Starting phenix.real_space_refine on Mon Sep 30 06:36:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/09_2024/8oxo_17266.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/09_2024/8oxo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/09_2024/8oxo_17266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/09_2024/8oxo_17266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/09_2024/8oxo_17266.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/09_2024/8oxo_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-5461/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: 14.98, per 1000 atoms: 0.62 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: 6.22 Conformation dependent library (CDL) restraints added in 3.0 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: 3.01 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: 9.34 Time building geometry restraints manager: 7.19 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: 0.00 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: 2.970 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: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 59.790 Find NCS groups from input model: 0.730 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: 0.010 Load rotamer database and sin/cos tables:14.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.720 ------------------------------------------------------------------------------- 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 24420 Z= 0.170 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 583 time to evaluate : 2.948 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: 1.2726 time to fit residues: 855.0398 Evaluate side-chains 305 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 2.793 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 24420 Z= 0.186 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 *********************** 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 fitting. rotamer outliers: 54 poor density : 344 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1556 TYR cc_start: 0.7235 (m-80) cc_final: 0.6965 (m-80) REVERT: A 1575 ARG cc_start: 0.8841 (mtt180) cc_final: 0.7948 (mmm160) REVERT: A 1630 ASP cc_start: 0.8960 (p0) cc_final: 0.8483 (m-30) REVERT: A 1793 ASN cc_start: 0.8846 (m-40) cc_final: 0.8551 (p0) REVERT: A 1844 TYR cc_start: 0.8945 (m-80) cc_final: 0.8616 (m-80) REVERT: A 1935 ASP cc_start: 0.9001 (t0) cc_final: 0.8683 (m-30) REVERT: A 1999 ILE cc_start: 0.9116 (mp) cc_final: 0.8852 (mp) REVERT: A 2196 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8555 (ppp80) REVERT: A 2407 SER cc_start: 0.8065 (p) cc_final: 0.7521 (p) REVERT: A 2411 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8820 (mm-30) REVERT: A 2446 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 2450 LEU cc_start: 0.9187 (tt) cc_final: 0.8634 (mm) REVERT: A 2475 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8973 (mm) REVERT: A 2503 MET cc_start: 0.8768 (ttm) cc_final: 0.8323 (ttm) REVERT: A 2507 ASP cc_start: 0.8514 (t0) cc_final: 0.7818 (m-30) REVERT: A 2596 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8561 (tm-30) REVERT: A 2597 ASP cc_start: 0.8945 (t0) cc_final: 0.8657 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9229 (tppp) cc_final: 0.8798 (tmtt) REVERT: A 2751 THR cc_start: 0.9194 (p) cc_final: 0.8854 (t) REVERT: A 2896 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6414 (tm-30) REVERT: A 3018 LYS cc_start: 0.9342 (mttt) cc_final: 0.9075 (mttp) REVERT: B 1556 TYR cc_start: 0.7262 (m-80) cc_final: 0.7043 (m-80) REVERT: B 1575 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8079 (mtp85) REVERT: B 1580 LYS cc_start: 0.8982 (mmpt) cc_final: 0.8738 (mmmt) REVERT: B 1630 ASP cc_start: 0.8988 (p0) cc_final: 0.8424 (m-30) REVERT: B 1714 MET cc_start: 0.9479 (tpp) cc_final: 0.9274 (tpp) REVERT: B 1793 ASN cc_start: 0.8843 (m-40) cc_final: 0.8433 (p0) REVERT: B 1844 TYR cc_start: 0.8941 (m-80) cc_final: 0.8548 (m-80) REVERT: B 1907 ARG cc_start: 0.8520 (ptp-170) cc_final: 0.8191 (mtt90) REVERT: B 2156 GLU cc_start: 0.7996 (pp20) cc_final: 0.7187 (pp20) REVERT: B 2411 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8819 (mm-30) REVERT: B 2428 ARG cc_start: 0.8938 (tpm170) cc_final: 0.8678 (tpm170) REVERT: B 2446 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8335 (tm-30) REVERT: B 2450 LEU cc_start: 0.9211 (tt) cc_final: 0.8649 (mm) REVERT: B 2475 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8893 (mm) REVERT: B 2503 MET cc_start: 0.8767 (ttm) cc_final: 0.8549 (ttm) REVERT: B 2507 ASP cc_start: 0.8518 (t0) cc_final: 0.7871 (m-30) REVERT: B 2597 ASP cc_start: 0.8931 (t0) cc_final: 0.8649 (m-30) REVERT: B 2670 LYS cc_start: 0.9239 (tppp) cc_final: 0.8800 (tmtt) REVERT: B 2751 THR cc_start: 0.9216 (p) cc_final: 0.8851 (t) REVERT: B 2962 MET cc_start: 0.7906 (mtm) cc_final: 0.7614 (mmm) REVERT: B 3018 LYS cc_start: 0.9359 (mttt) cc_final: 0.9073 (mttp) outliers start: 54 outliers final: 17 residues processed: 377 average time/residue: 1.1984 time to fit residues: 528.2827 Evaluate side-chains 323 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 303 time to evaluate : 2.625 ------------------------------------------------------------------------------- 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 148 optimal weight: 0.2980 chunk 83 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 266 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** A1946 GLN A2002 GLN A2632 ASN A2736 ASN A2809 GLN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2002 GLN B2106 ASN ** B2177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2197 GLN B2632 ASN B2736 ASN B2896 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24420 Z= 0.225 Angle : 0.610 9.584 32982 Z= 0.295 Chirality : 0.040 0.341 3736 Planarity : 0.003 0.045 4176 Dihedral : 4.688 103.674 3270 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.09 % Allowed : 14.10 % Favored : 83.81 % 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: 2.58 (0.16), residues: 2930 helix: 2.45 (0.12), residues: 2002 sheet: 0.86 (0.65), residues: 58 loop : 0.03 (0.22), residues: 870 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 *********************** 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 355 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 299 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 TYR cc_start: 0.9384 (m-80) cc_final: 0.8719 (t80) REVERT: A 1556 TYR cc_start: 0.7424 (m-80) cc_final: 0.7217 (m-80) REVERT: A 1565 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: A 1575 ARG cc_start: 0.8763 (mtt180) cc_final: 0.8188 (mmm160) REVERT: A 1630 ASP cc_start: 0.8997 (p0) cc_final: 0.8603 (m-30) REVERT: A 1714 MET cc_start: 0.9451 (tpp) cc_final: 0.9228 (tpp) REVERT: A 1720 ASN cc_start: 0.8653 (m-40) cc_final: 0.8220 (m110) REVERT: A 1793 ASN cc_start: 0.8900 (m-40) cc_final: 0.8604 (p0) REVERT: A 2051 LEU cc_start: 0.9009 (tm) cc_final: 0.8753 (tm) REVERT: A 2235 MET cc_start: 0.9012 (tpt) cc_final: 0.8744 (tpt) REVERT: A 2239 MET cc_start: 0.7202 (ppp) cc_final: 0.6825 (mmp) REVERT: A 2304 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: A 2407 SER cc_start: 0.7921 (p) cc_final: 0.7310 (p) REVERT: A 2411 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8733 (mm-30) REVERT: A 2446 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 2450 LEU cc_start: 0.9216 (tt) cc_final: 0.8657 (mm) REVERT: A 2475 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8903 (mm) REVERT: A 2503 MET cc_start: 0.8723 (ttm) cc_final: 0.8518 (ttm) REVERT: A 2507 ASP cc_start: 0.8613 (t0) cc_final: 0.7929 (m-30) REVERT: A 2596 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8513 (tm-30) REVERT: A 2597 ASP cc_start: 0.9015 (t0) cc_final: 0.8673 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9214 (tppp) cc_final: 0.8775 (tmtt) REVERT: A 2736 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8638 (m-40) REVERT: A 2751 THR cc_start: 0.9332 (p) cc_final: 0.9094 (t) REVERT: A 2896 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: A 2938 MET cc_start: 0.9255 (mmm) cc_final: 0.8958 (mtm) REVERT: A 3018 LYS cc_start: 0.9378 (mttt) cc_final: 0.9134 (mttp) REVERT: B 1470 TYR cc_start: 0.9361 (m-80) cc_final: 0.8657 (t80) REVERT: B 1556 TYR cc_start: 0.7416 (m-80) cc_final: 0.7130 (m-80) REVERT: B 1565 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: B 1575 ARG cc_start: 0.8523 (mtt180) cc_final: 0.8187 (mtp85) REVERT: B 1580 LYS cc_start: 0.9092 (mmpt) cc_final: 0.8885 (mmmt) REVERT: B 1630 ASP cc_start: 0.9072 (p0) cc_final: 0.8605 (m-30) REVERT: B 1793 ASN cc_start: 0.8869 (m-40) cc_final: 0.8495 (p0) REVERT: B 1844 TYR cc_start: 0.9039 (m-80) cc_final: 0.8671 (m-80) REVERT: B 1907 ARG cc_start: 0.8604 (ptp-170) cc_final: 0.8231 (mtt90) REVERT: B 1999 ILE cc_start: 0.8769 (mm) cc_final: 0.8547 (mp) REVERT: B 2008 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9003 (mp) REVERT: B 2411 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8854 (mm-30) REVERT: B 2475 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8910 (mm) REVERT: B 2503 MET cc_start: 0.8855 (ttm) cc_final: 0.8642 (ttm) REVERT: B 2507 ASP cc_start: 0.8617 (t0) cc_final: 0.7958 (m-30) REVERT: B 2519 LEU cc_start: 0.9178 (pp) cc_final: 0.8966 (pp) REVERT: B 2670 LYS cc_start: 0.9231 (tppp) cc_final: 0.8806 (tmtt) REVERT: B 2736 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8612 (m-40) REVERT: B 2751 THR cc_start: 0.9353 (p) cc_final: 0.9106 (t) REVERT: B 3018 LYS cc_start: 0.9393 (mttt) cc_final: 0.9138 (mttp) outliers start: 56 outliers final: 20 residues processed: 334 average time/residue: 1.1673 time to fit residues: 460.2374 Evaluate side-chains 291 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 263 time to evaluate : 2.930 ------------------------------------------------------------------------------- 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 2270 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 2557 LEU 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 1565 PHE 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 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 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 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 265 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 269 optimal weight: 0.0570 chunk 285 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 255 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- 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** A2632 ASN A2736 ASN B1847 HIS ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2736 ASN B2809 GLN B2896 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24420 Z= 0.181 Angle : 0.590 12.174 32982 Z= 0.281 Chirality : 0.039 0.317 3736 Planarity : 0.003 0.044 4176 Dihedral : 4.401 95.160 3270 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.51 % Allowed : 15.11 % Favored : 82.39 % 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: 2.48 (0.12), residues: 2006 sheet: 0.91 (0.64), residues: 58 loop : 0.03 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1805 HIS 0.012 0.001 HIS B1802 PHE 0.023 0.001 PHE A1712 TYR 0.016 0.001 TYR A1529 ARG 0.014 0.000 ARG A2428 *********************** 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 353 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 286 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 TYR cc_start: 0.9371 (m-80) cc_final: 0.8754 (t80) REVERT: A 1475 TYR cc_start: 0.8702 (m-80) cc_final: 0.8403 (m-10) REVERT: A 1556 TYR cc_start: 0.7451 (m-80) cc_final: 0.7131 (m-80) REVERT: A 1565 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: A 1575 ARG cc_start: 0.8697 (mtt180) cc_final: 0.8011 (mmm160) REVERT: A 1630 ASP cc_start: 0.9029 (p0) cc_final: 0.8647 (m-30) REVERT: A 1720 ASN cc_start: 0.8751 (m-40) cc_final: 0.8238 (m110) REVERT: A 2037 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8636 (mt-10) REVERT: A 2235 MET cc_start: 0.9019 (tpt) cc_final: 0.8798 (tpt) REVERT: A 2304 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: A 2407 SER cc_start: 0.7834 (p) cc_final: 0.7185 (p) REVERT: A 2411 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8739 (mm-30) REVERT: A 2428 ARG cc_start: 0.9024 (mmm160) cc_final: 0.8567 (tpm170) REVERT: A 2507 ASP cc_start: 0.8653 (t0) cc_final: 0.7963 (m-30) REVERT: A 2596 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8555 (tm-30) REVERT: A 2597 ASP cc_start: 0.8988 (t0) cc_final: 0.8739 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9212 (tppp) cc_final: 0.8739 (tmtt) REVERT: A 2736 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8656 (m-40) REVERT: A 2751 THR cc_start: 0.9369 (p) cc_final: 0.9121 (t) REVERT: A 2896 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6934 (tm-30) REVERT: A 3018 LYS cc_start: 0.9373 (mttt) cc_final: 0.9125 (mttp) REVERT: B 1475 TYR cc_start: 0.8698 (m-80) cc_final: 0.8418 (m-80) REVERT: B 1556 TYR cc_start: 0.7488 (m-80) cc_final: 0.7267 (m-80) REVERT: B 1565 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: B 1575 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8131 (mtp85) REVERT: B 1580 LYS cc_start: 0.9178 (mmpt) cc_final: 0.8857 (mmmt) REVERT: B 1793 ASN cc_start: 0.8902 (m-40) cc_final: 0.8527 (p0) REVERT: B 1844 TYR cc_start: 0.9046 (m-80) cc_final: 0.8665 (m-80) REVERT: B 1907 ARG cc_start: 0.8641 (ptp-170) cc_final: 0.8272 (mtt90) REVERT: B 1999 ILE cc_start: 0.8744 (mm) cc_final: 0.8540 (mp) REVERT: B 2008 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8975 (mp) REVERT: B 2051 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8765 (tm) REVERT: B 2239 MET cc_start: 0.7102 (ppp) cc_final: 0.6702 (mmp) REVERT: B 2304 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: B 2411 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8853 (mm-30) REVERT: B 2446 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8255 (tm-30) REVERT: B 2450 LEU cc_start: 0.9229 (tt) cc_final: 0.8708 (mm) REVERT: B 2503 MET cc_start: 0.8881 (ttm) cc_final: 0.8655 (ttm) REVERT: B 2507 ASP cc_start: 0.8662 (t0) cc_final: 0.8004 (m-30) REVERT: B 2519 LEU cc_start: 0.9183 (pp) cc_final: 0.8938 (pp) REVERT: B 2667 MET cc_start: 0.8803 (ttp) cc_final: 0.7793 (ptm) REVERT: B 2670 LYS cc_start: 0.9231 (tppp) cc_final: 0.8795 (tmtt) REVERT: B 2736 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8661 (m-40) REVERT: B 2751 THR cc_start: 0.9378 (p) cc_final: 0.9129 (t) REVERT: B 2752 ILE cc_start: 0.8678 (mm) cc_final: 0.8312 (mm) REVERT: B 3018 LYS cc_start: 0.9395 (mttt) cc_final: 0.9137 (mttp) outliers start: 67 outliers final: 22 residues processed: 329 average time/residue: 1.1202 time to fit residues: 435.6709 Evaluate side-chains 297 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 266 time to evaluate : 2.935 ------------------------------------------------------------------------------- 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 1611 LEU 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 2037 GLU 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 2557 LEU 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 1565 PHE Chi-restraints excluded: chain B residue 1581 ILE Chi-restraints excluded: chain B residue 1611 LEU Chi-restraints excluded: chain B residue 1764 LEU 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 Chi-restraints excluded: chain B residue 2736 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 243 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 0.0670 chunk 255 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2210 GLN A2632 ASN A2736 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24420 Z= 0.188 Angle : 0.599 12.205 32982 Z= 0.283 Chirality : 0.039 0.276 3736 Planarity : 0.003 0.044 4176 Dihedral : 4.320 87.600 3270 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.69 % Allowed : 15.93 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.46 (0.12), residues: 2008 sheet: 0.97 (0.64), residues: 58 loop : 0.06 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1805 HIS 0.011 0.001 HIS B1802 PHE 0.019 0.001 PHE A1712 TYR 0.017 0.001 TYR B1470 ARG 0.006 0.000 ARG A2428 *********************** 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 fitting. rotamer outliers: 72 poor density : 283 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 TYR cc_start: 0.9390 (m-80) cc_final: 0.8814 (t80) REVERT: A 1556 TYR cc_start: 0.7451 (m-80) cc_final: 0.7125 (m-80) REVERT: A 1565 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: A 1575 ARG cc_start: 0.8678 (mtt180) cc_final: 0.7989 (mmm160) REVERT: A 1630 ASP cc_start: 0.9030 (p0) cc_final: 0.8662 (m-30) REVERT: A 1701 LYS cc_start: 0.9260 (pttm) cc_final: 0.9011 (pttp) REVERT: A 1706 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8464 (tmmm) REVERT: A 1720 ASN cc_start: 0.8846 (m-40) cc_final: 0.8617 (m-40) REVERT: A 2051 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8902 (tm) REVERT: A 2235 MET cc_start: 0.8991 (tpt) cc_final: 0.8785 (ttm) REVERT: A 2239 MET cc_start: 0.7050 (ppp) cc_final: 0.6563 (mmp) REVERT: A 2304 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: A 2407 SER cc_start: 0.7758 (p) cc_final: 0.7189 (p) REVERT: A 2411 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8698 (mm-30) REVERT: A 2428 ARG cc_start: 0.9028 (mmm160) cc_final: 0.8593 (tpm170) REVERT: A 2446 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 2450 LEU cc_start: 0.9216 (tt) cc_final: 0.8692 (mm) REVERT: A 2507 ASP cc_start: 0.8687 (t0) cc_final: 0.8009 (m-30) REVERT: A 2596 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8570 (tm-30) REVERT: A 2597 ASP cc_start: 0.8987 (t0) cc_final: 0.8743 (OUTLIER) REVERT: A 2667 MET cc_start: 0.8797 (ttp) cc_final: 0.8146 (ptm) REVERT: A 2670 LYS cc_start: 0.9214 (tppp) cc_final: 0.8716 (tmtt) REVERT: A 2736 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8685 (m-40) REVERT: A 2751 THR cc_start: 0.9381 (p) cc_final: 0.9145 (t) REVERT: A 2752 ILE cc_start: 0.8711 (mm) cc_final: 0.8420 (mm) REVERT: A 2896 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: A 3018 LYS cc_start: 0.9389 (mttt) cc_final: 0.9148 (mttp) REVERT: B 1475 TYR cc_start: 0.8691 (m-80) cc_final: 0.8408 (m-80) REVERT: B 1539 LEU cc_start: 0.9318 (mm) cc_final: 0.9043 (pp) REVERT: B 1556 TYR cc_start: 0.7472 (m-80) cc_final: 0.7192 (m-80) REVERT: B 1565 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: B 1575 ARG cc_start: 0.8609 (mtt180) cc_final: 0.7924 (mtp85) REVERT: B 1580 LYS cc_start: 0.9175 (mmpt) cc_final: 0.8861 (mmmt) REVERT: B 1706 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8541 (tmmm) REVERT: B 1844 TYR cc_start: 0.9054 (m-80) cc_final: 0.8742 (m-80) REVERT: B 1907 ARG cc_start: 0.8672 (ptp-170) cc_final: 0.8255 (mtt90) REVERT: B 1999 ILE cc_start: 0.8737 (mm) cc_final: 0.8536 (mp) REVERT: B 2008 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8965 (mp) REVERT: B 2051 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8851 (tm) REVERT: B 2304 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: B 2411 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8861 (mm-30) REVERT: B 2446 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8294 (tm-30) REVERT: B 2448 ASP cc_start: 0.8792 (m-30) cc_final: 0.8446 (m-30) REVERT: B 2450 LEU cc_start: 0.9227 (tt) cc_final: 0.8709 (mm) REVERT: B 2519 LEU cc_start: 0.9191 (pp) cc_final: 0.8941 (pp) REVERT: B 2667 MET cc_start: 0.8785 (ttp) cc_final: 0.7836 (ptm) REVERT: B 2670 LYS cc_start: 0.9212 (tppp) cc_final: 0.8733 (tmtt) REVERT: B 2736 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8680 (m-40) REVERT: B 2751 THR cc_start: 0.9390 (p) cc_final: 0.9137 (t) REVERT: B 2752 ILE cc_start: 0.8706 (mm) cc_final: 0.8394 (mm) REVERT: B 2938 MET cc_start: 0.9328 (mmm) cc_final: 0.8944 (mtm) REVERT: B 3018 LYS cc_start: 0.9389 (mttt) cc_final: 0.9140 (mttp) outliers start: 72 outliers final: 25 residues processed: 330 average time/residue: 1.0769 time to fit residues: 424.0471 Evaluate side-chains 302 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 266 time to evaluate : 2.759 ------------------------------------------------------------------------------- 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 1611 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 2557 LEU 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 1565 PHE Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1609 THR 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 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 2304 GLU Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2736 ASN Chi-restraints excluded: chain B residue 2942 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 0.7980 chunk 256 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2210 GLN A2632 ASN A2736 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2736 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24420 Z= 0.199 Angle : 0.613 12.134 32982 Z= 0.288 Chirality : 0.040 0.294 3736 Planarity : 0.003 0.058 4176 Dihedral : 4.282 79.180 3270 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.73 % Allowed : 16.64 % 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: 2.60 (0.16), residues: 2930 helix: 2.44 (0.12), residues: 2012 sheet: 1.03 (0.64), residues: 58 loop : 0.06 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1805 HIS 0.012 0.001 HIS B2208 PHE 0.023 0.001 PHE A1712 TYR 0.015 0.001 TYR A1753 ARG 0.014 0.000 ARG B2428 *********************** 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 357 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 284 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 TYR cc_start: 0.9384 (m-80) cc_final: 0.8822 (t80) REVERT: A 1475 TYR cc_start: 0.8759 (m-80) cc_final: 0.8454 (m-80) REVERT: A 1539 LEU cc_start: 0.9323 (mm) cc_final: 0.9023 (pp) REVERT: A 1556 TYR cc_start: 0.7445 (m-80) cc_final: 0.7217 (m-80) REVERT: A 1565 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: A 1575 ARG cc_start: 0.8666 (mtt180) cc_final: 0.7978 (mmm160) REVERT: A 1630 ASP cc_start: 0.9019 (p0) cc_final: 0.8643 (m-30) REVERT: A 1701 LYS cc_start: 0.9269 (pttm) cc_final: 0.9014 (pttp) REVERT: A 1706 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8473 (tmmm) REVERT: A 1720 ASN cc_start: 0.8881 (m-40) cc_final: 0.8620 (m-40) REVERT: A 2304 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: A 2407 SER cc_start: 0.7723 (p) cc_final: 0.7145 (p) REVERT: A 2411 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8696 (mm-30) REVERT: A 2428 ARG cc_start: 0.9050 (mmm160) cc_final: 0.8637 (tpm170) REVERT: A 2448 ASP cc_start: 0.8780 (m-30) cc_final: 0.8436 (m-30) REVERT: A 2596 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8557 (tm-30) REVERT: A 2597 ASP cc_start: 0.8998 (t0) cc_final: 0.8748 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9179 (tppp) cc_final: 0.8674 (tmtt) REVERT: A 2736 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8687 (m-40) REVERT: A 2751 THR cc_start: 0.9393 (p) cc_final: 0.9149 (t) REVERT: A 2752 ILE cc_start: 0.8744 (mm) cc_final: 0.8460 (mm) REVERT: A 2896 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: A 3018 LYS cc_start: 0.9395 (mttt) cc_final: 0.9091 (mttm) REVERT: B 1475 TYR cc_start: 0.8724 (m-80) cc_final: 0.8439 (m-80) REVERT: B 1539 LEU cc_start: 0.9298 (mm) cc_final: 0.9033 (pp) REVERT: B 1556 TYR cc_start: 0.7478 (m-80) cc_final: 0.7179 (m-80) REVERT: B 1565 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7324 (m-80) REVERT: B 1575 ARG cc_start: 0.8560 (mtt180) cc_final: 0.7963 (mtp85) REVERT: B 1580 LYS cc_start: 0.9156 (mmpt) cc_final: 0.8807 (mmmt) REVERT: B 1701 LYS cc_start: 0.9278 (pttm) cc_final: 0.8974 (pttp) REVERT: B 1706 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8559 (tmmm) REVERT: B 1844 TYR cc_start: 0.9067 (m-80) cc_final: 0.8771 (m-80) REVERT: B 1907 ARG cc_start: 0.8711 (ptp-170) cc_final: 0.8413 (mtm-85) REVERT: B 1999 ILE cc_start: 0.8742 (mm) cc_final: 0.8539 (mp) REVERT: B 2008 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8956 (mp) REVERT: B 2051 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8925 (tm) REVERT: B 2239 MET cc_start: 0.6991 (ppp) cc_final: 0.6529 (mmp) REVERT: B 2304 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: B 2411 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8880 (mm-30) REVERT: B 2428 ARG cc_start: 0.9154 (mmm160) cc_final: 0.8626 (tpm170) REVERT: B 2448 ASP cc_start: 0.8801 (m-30) cc_final: 0.8459 (m-30) REVERT: B 2670 LYS cc_start: 0.9210 (tppp) cc_final: 0.8709 (tmtt) REVERT: B 2736 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8662 (m-40) REVERT: B 2751 THR cc_start: 0.9396 (p) cc_final: 0.9146 (t) REVERT: B 2752 ILE cc_start: 0.8738 (mm) cc_final: 0.8436 (mm) REVERT: B 2938 MET cc_start: 0.9273 (mmm) cc_final: 0.8962 (mtm) REVERT: B 3018 LYS cc_start: 0.9409 (mttt) cc_final: 0.9156 (mttp) outliers start: 73 outliers final: 30 residues processed: 330 average time/residue: 1.1131 time to fit residues: 434.7679 Evaluate side-chains 301 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 261 time to evaluate : 2.763 ------------------------------------------------------------------------------- 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 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 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 2557 LEU 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 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 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 2176 LEU 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 2550 MET Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2736 ASN Chi-restraints excluded: chain B residue 2942 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 284 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1552 ASN A2210 GLN A2632 ASN A2736 ASN B1552 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2736 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24420 Z= 0.210 Angle : 0.631 12.688 32982 Z= 0.295 Chirality : 0.041 0.332 3736 Planarity : 0.003 0.045 4176 Dihedral : 4.272 70.233 3270 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.47 % Allowed : 17.88 % Favored : 79.66 % 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: 2.58 (0.16), residues: 2930 helix: 2.43 (0.12), residues: 2010 sheet: 1.09 (0.65), residues: 58 loop : 0.04 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1805 HIS 0.012 0.001 HIS B2208 PHE 0.027 0.001 PHE B1749 TYR 0.015 0.001 TYR B1717 ARG 0.010 0.000 ARG B2428 *********************** 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 349 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 283 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1475 TYR cc_start: 0.8734 (m-80) cc_final: 0.8434 (m-10) REVERT: A 1539 LEU cc_start: 0.9328 (mm) cc_final: 0.9033 (pp) REVERT: A 1556 TYR cc_start: 0.7479 (m-80) cc_final: 0.7212 (m-80) REVERT: A 1565 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: A 1575 ARG cc_start: 0.8657 (mtt180) cc_final: 0.7973 (mmm160) REVERT: A 1701 LYS cc_start: 0.9276 (pttm) cc_final: 0.8984 (pttp) REVERT: A 1706 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8460 (tmmm) REVERT: A 1720 ASN cc_start: 0.8911 (m-40) cc_final: 0.8652 (m-40) REVERT: A 2239 MET cc_start: 0.6930 (ppp) cc_final: 0.6499 (mmp) REVERT: A 2304 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: A 2407 SER cc_start: 0.7709 (p) cc_final: 0.6961 (p) REVERT: A 2411 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8780 (mm-30) REVERT: A 2428 ARG cc_start: 0.9078 (mmm160) cc_final: 0.8645 (tpm170) REVERT: A 2448 ASP cc_start: 0.8794 (m-30) cc_final: 0.8424 (m-30) REVERT: A 2596 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8581 (tm-30) REVERT: A 2597 ASP cc_start: 0.8989 (t0) cc_final: 0.8752 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9182 (tppp) cc_final: 0.8693 (tmtt) REVERT: A 2736 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8693 (m-40) REVERT: A 2751 THR cc_start: 0.9404 (p) cc_final: 0.9153 (t) REVERT: A 2752 ILE cc_start: 0.8780 (mm) cc_final: 0.8519 (mm) REVERT: A 2896 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: A 2938 MET cc_start: 0.9314 (mmm) cc_final: 0.8967 (mtm) REVERT: A 3018 LYS cc_start: 0.9404 (mttt) cc_final: 0.9083 (mttm) REVERT: B 1470 TYR cc_start: 0.9392 (m-80) cc_final: 0.8668 (t80) REVERT: B 1475 TYR cc_start: 0.8692 (m-80) cc_final: 0.8428 (m-80) REVERT: B 1539 LEU cc_start: 0.9287 (mm) cc_final: 0.9040 (pp) REVERT: B 1556 TYR cc_start: 0.7483 (m-80) cc_final: 0.7263 (m-80) REVERT: B 1565 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: B 1575 ARG cc_start: 0.8472 (mtt180) cc_final: 0.7898 (mtp85) REVERT: B 1580 LYS cc_start: 0.9171 (mmpt) cc_final: 0.8811 (mmmt) REVERT: B 1701 LYS cc_start: 0.9295 (pttm) cc_final: 0.8971 (pttp) REVERT: B 1706 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8540 (tmmm) REVERT: B 1844 TYR cc_start: 0.9063 (m-80) cc_final: 0.8823 (m-80) REVERT: B 1907 ARG cc_start: 0.8738 (ptp-170) cc_final: 0.8399 (mtm-85) REVERT: B 1935 ASP cc_start: 0.9001 (t0) cc_final: 0.8728 (m-30) REVERT: B 1999 ILE cc_start: 0.8766 (mm) cc_final: 0.8566 (mp) REVERT: B 2008 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8952 (mp) REVERT: B 2051 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8962 (tm) REVERT: B 2304 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: B 2411 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8877 (mm-30) REVERT: B 2428 ARG cc_start: 0.9129 (mmm160) cc_final: 0.8521 (tpm170) REVERT: B 2448 ASP cc_start: 0.8799 (m-30) cc_final: 0.8428 (m-30) REVERT: B 2670 LYS cc_start: 0.9202 (tppp) cc_final: 0.8699 (tmtt) REVERT: B 2736 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8720 (m-40) REVERT: B 2751 THR cc_start: 0.9405 (p) cc_final: 0.9146 (t) REVERT: B 2752 ILE cc_start: 0.8784 (mm) cc_final: 0.8506 (mm) REVERT: B 2896 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: B 2938 MET cc_start: 0.9248 (mmm) cc_final: 0.8965 (mtm) REVERT: B 3018 LYS cc_start: 0.9417 (mttt) cc_final: 0.9093 (mttm) outliers start: 66 outliers final: 33 residues processed: 321 average time/residue: 1.1850 time to fit residues: 450.3924 Evaluate side-chains 311 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 267 time to evaluate : 2.688 ------------------------------------------------------------------------------- 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 1609 THR Chi-restraints excluded: chain A residue 1611 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 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 2557 LEU 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 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 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 2176 LEU 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 2493 GLU Chi-restraints excluded: chain B residue 2550 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2632 ASN A2736 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2106 ASN B2632 ASN B2736 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24420 Z= 0.200 Angle : 0.643 13.515 32982 Z= 0.299 Chirality : 0.041 0.350 3736 Planarity : 0.003 0.045 4176 Dihedral : 4.279 67.446 3270 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.58 % Allowed : 18.03 % Favored : 79.39 % 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: 2.59 (0.16), residues: 2930 helix: 2.42 (0.12), residues: 2008 sheet: 1.15 (0.65), residues: 58 loop : 0.09 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1805 HIS 0.012 0.001 HIS B2208 PHE 0.030 0.001 PHE B1749 TYR 0.013 0.001 TYR B1696 ARG 0.008 0.000 ARG B2428 *********************** 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 352 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 283 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 LEU cc_start: 0.9326 (mm) cc_final: 0.9035 (pp) REVERT: A 1556 TYR cc_start: 0.7485 (m-80) cc_final: 0.7222 (m-80) REVERT: A 1565 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: A 1575 ARG cc_start: 0.8658 (mtt180) cc_final: 0.7977 (mmm160) REVERT: A 1701 LYS cc_start: 0.9336 (pttm) cc_final: 0.9046 (pttp) REVERT: A 1706 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8485 (tmmm) REVERT: A 1717 TYR cc_start: 0.9306 (t80) cc_final: 0.8912 (t80) REVERT: A 1720 ASN cc_start: 0.8939 (m-40) cc_final: 0.8685 (m-40) REVERT: A 1836 ASP cc_start: 0.9453 (m-30) cc_final: 0.8910 (t0) REVERT: A 2239 MET cc_start: 0.6907 (ppp) cc_final: 0.6451 (mmp) REVERT: A 2304 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: A 2407 SER cc_start: 0.7680 (p) cc_final: 0.6933 (p) REVERT: A 2411 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8780 (mm-30) REVERT: A 2428 ARG cc_start: 0.9081 (mmm160) cc_final: 0.8668 (tpm170) REVERT: A 2448 ASP cc_start: 0.8802 (m-30) cc_final: 0.8427 (m-30) REVERT: A 2596 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8578 (tm-30) REVERT: A 2597 ASP cc_start: 0.8985 (t0) cc_final: 0.8749 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9183 (tppp) cc_final: 0.8680 (tmtt) REVERT: A 2736 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8683 (m-40) REVERT: A 2751 THR cc_start: 0.9424 (p) cc_final: 0.9163 (t) REVERT: A 2752 ILE cc_start: 0.8808 (mm) cc_final: 0.8536 (mm) REVERT: A 2938 MET cc_start: 0.9311 (mmm) cc_final: 0.8979 (mtm) REVERT: A 3018 LYS cc_start: 0.9411 (mttt) cc_final: 0.9087 (mttm) REVERT: B 1475 TYR cc_start: 0.8687 (m-80) cc_final: 0.8380 (m-10) REVERT: B 1565 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: B 1575 ARG cc_start: 0.8454 (mtt180) cc_final: 0.7972 (mtp85) REVERT: B 1580 LYS cc_start: 0.9189 (mmpt) cc_final: 0.8800 (mmmt) REVERT: B 1701 LYS cc_start: 0.9307 (pttm) cc_final: 0.9045 (pttp) REVERT: B 1706 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8528 (tmmm) REVERT: B 1793 ASN cc_start: 0.8935 (m-40) cc_final: 0.8578 (p0) REVERT: B 1844 TYR cc_start: 0.9064 (m-80) cc_final: 0.8840 (m-80) REVERT: B 2008 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8949 (mp) REVERT: B 2051 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8986 (tm) REVERT: B 2239 MET cc_start: 0.6878 (ppp) cc_final: 0.6576 (mmp) REVERT: B 2304 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: B 2350 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8756 (mp) REVERT: B 2411 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8858 (mm-30) REVERT: B 2428 ARG cc_start: 0.9110 (mmm160) cc_final: 0.8485 (tpm170) REVERT: B 2670 LYS cc_start: 0.9198 (tppp) cc_final: 0.8678 (tmtt) REVERT: B 2736 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8703 (m-40) REVERT: B 2751 THR cc_start: 0.9421 (p) cc_final: 0.9156 (t) REVERT: B 2752 ILE cc_start: 0.8814 (mm) cc_final: 0.8531 (mm) REVERT: B 2896 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: B 2938 MET cc_start: 0.9251 (mmm) cc_final: 0.8963 (mtm) REVERT: B 3018 LYS cc_start: 0.9416 (mttt) cc_final: 0.9124 (mttp) outliers start: 69 outliers final: 33 residues processed: 324 average time/residue: 1.0671 time to fit residues: 411.5211 Evaluate side-chains 304 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 2.694 ------------------------------------------------------------------------------- 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 1609 THR 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 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 2557 LEU Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2736 ASN 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 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 2176 LEU 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 2350 LEU Chi-restraints excluded: chain B residue 2493 GLU Chi-restraints excluded: chain B residue 2597 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 0.9990 chunk 248 optimal weight: 0.1980 chunk 264 optimal weight: 0.0070 chunk 159 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 280 optimal weight: 6.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2632 ASN A2736 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2736 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24420 Z= 0.172 Angle : 0.666 14.371 32982 Z= 0.306 Chirality : 0.041 0.392 3736 Planarity : 0.003 0.046 4176 Dihedral : 4.265 67.757 3270 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.28 % Allowed : 18.55 % 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: 2.59 (0.16), residues: 2930 helix: 2.43 (0.12), residues: 2010 sheet: 1.12 (0.65), residues: 58 loop : 0.07 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1805 HIS 0.011 0.001 HIS B2208 PHE 0.041 0.001 PHE B1749 TYR 0.014 0.001 TYR B1696 ARG 0.008 0.000 ARG B2428 *********************** 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 337 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 276 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1475 TYR cc_start: 0.8754 (m-80) cc_final: 0.8451 (m-80) REVERT: A 1539 LEU cc_start: 0.9322 (mm) cc_final: 0.9032 (pp) REVERT: A 1556 TYR cc_start: 0.7475 (m-80) cc_final: 0.7205 (m-80) REVERT: A 1565 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: A 1575 ARG cc_start: 0.8644 (mtt180) cc_final: 0.7972 (mmm160) REVERT: A 1701 LYS cc_start: 0.9355 (pttm) cc_final: 0.9060 (pttp) REVERT: A 1706 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8497 (tmmm) REVERT: A 1717 TYR cc_start: 0.9265 (t80) cc_final: 0.8936 (t80) REVERT: A 1720 ASN cc_start: 0.8931 (m-40) cc_final: 0.8677 (m-40) REVERT: A 1836 ASP cc_start: 0.9438 (m-30) cc_final: 0.8902 (t0) REVERT: A 2126 GLU cc_start: 0.9359 (tt0) cc_final: 0.9037 (tt0) REVERT: A 2239 MET cc_start: 0.6896 (ppp) cc_final: 0.6419 (mmp) REVERT: A 2304 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: A 2407 SER cc_start: 0.7691 (p) cc_final: 0.7155 (p) REVERT: A 2411 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8707 (mm-30) REVERT: A 2428 ARG cc_start: 0.9067 (mmm160) cc_final: 0.8633 (tpm170) REVERT: A 2448 ASP cc_start: 0.8796 (m-30) cc_final: 0.8416 (m-30) REVERT: A 2475 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8493 (mm) REVERT: A 2596 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8575 (tm-30) REVERT: A 2597 ASP cc_start: 0.8974 (t0) cc_final: 0.8746 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9164 (tppp) cc_final: 0.8640 (tmtt) REVERT: A 2736 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8701 (m-40) REVERT: A 2751 THR cc_start: 0.9408 (p) cc_final: 0.9137 (t) REVERT: A 2752 ILE cc_start: 0.8808 (mm) cc_final: 0.8542 (mm) REVERT: A 2938 MET cc_start: 0.9282 (mmm) cc_final: 0.9008 (mtm) REVERT: A 3018 LYS cc_start: 0.9404 (mttt) cc_final: 0.9076 (mttm) REVERT: B 1475 TYR cc_start: 0.8665 (m-80) cc_final: 0.8357 (m-10) REVERT: B 1565 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: B 1575 ARG cc_start: 0.8434 (mtt180) cc_final: 0.8068 (mtp85) REVERT: B 1580 LYS cc_start: 0.9180 (mmpt) cc_final: 0.8782 (mmmt) REVERT: B 1701 LYS cc_start: 0.9319 (pttm) cc_final: 0.9049 (pttp) REVERT: B 1706 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8636 (tmmm) REVERT: B 1793 ASN cc_start: 0.8931 (m-40) cc_final: 0.8567 (p0) REVERT: B 2008 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8901 (mp) REVERT: B 2239 MET cc_start: 0.6878 (ppp) cc_final: 0.6500 (mmp) REVERT: B 2411 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8870 (mm-30) REVERT: B 2428 ARG cc_start: 0.9096 (mmm160) cc_final: 0.8520 (tpm170) REVERT: B 2448 ASP cc_start: 0.8818 (m-30) cc_final: 0.8439 (m-30) REVERT: B 2475 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8494 (mm) REVERT: B 2670 LYS cc_start: 0.9202 (tppp) cc_final: 0.8673 (tmtt) REVERT: B 2736 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8735 (m-40) REVERT: B 2751 THR cc_start: 0.9418 (p) cc_final: 0.9157 (t) REVERT: B 2752 ILE cc_start: 0.8809 (mm) cc_final: 0.8535 (mm) REVERT: B 2938 MET cc_start: 0.9245 (mmm) cc_final: 0.9007 (mtm) REVERT: B 3018 LYS cc_start: 0.9409 (mttt) cc_final: 0.9071 (mttm) outliers start: 61 outliers final: 30 residues processed: 315 average time/residue: 1.1384 time to fit residues: 426.3830 Evaluate side-chains 306 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 267 time to evaluate : 2.558 ------------------------------------------------------------------------------- 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 1609 THR Chi-restraints excluded: chain A residue 1611 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 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 2475 LEU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2736 ASN 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 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 2008 ILE Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 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 2493 GLU Chi-restraints excluded: chain B residue 2597 ASP Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2736 ASN Chi-restraints excluded: chain B residue 2942 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 194 optimal weight: 0.3980 chunk 293 optimal weight: 3.9990 chunk 270 optimal weight: 0.4980 chunk 234 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 249 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2206 GLN A2632 ASN A2736 ASN ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2736 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24420 Z= 0.177 Angle : 0.676 14.937 32982 Z= 0.311 Chirality : 0.041 0.374 3736 Planarity : 0.003 0.047 4176 Dihedral : 4.266 67.557 3270 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.80 % Allowed : 19.00 % 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: 2.57 (0.16), residues: 2930 helix: 2.41 (0.12), residues: 2010 sheet: 1.14 (0.65), residues: 58 loop : 0.06 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1710 HIS 0.011 0.001 HIS B2208 PHE 0.049 0.001 PHE A1749 TYR 0.015 0.001 TYR A1753 ARG 0.007 0.000 ARG B2428 ********************** 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 319 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 271 time to evaluate : 2.725 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 1475 TYR cc_start: 0.8723 (m-80) cc_final: 0.8399 (m-10) REVERT: A 1539 LEU cc_start: 0.9315 (mm) cc_final: 0.9043 (pp) REVERT: A 1556 TYR cc_start: 0.7435 (m-80) cc_final: 0.7190 (m-80) REVERT: A 1565 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: A 1575 ARG cc_start: 0.8642 (mtt180) cc_final: 0.7973 (mmm160) REVERT: A 1701 LYS cc_start: 0.9357 (pttm) cc_final: 0.9071 (pttp) REVERT: A 1706 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8512 (tmmm) REVERT: A 1717 TYR cc_start: 0.9252 (t80) cc_final: 0.8923 (t80) REVERT: A 1720 ASN cc_start: 0.8924 (m-40) cc_final: 0.8668 (m-40) REVERT: A 1836 ASP cc_start: 0.9446 (m-30) cc_final: 0.8898 (t0) REVERT: A 2051 LEU cc_start: 0.9182 (tm) cc_final: 0.8958 (tm) REVERT: A 2126 GLU cc_start: 0.9358 (tt0) cc_final: 0.9037 (tt0) REVERT: A 2304 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: A 2407 SER cc_start: 0.7720 (p) cc_final: 0.7273 (p) REVERT: A 2411 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8707 (mm-30) REVERT: A 2428 ARG cc_start: 0.9084 (mmm160) cc_final: 0.8661 (tpm170) REVERT: A 2448 ASP cc_start: 0.8793 (m-30) cc_final: 0.8408 (m-30) REVERT: A 2475 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8481 (mm) REVERT: A 2596 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8614 (tm-30) REVERT: A 2597 ASP cc_start: 0.8971 (t0) cc_final: 0.8742 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9166 (tppp) cc_final: 0.8636 (tmtt) REVERT: A 2736 ASN cc_start: 0.9003 (OUTLIER) cc_final: 0.8699 (m-40) REVERT: A 2751 THR cc_start: 0.9404 (p) cc_final: 0.9142 (t) REVERT: A 2752 ILE cc_start: 0.8803 (mm) cc_final: 0.8548 (mm) REVERT: A 2938 MET cc_start: 0.9285 (mmm) cc_final: 0.9025 (mtm) REVERT: A 3018 LYS cc_start: 0.9404 (mttt) cc_final: 0.9067 (mttm) REVERT: B 1475 TYR cc_start: 0.8652 (m-80) cc_final: 0.8352 (m-10) REVERT: B 1565 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.7518 (m-80) REVERT: B 1575 ARG cc_start: 0.8491 (mtt180) cc_final: 0.8001 (mtp85) REVERT: B 1580 LYS cc_start: 0.9179 (mmpt) cc_final: 0.8785 (mmmt) REVERT: B 1701 LYS cc_start: 0.9331 (pttm) cc_final: 0.9056 (pttp) REVERT: B 1706 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8651 (tmmm) REVERT: B 1793 ASN cc_start: 0.8932 (m-40) cc_final: 0.8570 (p0) REVERT: B 1844 TYR cc_start: 0.9063 (m-80) cc_final: 0.8702 (m-80) REVERT: B 2008 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8926 (mp) REVERT: B 2239 MET cc_start: 0.6887 (ppp) cc_final: 0.6528 (mmp) REVERT: B 2411 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8871 (mm-30) REVERT: B 2428 ARG cc_start: 0.9099 (mmm160) cc_final: 0.8564 (tpm170) REVERT: B 2448 ASP cc_start: 0.8817 (m-30) cc_final: 0.8428 (m-30) REVERT: B 2475 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8480 (mm) REVERT: B 2670 LYS cc_start: 0.9184 (tppp) cc_final: 0.8658 (tmtt) REVERT: B 2736 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8723 (m-40) REVERT: B 2751 THR cc_start: 0.9401 (p) cc_final: 0.9135 (t) REVERT: B 2752 ILE cc_start: 0.8805 (mm) cc_final: 0.8542 (mm) REVERT: B 2938 MET cc_start: 0.9254 (mmm) cc_final: 0.9018 (mtm) REVERT: B 3018 LYS cc_start: 0.9424 (mttt) cc_final: 0.9086 (mttm) outliers start: 48 outliers final: 29 residues processed: 299 average time/residue: 1.1356 time to fit residues: 400.5223 Evaluate side-chains 304 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 266 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1609 THR 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 2185 ILE Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2475 LEU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2736 ASN Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain A residue 3011 MET 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 1824 LEU 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 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 2493 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 65 optimal weight: 0.9980 chunk 234 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 205 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2632 ASN A2736 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 = 0.3584 r_free = 0.3584 target = 0.094599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068490 restraints weight = 54246.846| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.75 r_work: 0.2907 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24420 Z= 0.171 Angle : 0.674 14.913 32982 Z= 0.310 Chirality : 0.041 0.348 3736 Planarity : 0.003 0.048 4176 Dihedral : 4.238 67.659 3270 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.57 % Allowed : 19.26 % 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: 2.59 (0.16), residues: 2930 helix: 2.43 (0.12), residues: 2004 sheet: 1.13 (0.65), residues: 58 loop : 0.05 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1710 HIS 0.010 0.001 HIS B2208 PHE 0.053 0.001 PHE B1749 TYR 0.019 0.001 TYR A1753 ARG 0.006 0.000 ARG B2428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8070.38 seconds wall clock time: 142 minutes 29.33 seconds (8549.33 seconds total)