARG B3008 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 1498) hydrogen bonds : angle 3.52826 ( 4461) metal coordination : bond 0.00396 ( 6) covalent geometry : bond 0.00473 (24420) covalent geometry : angle 0.64344 (32982) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 285 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 TYR cc_start: 0.9353 (m-80) cc_final: 0.8833 (t80) REVERT: A 1556 TYR cc_start: 0.7510 (m-80) cc_final: 0.7248 (m-80) REVERT: A 1565 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: A 1575 ARG cc_start: 0.8802 (mtt180) cc_final: 0.8083 (mmm160) REVERT: A 1630 ASP cc_start: 0.9024 (p0) cc_final: 0.8623 (m-30) REVERT: A 1701 LYS cc_start: 0.9289 (pttm) cc_final: 0.9044 (pttp) REVERT: A 1706 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8421 (tmmm) REVERT: A 1720 ASN cc_start: 0.8899 (m-40) cc_final: 0.8693 (m-40) REVERT: A 2051 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9039 (tm) REVERT: A 2239 MET cc_start: 0.7180 (ppp) cc_final: 0.6762 (mmp) REVERT: A 2304 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: A 2407 SER cc_start: 0.7932 (p) cc_final: 0.7321 (p) REVERT: A 2411 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8844 (mm-30) REVERT: A 2448 ASP cc_start: 0.8872 (m-30) cc_final: 0.8585 (m-30) REVERT: A 2450 LEU cc_start: 0.9202 (tt) cc_final: 0.8799 (mm) REVERT: A 2596 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8586 (tm-30) REVERT: A 2597 ASP cc_start: 0.8988 (t0) cc_final: 0.8766 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9259 (tppp) cc_final: 0.8729 (tmtt) REVERT: A 2896 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: A 3018 LYS cc_start: 0.9412 (mttt) cc_final: 0.9165 (mttp) REVERT: B 1556 TYR cc_start: 0.7607 (m-80) cc_final: 0.7388 (m-80) REVERT: B 1565 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: B 1575 ARG cc_start: 0.8633 (mtt180) cc_final: 0.7885 (mmm160) REVERT: B 1580 LYS cc_start: 0.9139 (mmmt) cc_final: 0.8866 (mmmm) REVERT: B 1701 LYS cc_start: 0.9290 (pttm) cc_final: 0.9018 (pttp) REVERT: B 1706 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8522 (tmmm) REVERT: B 1844 TYR cc_start: 0.9118 (m-80) cc_final: 0.8863 (m-80) REVERT: B 1935 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8825 (m-30) REVERT: B 2008 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8982 (mp) REVERT: B 2051 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9016 (tm) REVERT: B 2177 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8928 (tt0) REVERT: B 2239 MET cc_start: 0.7186 (ppp) cc_final: 0.6792 (mmp) REVERT: B 2304 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: B 2411 GLU cc_start: 0.9337 (mm-30) cc_final: 0.8923 (mm-30) REVERT: B 2448 ASP cc_start: 0.8851 (m-30) cc_final: 0.8569 (m-30) REVERT: B 2450 LEU cc_start: 0.9178 (tt) cc_final: 0.8769 (mm) REVERT: B 2670 LYS cc_start: 0.9275 (tppp) cc_final: 0.8768 (tmtt) REVERT: B 2751 THR cc_start: 0.9412 (p) cc_final: 0.9184 (t) REVERT: B 2896 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: B 3018 LYS cc_start: 0.9427 (mttt) cc_final: 0.9158 (mttp) outliers start: 70 outliers final: 27 residues processed: 332 average time/residue: 1.1046 time to fit residues: 434.7738 Evaluate side-chains 290 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1516 HIS Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2493 GLU Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain A residue 2942 GLN Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain B residue 1516 HIS Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1706 LYS Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2008 ILE Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 LEU Chi-restraints excluded: chain B residue 2051 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2177 GLN Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2304 GLU Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2597 ASP Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2896 GLN Chi-restraints excluded: chain B residue 2945 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 250 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 278 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 243 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 chunk 251 optimal weight: 0.6980 chunk 258 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1552 ASN A2632 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.093926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067803 restraints weight = 53958.741| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.73 r_work: 0.2885 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24426 Z= 0.116 Angle : 0.619 12.688 32982 Z= 0.291 Chirality : 0.040 0.304 3736 Planarity : 0.003 0.056 4176 Dihedral : 4.309 72.100 3270 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.69 % Allowed : 16.68 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.16), residues: 2930 helix: 2.40 (0.12), residues: 2014 sheet: 1.10 (0.65), residues: 58 loop : 0.04 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1933 HIS 0.013 0.001 HIS B2208 PHE 0.024 0.001 PHE A1712 TYR 0.018 0.001 TYR A1753 ARG 0.015 0.000 ARG B2428 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 1498) hydrogen bonds : angle 3.41944 ( 4461) metal coordination : bond 0.00405 ( 6) covalent geometry : bond 0.00273 (24420) covalent geometry : angle 0.61950 (32982) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 282 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 TYR cc_start: 0.9334 (m-80) cc_final: 0.8670 (t80) REVERT: A 1474 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8249 (m-70) REVERT: A 1475 TYR cc_start: 0.8849 (m-80) cc_final: 0.8538 (m-10) REVERT: A 1539 LEU cc_start: 0.9360 (mm) cc_final: 0.9084 (pp) REVERT: A 1556 TYR cc_start: 0.7383 (m-80) cc_final: 0.7148 (m-80) REVERT: A 1565 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: A 1575 ARG cc_start: 0.8729 (mtt180) cc_final: 0.8002 (mmm160) REVERT: A 1701 LYS cc_start: 0.9281 (pttm) cc_final: 0.9041 (pttp) REVERT: A 1706 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8374 (tmmm) REVERT: A 1720 ASN cc_start: 0.8863 (m-40) cc_final: 0.8640 (m-40) REVERT: A 1935 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8582 (m-30) REVERT: A 2051 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8878 (tm) REVERT: A 2126 GLU cc_start: 0.9451 (tt0) cc_final: 0.9121 (tt0) REVERT: A 2304 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: A 2407 SER cc_start: 0.7564 (p) cc_final: 0.7097 (p) REVERT: A 2411 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8777 (mm-30) REVERT: A 2448 ASP cc_start: 0.8858 (m-30) cc_final: 0.8590 (m-30) REVERT: A 2596 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8588 (tm-30) REVERT: A 2670 LYS cc_start: 0.9222 (tppp) cc_final: 0.8629 (tmtt) REVERT: A 2895 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8978 (mp0) REVERT: A 2896 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: A 3018 LYS cc_start: 0.9396 (mttt) cc_final: 0.9078 (mttm) REVERT: B 1539 LEU cc_start: 0.9323 (mm) cc_final: 0.9087 (pp) REVERT: B 1556 TYR cc_start: 0.7493 (m-80) cc_final: 0.7218 (m-80) REVERT: B 1575 ARG cc_start: 0.8549 (mtt180) cc_final: 0.7909 (mmm160) REVERT: B 1580 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8850 (mmtp) REVERT: B 1701 LYS cc_start: 0.9277 (pttm) cc_final: 0.9023 (pttp) REVERT: B 1706 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8427 (tmmm) REVERT: B 1717 TYR cc_start: 0.9311 (t80) cc_final: 0.9030 (t80) REVERT: B 1836 ASP cc_start: 0.9543 (m-30) cc_final: 0.8907 (t0) REVERT: B 1844 TYR cc_start: 0.8996 (m-80) cc_final: 0.8795 (m-80) REVERT: B 1935 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8859 (m-30) REVERT: B 2008 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8817 (mp) REVERT: B 2051 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8888 (tm) REVERT: B 2411 GLU cc_start: 0.9375 (mm-30) cc_final: 0.8939 (mm-30) REVERT: B 2428 ARG cc_start: 0.9205 (mmm160) cc_final: 0.8734 (tpm170) REVERT: B 2448 ASP cc_start: 0.8857 (m-30) cc_final: 0.8573 (m-30) REVERT: B 2670 LYS cc_start: 0.9247 (tppp) cc_final: 0.8641 (tmtt) REVERT: B 2751 THR cc_start: 0.9387 (p) cc_final: 0.9153 (t) REVERT: B 2896 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7117 (mm-40) REVERT: B 3018 LYS cc_start: 0.9412 (mttt) cc_final: 0.9090 (mttm) outliers start: 72 outliers final: 29 residues processed: 323 average time/residue: 1.0743 time to fit residues: 411.2319 Evaluate side-chains 302 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1474 HIS Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 1935 ASP Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2210 GLN Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2493 GLU Chi-restraints excluded: chain A residue 2597 ASP Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain B residue 1516 HIS Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1581 ILE Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1706 LYS Chi-restraints excluded: chain B residue 1823 ILE Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2008 ILE Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 LEU Chi-restraints excluded: chain B residue 2051 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2896 GLN Chi-restraints excluded: chain B residue 2942 GLN Chi-restraints excluded: chain B residue 2945 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 161 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 245 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 99 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2632 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.093846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067679 restraints weight = 54319.325| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.73 r_work: 0.2886 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24426 Z= 0.124 Angle : 0.643 12.795 32982 Z= 0.299 Chirality : 0.041 0.319 3736 Planarity : 0.003 0.043 4176 Dihedral : 4.289 67.730 3270 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.62 % Allowed : 17.54 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.16), residues: 2930 helix: 2.41 (0.12), residues: 2012 sheet: 1.13 (0.65), residues: 58 loop : 0.05 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1933 HIS 0.012 0.001 HIS B2208 PHE 0.032 0.001 PHE A1749 TYR 0.014 0.001 TYR B1696 ARG 0.011 0.000 ARG B2428 Details of bonding type rmsd hydrogen bonds : bond 0.03016 ( 1498) hydrogen bonds : angle 3.44553 ( 4461) metal coordination : bond 0.00329 ( 6) covalent geometry : bond 0.00291 (24420) covalent geometry : angle 0.64304 (32982) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 278 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1474 HIS cc_start: 0.8581 (OUTLIER) cc_final: 0.8344 (m-70) REVERT: A 1475 TYR cc_start: 0.8792 (m-80) cc_final: 0.8490 (m-10) REVERT: A 1539 LEU cc_start: 0.9350 (mm) cc_final: 0.9083 (pp) REVERT: A 1556 TYR cc_start: 0.7332 (m-80) cc_final: 0.7062 (m-80) REVERT: A 1565 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: A 1575 ARG cc_start: 0.8740 (mtt180) cc_final: 0.8011 (mmm160) REVERT: A 1701 LYS cc_start: 0.9309 (pttm) cc_final: 0.9051 (pttp) REVERT: A 1706 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8414 (tmmm) REVERT: A 1720 ASN cc_start: 0.8909 (m-40) cc_final: 0.8685 (m-40) REVERT: A 2051 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8891 (tm) REVERT: A 2126 GLU cc_start: 0.9441 (tt0) cc_final: 0.9115 (tt0) REVERT: A 2239 MET cc_start: 0.6937 (ppp) cc_final: 0.6508 (mmp) REVERT: A 2304 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: A 2407 SER cc_start: 0.7549 (p) cc_final: 0.7055 (p) REVERT: A 2411 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8787 (mm-30) REVERT: A 2448 ASP cc_start: 0.8871 (m-30) cc_final: 0.8591 (m-30) REVERT: A 2596 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8693 (tm-30) REVERT: A 2670 LYS cc_start: 0.9218 (tppp) cc_final: 0.8622 (tmtt) REVERT: A 2896 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: A 2938 MET cc_start: 0.9400 (mmm) cc_final: 0.9055 (mtm) REVERT: A 3018 LYS cc_start: 0.9403 (mttt) cc_final: 0.9119 (mttp) REVERT: B 1474 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.8284 (m-70) REVERT: B 1475 TYR cc_start: 0.8826 (m-80) cc_final: 0.8521 (m-80) REVERT: B 1539 LEU cc_start: 0.9306 (mm) cc_final: 0.9099 (pp) REVERT: B 1556 TYR cc_start: 0.7504 (m-80) cc_final: 0.7271 (m-80) REVERT: B 1565 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: B 1575 ARG cc_start: 0.8477 (mtt180) cc_final: 0.7856 (mmm160) REVERT: B 1701 LYS cc_start: 0.9276 (pttm) cc_final: 0.8990 (pttp) REVERT: B 1706 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8454 (tmmm) REVERT: B 1717 TYR cc_start: 0.9269 (t80) cc_final: 0.8988 (t80) REVERT: B 1836 ASP cc_start: 0.9557 (m-30) cc_final: 0.8907 (t0) REVERT: B 1935 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8829 (m-30) REVERT: B 2008 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8825 (mp) REVERT: B 2051 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8915 (tm) REVERT: B 2239 MET cc_start: 0.6901 (ppp) cc_final: 0.6512 (mmp) REVERT: B 2411 GLU cc_start: 0.9388 (mm-30) cc_final: 0.8955 (mm-30) REVERT: B 2428 ARG cc_start: 0.9224 (mmm160) cc_final: 0.8620 (tpm170) REVERT: B 2448 ASP cc_start: 0.8859 (m-30) cc_final: 0.8564 (m-30) REVERT: B 2670 LYS cc_start: 0.9228 (tppp) cc_final: 0.8644 (tmtt) REVERT: B 2751 THR cc_start: 0.9376 (p) cc_final: 0.9146 (t) REVERT: B 2896 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7055 (mm-40) REVERT: B 3018 LYS cc_start: 0.9427 (mttt) cc_final: 0.9109 (mttm) outliers start: 70 outliers final: 28 residues processed: 317 average time/residue: 1.1947 time to fit residues: 445.9280 Evaluate side-chains 299 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1474 HIS Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2493 GLU Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain A residue 2942 GLN Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain B residue 1474 HIS Chi-restraints excluded: chain B residue 1516 HIS Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1559 ILE Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1706 LYS Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2008 ILE Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 LEU Chi-restraints excluded: chain B residue 2051 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2896 GLN Chi-restraints excluded: chain B residue 2945 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 8 optimal weight: 0.5980 chunk 245 optimal weight: 0.6980 chunk 247 optimal weight: 0.9980 chunk 252 optimal weight: 0.0770 chunk 244 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2632 ASN B1552 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.067965 restraints weight = 55271.982| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.87 r_work: 0.2896 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24426 Z= 0.115 Angle : 0.650 13.410 32982 Z= 0.301 Chirality : 0.041 0.358 3736 Planarity : 0.004 0.069 4176 Dihedral : 4.270 68.103 3270 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.28 % Allowed : 18.51 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.16), residues: 2930 helix: 2.40 (0.12), residues: 2012 sheet: 1.14 (0.65), residues: 58 loop : 0.03 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1710 HIS 0.010 0.001 HIS B2208 PHE 0.022 0.001 PHE A1712 TYR 0.015 0.001 TYR B1844 ARG 0.018 0.000 ARG A2428 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 1498) hydrogen bonds : angle 3.42188 ( 4461) metal coordination : bond 0.00282 ( 6) covalent geometry : bond 0.00268 (24420) covalent geometry : angle 0.64979 (32982) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 283 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1474 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8319 (m-70) REVERT: A 1539 LEU cc_start: 0.9348 (mm) cc_final: 0.9093 (pp) REVERT: A 1556 TYR cc_start: 0.7300 (m-80) cc_final: 0.7043 (m-80) REVERT: A 1565 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: A 1575 ARG cc_start: 0.8738 (mtt180) cc_final: 0.7993 (mmm160) REVERT: A 1701 LYS cc_start: 0.9355 (pttm) cc_final: 0.9111 (pttp) REVERT: A 1706 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8433 (tmmm) REVERT: A 1720 ASN cc_start: 0.8900 (m-40) cc_final: 0.8671 (m-40) REVERT: A 2051 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8894 (tm) REVERT: A 2126 GLU cc_start: 0.9433 (tt0) cc_final: 0.9133 (tt0) REVERT: A 2239 MET cc_start: 0.6901 (ppp) cc_final: 0.6415 (mmp) REVERT: A 2304 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: A 2407 SER cc_start: 0.7559 (p) cc_final: 0.7096 (p) REVERT: A 2411 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8801 (mm-30) REVERT: A 2428 ARG cc_start: 0.9192 (mmm160) cc_final: 0.8740 (tpm170) REVERT: A 2448 ASP cc_start: 0.8883 (m-30) cc_final: 0.8602 (m-30) REVERT: A 2527 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.6417 (mpp) REVERT: A 2596 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8696 (tm-30) REVERT: A 2670 LYS cc_start: 0.9208 (tppp) cc_final: 0.8600 (tmtt) REVERT: A 2938 MET cc_start: 0.9376 (mmm) cc_final: 0.9122 (mtm) REVERT: A 3018 LYS cc_start: 0.9409 (mttt) cc_final: 0.9080 (mttm) REVERT: B 1474 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.8243 (m-70) REVERT: B 1539 LEU cc_start: 0.9300 (mm) cc_final: 0.9097 (pp) REVERT: B 1556 TYR cc_start: 0.7446 (m-80) cc_final: 0.7145 (m-80) REVERT: B 1565 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7565 (m-80) REVERT: B 1575 ARG cc_start: 0.8484 (mtt180) cc_final: 0.7878 (mmm160) REVERT: B 1580 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8818 (mmmm) REVERT: B 1701 LYS cc_start: 0.9296 (pttm) cc_final: 0.9058 (pttp) REVERT: B 1706 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8440 (tmmm) REVERT: B 1717 TYR cc_start: 0.9268 (t80) cc_final: 0.9024 (t80) REVERT: B 1793 ASN cc_start: 0.8935 (m-40) cc_final: 0.8563 (p0) REVERT: B 1830 MET cc_start: 0.8542 (tmm) cc_final: 0.8010 (ppp) REVERT: B 1836 ASP cc_start: 0.9530 (m-30) cc_final: 0.8900 (t0) REVERT: B 1844 TYR cc_start: 0.9016 (m-80) cc_final: 0.8695 (m-80) REVERT: B 1935 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8851 (m-30) REVERT: B 2008 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8762 (mp) REVERT: B 2051 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8913 (tm) REVERT: B 2126 GLU cc_start: 0.9437 (tt0) cc_final: 0.9093 (tt0) REVERT: B 2156 GLU cc_start: 0.8187 (pp20) cc_final: 0.7889 (pp20) REVERT: B 2157 GLU cc_start: 0.8418 (tp30) cc_final: 0.8094 (tp30) REVERT: B 2239 MET cc_start: 0.6903 (ppp) cc_final: 0.6454 (mmp) REVERT: B 2411 GLU cc_start: 0.9395 (mm-30) cc_final: 0.8961 (mm-30) REVERT: B 2428 ARG cc_start: 0.9225 (mmm160) cc_final: 0.8666 (tpm170) REVERT: B 2448 ASP cc_start: 0.8867 (m-30) cc_final: 0.8577 (m-30) REVERT: B 2670 LYS cc_start: 0.9229 (tppp) cc_final: 0.8635 (tmtt) REVERT: B 2895 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9057 (mp0) REVERT: B 3018 LYS cc_start: 0.9420 (mttt) cc_final: 0.9142 (mttp) outliers start: 61 outliers final: 31 residues processed: 313 average time/residue: 1.1358 time to fit residues: 419.4543 Evaluate side-chains 309 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1474 HIS Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2493 GLU Chi-restraints excluded: chain A residue 2527 MET Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain A residue 2942 GLN Chi-restraints excluded: chain B residue 1474 HIS Chi-restraints excluded: chain B residue 1516 HIS Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1706 LYS Chi-restraints excluded: chain B residue 1823 ILE Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2008 ILE Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 LEU Chi-restraints excluded: chain B residue 2051 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2896 GLN Chi-restraints excluded: chain B residue 2942 GLN Chi-restraints excluded: chain B residue 2945 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 93 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 chunk 219 optimal weight: 0.0770 chunk 112 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2206 GLN A2632 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2106 ASN B2632 ASN B2736 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.068027 restraints weight = 55231.721| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.86 r_work: 0.2896 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24426 Z= 0.120 Angle : 0.667 14.605 32982 Z= 0.308 Chirality : 0.041 0.382 3736 Planarity : 0.004 0.063 4176 Dihedral : 4.256 67.818 3270 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.32 % Allowed : 18.51 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.16), residues: 2930 helix: 2.43 (0.12), residues: 2008 sheet: 1.12 (0.65), residues: 58 loop : 0.01 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1710 HIS 0.010 0.001 HIS B2208 PHE 0.032 0.001 PHE B1749 TYR 0.033 0.001 TYR B1475 ARG 0.017 0.000 ARG A2428 Details of bonding type rmsd hydrogen bonds : bond 0.02928 ( 1498) hydrogen bonds : angle 3.43791 ( 4461) metal coordination : bond 0.00217 ( 6) covalent geometry : bond 0.00282 (24420) covalent geometry : angle 0.66684 (32982) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1474 HIS cc_start: 0.8552 (OUTLIER) cc_final: 0.8321 (m-70) REVERT: A 1539 LEU cc_start: 0.9329 (mm) cc_final: 0.9085 (pp) REVERT: A 1556 TYR cc_start: 0.7289 (m-80) cc_final: 0.7016 (m-80) REVERT: A 1565 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: A 1575 ARG cc_start: 0.8754 (mtt180) cc_final: 0.8032 (mmm160) REVERT: A 1701 LYS cc_start: 0.9359 (pttm) cc_final: 0.9105 (pttp) REVERT: A 1706 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8444 (tmmm) REVERT: A 1720 ASN cc_start: 0.8897 (m-40) cc_final: 0.8656 (m-40) REVERT: A 1935 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8627 (m-30) REVERT: A 2051 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8910 (tm) REVERT: A 2126 GLU cc_start: 0.9436 (tt0) cc_final: 0.9138 (tt0) REVERT: A 2239 MET cc_start: 0.6905 (ppp) cc_final: 0.6402 (mmp) REVERT: A 2304 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: A 2407 SER cc_start: 0.7569 (p) cc_final: 0.7110 (p) REVERT: A 2411 GLU cc_start: 0.9373 (mm-30) cc_final: 0.8809 (mm-30) REVERT: A 2428 ARG cc_start: 0.9202 (mmm160) cc_final: 0.8758 (tpm170) REVERT: A 2448 ASP cc_start: 0.8868 (m-30) cc_final: 0.8583 (m-30) REVERT: A 2475 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8507 (mm) REVERT: A 2596 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8712 (tm-30) REVERT: A 2670 LYS cc_start: 0.9191 (tppp) cc_final: 0.8565 (tmtt) REVERT: A 3018 LYS cc_start: 0.9418 (mttt) cc_final: 0.9089 (mttm) REVERT: B 1474 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8287 (m-70) REVERT: B 1539 LEU cc_start: 0.9304 (mm) cc_final: 0.9104 (pp) REVERT: B 1556 TYR cc_start: 0.7469 (m-80) cc_final: 0.7246 (m-80) REVERT: B 1565 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: B 1575 ARG cc_start: 0.8519 (mtt180) cc_final: 0.7892 (mmm160) REVERT: B 1580 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8760 (mmmm) REVERT: B 1701 LYS cc_start: 0.9306 (pttm) cc_final: 0.9066 (pttp) REVERT: B 1706 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8468 (tmmm) REVERT: B 1717 TYR cc_start: 0.9256 (t80) cc_final: 0.8922 (t80) REVERT: B 1793 ASN cc_start: 0.8939 (m-40) cc_final: 0.8568 (p0) REVERT: B 1830 MET cc_start: 0.8579 (tmm) cc_final: 0.8039 (ppp) REVERT: B 1836 ASP cc_start: 0.9545 (m-30) cc_final: 0.8889 (t0) REVERT: B 1844 TYR cc_start: 0.9063 (m-80) cc_final: 0.8734 (m-80) REVERT: B 1935 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8821 (m-30) REVERT: B 2008 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8781 (mp) REVERT: B 2051 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8951 (tm) REVERT: B 2126 GLU cc_start: 0.9441 (tt0) cc_final: 0.9103 (tt0) REVERT: B 2145 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8955 (mm-30) REVERT: B 2239 MET cc_start: 0.6936 (ppp) cc_final: 0.6475 (mmp) REVERT: B 2411 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8954 (mm-30) REVERT: B 2428 ARG cc_start: 0.9227 (mmm160) cc_final: 0.8700 (tpm170) REVERT: B 2448 ASP cc_start: 0.8870 (m-30) cc_final: 0.8560 (m-30) REVERT: B 2475 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8520 (mm) REVERT: B 2670 LYS cc_start: 0.9216 (tppp) cc_final: 0.8620 (tmtt) REVERT: B 2736 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8596 (m-40) REVERT: B 2751 THR cc_start: 0.9355 (p) cc_final: 0.9139 (t) REVERT: B 2895 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9069 (mp0) REVERT: B 3018 LYS cc_start: 0.9428 (mttt) cc_final: 0.9103 (mttm) outliers start: 62 outliers final: 30 residues processed: 312 average time/residue: 1.1902 time to fit residues: 440.2957 Evaluate side-chains 311 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1474 HIS Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 1935 ASP Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2475 LEU Chi-restraints excluded: chain A residue 2493 GLU Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain A residue 2942 GLN Chi-restraints excluded: chain B residue 1474 HIS Chi-restraints excluded: chain B residue 1516 HIS Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1706 LYS Chi-restraints excluded: chain B residue 1823 ILE Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2008 ILE Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 LEU Chi-restraints excluded: chain B residue 2051 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2736 ASN Chi-restraints excluded: chain B residue 2896 GLN Chi-restraints excluded: chain B residue 2942 GLN Chi-restraints excluded: chain B residue 2945 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 278 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 260 optimal weight: 8.9990 chunk 238 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 263 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2106 ASN ** A2469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2632 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2736 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068055 restraints weight = 55405.014| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.73 r_work: 0.2906 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24426 Z= 0.127 Angle : 0.688 15.184 32982 Z= 0.319 Chirality : 0.042 0.383 3736 Planarity : 0.004 0.061 4176 Dihedral : 4.282 67.462 3270 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.98 % Allowed : 19.15 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.16), residues: 2930 helix: 2.41 (0.12), residues: 2006 sheet: 1.10 (0.65), residues: 58 loop : 0.02 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1710 HIS 0.010 0.001 HIS B2208 PHE 0.048 0.001 PHE A1749 TYR 0.015 0.001 TYR B1753 ARG 0.015 0.000 ARG A2428 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 1498) hydrogen bonds : angle 3.50755 ( 4461) metal coordination : bond 0.00185 ( 6) covalent geometry : bond 0.00302 (24420) covalent geometry : angle 0.68805 (32982) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 281 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1474 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8349 (m-70) REVERT: A 1475 TYR cc_start: 0.8871 (m-80) cc_final: 0.8588 (m-80) REVERT: A 1539 LEU cc_start: 0.9337 (mm) cc_final: 0.9081 (pp) REVERT: A 1556 TYR cc_start: 0.7280 (m-80) cc_final: 0.7017 (m-80) REVERT: A 1565 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: A 1575 ARG cc_start: 0.8761 (mtt180) cc_final: 0.8018 (mmm160) REVERT: A 1701 LYS cc_start: 0.9367 (pttm) cc_final: 0.9104 (pttp) REVERT: A 1706 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8453 (tmmm) REVERT: A 1720 ASN cc_start: 0.8889 (m-40) cc_final: 0.8656 (m-40) REVERT: A 1749 PHE cc_start: 0.9020 (t80) cc_final: 0.8812 (t80) REVERT: A 1836 ASP cc_start: 0.9436 (m-30) cc_final: 0.8892 (t0) REVERT: A 1844 TYR cc_start: 0.9011 (m-80) cc_final: 0.8735 (m-80) REVERT: A 1935 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8618 (m-30) REVERT: A 2051 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8956 (tm) REVERT: A 2126 GLU cc_start: 0.9439 (tt0) cc_final: 0.9112 (tt0) REVERT: A 2239 MET cc_start: 0.6923 (ppp) cc_final: 0.6379 (mmp) REVERT: A 2304 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: A 2407 SER cc_start: 0.7569 (p) cc_final: 0.7111 (p) REVERT: A 2411 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8782 (mm-30) REVERT: A 2428 ARG cc_start: 0.9202 (mmm160) cc_final: 0.8770 (tpm170) REVERT: A 2446 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8746 (pp20) REVERT: A 2448 ASP cc_start: 0.8884 (m-30) cc_final: 0.8584 (m-30) REVERT: A 2475 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8419 (mm) REVERT: A 2507 ASP cc_start: 0.8958 (t0) cc_final: 0.8584 (t0) REVERT: A 2527 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6427 (mpp) REVERT: A 2532 MET cc_start: 0.6760 (tpt) cc_final: 0.6467 (tpp) REVERT: A 2596 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8700 (tm-30) REVERT: A 2670 LYS cc_start: 0.9201 (tppp) cc_final: 0.8558 (tmtt) REVERT: A 3018 LYS cc_start: 0.9420 (mttt) cc_final: 0.9096 (mttm) REVERT: B 1474 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.8287 (m-70) REVERT: B 1539 LEU cc_start: 0.9298 (mm) cc_final: 0.9090 (pp) REVERT: B 1575 ARG cc_start: 0.8540 (mtt180) cc_final: 0.7918 (mmm160) REVERT: B 1580 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8764 (mmmm) REVERT: B 1701 LYS cc_start: 0.9314 (pttm) cc_final: 0.9099 (pttp) REVERT: B 1706 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8484 (tmmm) REVERT: B 1717 TYR cc_start: 0.9259 (t80) cc_final: 0.8908 (t80) REVERT: B 1793 ASN cc_start: 0.8945 (m-40) cc_final: 0.8581 (p0) REVERT: B 1830 MET cc_start: 0.8486 (tmm) cc_final: 0.8017 (ppp) REVERT: B 1836 ASP cc_start: 0.9542 (m-30) cc_final: 0.8885 (t0) REVERT: B 1844 TYR cc_start: 0.9074 (m-80) cc_final: 0.8755 (m-80) REVERT: B 2008 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8827 (mp) REVERT: B 2051 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8984 (tm) REVERT: B 2145 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8913 (mm-30) REVERT: B 2239 MET cc_start: 0.7007 (ppp) cc_final: 0.6547 (mmp) REVERT: B 2411 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8952 (mm-30) REVERT: B 2428 ARG cc_start: 0.9212 (mmm160) cc_final: 0.8700 (tpm170) REVERT: B 2450 LEU cc_start: 0.9094 (tt) cc_final: 0.8677 (mm) REVERT: B 2475 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8391 (mm) REVERT: B 2507 ASP cc_start: 0.8782 (t0) cc_final: 0.8296 (t0) REVERT: B 2532 MET cc_start: 0.6805 (tpt) cc_final: 0.6517 (tpp) REVERT: B 2670 LYS cc_start: 0.9200 (tppp) cc_final: 0.8588 (tmtt) REVERT: B 2736 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8640 (m-40) REVERT: B 2740 GLN cc_start: 0.9545 (tp-100) cc_final: 0.8959 (tp-100) REVERT: B 2751 THR cc_start: 0.9384 (p) cc_final: 0.9163 (t) REVERT: B 2895 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9060 (mp0) REVERT: B 3018 LYS cc_start: 0.9429 (mttt) cc_final: 0.9114 (mttm) outliers start: 53 outliers final: 30 residues processed: 308 average time/residue: 1.1434 time to fit residues: 413.2509 Evaluate side-chains 313 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1474 HIS Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1611 LEU Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 1935 ASP Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2356 ILE Chi-restraints excluded: chain A residue 2475 LEU Chi-restraints excluded: chain A residue 2493 GLU Chi-restraints excluded: chain A residue 2527 MET Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2942 GLN Chi-restraints excluded: chain B residue 1474 HIS Chi-restraints excluded: chain B residue 1516 HIS Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1706 LYS Chi-restraints excluded: chain B residue 1823 ILE Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 2008 ILE Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 LEU Chi-restraints excluded: chain B residue 2051 LEU Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2356 ILE Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2736 ASN Chi-restraints excluded: chain B residue 2896 GLN Chi-restraints excluded: chain B residue 2942 GLN Chi-restraints excluded: chain B residue 2945 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 85 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 287 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 269 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 47 optimal weight: 0.0020 chunk 286 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2632 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.095153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.069044 restraints weight = 54210.824| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.75 r_work: 0.2920 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24426 Z= 0.118 Angle : 0.691 15.314 32982 Z= 0.319 Chirality : 0.042 0.366 3736 Planarity : 0.004 0.057 4176 Dihedral : 4.306 67.962 3270 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.80 % Allowed : 19.37 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.16), residues: 2930 helix: 2.36 (0.12), residues: 2008 sheet: 1.08 (0.65), residues: 58 loop : 0.02 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B1710 HIS 0.009 0.001 HIS B2208 PHE 0.049 0.001 PHE B1749 TYR 0.056 0.001 TYR B1475 ARG 0.014 0.000 ARG A2428 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 1498) hydrogen bonds : angle 3.49702 ( 4461) metal coordination : bond 0.00170 ( 6) covalent geometry : bond 0.00275 (24420) covalent geometry : angle 0.69125 (32982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14255.42 seconds wall clock time: 246 minutes 59.02 seconds (14819.02 seconds total)