Starting phenix.real_space_refine on Thu Apr 11 23:09:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/04_2024/8oxo_17266_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/04_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_17266/04_2024/8oxo_17266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/04_2024/8oxo_17266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/04_2024/8oxo_17266_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxo_17266/04_2024/8oxo_17266_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 12.18, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 10.06 Conformation dependent library (CDL) restraints added in 4.2 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... running ksdssp... Secondary structure from input PDB file: 154 helices and 4 sheets defined 66.3% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.11 Creating SS restraints... Processing helix chain 'A' and resid 1463 through 1477 Processing helix chain 'A' and resid 1491 through 1508 Processing helix chain 'A' and resid 1518 through 1523 Processing helix chain 'A' and resid 1525 through 1528 Processing helix chain 'A' and resid 1532 through 1547 Processing helix chain 'A' and resid 1553 through 1560 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 1569 through 1582 removed outlier: 4.869A pdb=" N ASP A1573 " --> pdb=" O VAL A1570 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A1579 " --> pdb=" O ILE A1576 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A1580 " --> pdb=" O THR A1577 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1581 " --> pdb=" O GLN A1578 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A1582 " --> pdb=" O GLN A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1603 Processing helix chain 'A' and resid 1608 through 1623 removed outlier: 3.510A pdb=" N LEU A1611 " --> pdb=" O LEU A1608 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU A1612 " --> pdb=" O THR A1609 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A1623 " --> pdb=" O GLN A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1634 removed outlier: 3.513A pdb=" N MET A1628 " --> pdb=" O LYS A1625 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A1629 " --> pdb=" O ASP A1626 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP A1630 " --> pdb=" O GLN A1627 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A1631 " --> pdb=" O MET A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1641 No H-bonds generated for 'chain 'A' and resid 1639 through 1641' Processing helix chain 'A' and resid 1643 through 1660 removed outlier: 5.145A pdb=" N ASN A1660 " --> pdb=" O LYS A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1676 removed outlier: 3.537A pdb=" N GLU A1669 " --> pdb=" O LYS A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1702 Processing helix chain 'A' and resid 1706 through 1722 Processing helix chain 'A' and resid 1727 through 1741 Processing helix chain 'A' and resid 1744 through 1754 Processing helix chain 'A' and resid 1760 through 1767 Proline residue: A1766 - end of helix Processing helix chain 'A' and resid 1786 through 1788 No H-bonds generated for 'chain 'A' and resid 1786 through 1788' Processing helix chain 'A' and resid 1792 through 1795 No H-bonds generated for 'chain 'A' and resid 1792 through 1795' Processing helix chain 'A' and resid 1802 through 1815 Processing helix chain 'A' and resid 1828 through 1831 No H-bonds generated for 'chain 'A' and resid 1828 through 1831' Processing helix chain 'A' and resid 1835 through 1851 Proline residue: A1843 - end of helix Processing helix chain 'A' and resid 1857 through 1874 removed outlier: 3.720A pdb=" N LEU A1861 " --> pdb=" O SER A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1903 through 1918 removed outlier: 3.633A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1932 removed outlier: 3.543A pdb=" N PHE A1932 " --> pdb=" O PHE A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1947 Processing helix chain 'A' and resid 1951 through 1973 Processing helix chain 'A' and resid 1986 through 1996 Processing helix chain 'A' and resid 2001 through 2011 Processing helix chain 'A' and resid 2029 through 2038 Processing helix chain 'A' and resid 2042 through 2051 removed outlier: 3.546A pdb=" N VAL A2047 " --> pdb=" O GLY A2043 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2070 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 2075 through 2087 Processing helix chain 'A' and resid 2093 through 2105 Processing helix chain 'A' and resid 2124 through 2136 Processing helix chain 'A' and resid 2141 through 2160 Processing helix chain 'A' and resid 2167 through 2190 Proline residue: A2171 - end of helix Processing helix chain 'A' and resid 2195 through 2211 Processing helix chain 'A' and resid 2217 through 2236 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2242 through 2265 removed outlier: 3.746A pdb=" N PHE A2265 " --> pdb=" O LEU A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2269 through 2281 Processing helix chain 'A' and resid 2290 through 2301 Processing helix chain 'A' and resid 2305 through 2321 removed outlier: 3.522A pdb=" N ALA A2321 " --> pdb=" O LYS A2317 " (cutoff:3.500A) Processing helix chain 'A' and resid 2328 through 2348 Processing helix chain 'A' and resid 2353 through 2371 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 2377 through 2405 removed outlier: 4.141A pdb=" N GLY A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2408 through 2429 Processing helix chain 'A' and resid 2436 through 2475 Processing helix chain 'A' and resid 2481 through 2493 removed outlier: 3.765A pdb=" N VAL A2484 " --> pdb=" O ASP A2481 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A2485 " --> pdb=" O MET A2482 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A2492 " --> pdb=" O SER A2489 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A2493 " --> pdb=" O LEU A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2506 Processing helix chain 'A' and resid 2508 through 2510 No H-bonds generated for 'chain 'A' and resid 2508 through 2510' Processing helix chain 'A' and resid 2513 through 2515 No H-bonds generated for 'chain 'A' and resid 2513 through 2515' Processing helix chain 'A' and resid 2520 through 2525 Processing helix chain 'A' and resid 2535 through 2551 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 2557 through 2564 Processing helix chain 'A' and resid 2568 through 2572 Processing helix chain 'A' and resid 2593 through 2612 removed outlier: 3.799A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2614 through 2632 Processing helix chain 'A' and resid 2636 through 2638 No H-bonds generated for 'chain 'A' and resid 2636 through 2638' Processing helix chain 'A' and resid 2652 through 2655 No H-bonds generated for 'chain 'A' and resid 2652 through 2655' Processing helix chain 'A' and resid 2723 through 2741 Processing helix chain 'A' and resid 2743 through 2748 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) No H-bonds generated for 'chain 'A' and resid 2743 through 2748' Processing helix chain 'A' and resid 2776 through 2780 Processing helix chain 'A' and resid 2787 through 2791 Processing helix chain 'A' and resid 2798 through 2808 Processing helix chain 'A' and resid 2813 through 2825 Processing helix chain 'A' and resid 2831 through 2838 removed outlier: 4.427A pdb=" N CYS A2835 " --> pdb=" O ARG A2832 " (cutoff:3.500A) Processing helix chain 'A' and resid 2842 through 2866 Processing helix chain 'A' and resid 2873 through 2875 No H-bonds generated for 'chain 'A' and resid 2873 through 2875' Processing helix chain 'A' and resid 2912 through 2918 Processing helix chain 'A' and resid 2926 through 2951 removed outlier: 3.608A pdb=" N GLN A2942 " --> pdb=" O MET A2938 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU A2943 " --> pdb=" O ARG A2939 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A2944 " --> pdb=" O ASN A2940 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A2951 " --> pdb=" O THR A2947 " (cutoff:3.500A) Processing helix chain 'A' and resid 3004 through 3018 Processing helix chain 'A' and resid 3028 through 3040 Processing helix chain 'A' and resid 3042 through 3046 Processing helix chain 'A' and resid 3050 through 3052 No H-bonds generated for 'chain 'A' and resid 3050 through 3052' Processing helix chain 'B' and resid 1463 through 1477 Processing helix chain 'B' and resid 1491 through 1508 Processing helix chain 'B' and resid 1518 through 1528 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) Proline residue: B1526 - end of helix Processing helix chain 'B' and resid 1532 through 1547 Processing helix chain 'B' and resid 1553 through 1560 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 1569 through 1582 removed outlier: 4.905A pdb=" N ASP B1573 " --> pdb=" O VAL B1570 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B1580 " --> pdb=" O THR B1577 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B1581 " --> pdb=" O GLN B1578 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B1582 " --> pdb=" O GLN B1579 " (cutoff:3.500A) Processing helix chain 'B' and resid 1590 through 1603 Processing helix chain 'B' and resid 1608 through 1623 removed outlier: 4.696A pdb=" N GLU B1612 " --> pdb=" O THR B1609 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B1623 " --> pdb=" O GLN B1620 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1634 removed outlier: 3.503A pdb=" N MET B1628 " --> pdb=" O LYS B1625 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B1629 " --> pdb=" O ASP B1626 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP B1630 " --> pdb=" O GLN B1627 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B1631 " --> pdb=" O MET B1628 " (cutoff:3.500A) Processing helix chain 'B' and resid 1639 through 1641 No H-bonds generated for 'chain 'B' and resid 1639 through 1641' Processing helix chain 'B' and resid 1643 through 1660 removed outlier: 5.138A pdb=" N ASN B1660 " --> pdb=" O LYS B1656 " (cutoff:3.500A) Processing helix chain 'B' and resid 1664 through 1676 removed outlier: 3.546A pdb=" N GLU B1669 " --> pdb=" O LYS B1665 " (cutoff:3.500A) Processing helix chain 'B' and resid 1694 through 1702 Processing helix chain 'B' and resid 1706 through 1722 Processing helix chain 'B' and resid 1727 through 1741 Processing helix chain 'B' and resid 1744 through 1754 Processing helix chain 'B' and resid 1760 through 1767 Proline residue: B1766 - end of helix Processing helix chain 'B' and resid 1786 through 1788 No H-bonds generated for 'chain 'B' and resid 1786 through 1788' Processing helix chain 'B' and resid 1792 through 1795 No H-bonds generated for 'chain 'B' and resid 1792 through 1795' Processing helix chain 'B' and resid 1802 through 1815 Processing helix chain 'B' and resid 1828 through 1831 No H-bonds generated for 'chain 'B' and resid 1828 through 1831' Processing helix chain 'B' and resid 1835 through 1851 removed outlier: 3.550A pdb=" N GLN B1839 " --> pdb=" O THR B1835 " (cutoff:3.500A) Proline residue: B1843 - end of helix Processing helix chain 'B' and resid 1857 through 1874 removed outlier: 3.706A pdb=" N LEU B1861 " --> pdb=" O SER B1857 " (cutoff:3.500A) Processing helix chain 'B' and resid 1903 through 1918 removed outlier: 3.610A pdb=" N ARG B1918 " --> pdb=" O ASP B1914 " (cutoff:3.500A) Processing helix chain 'B' and resid 1927 through 1932 removed outlier: 3.611A pdb=" N PHE B1932 " --> pdb=" O PHE B1928 " (cutoff:3.500A) Processing helix chain 'B' and resid 1938 through 1947 Processing helix chain 'B' and resid 1951 through 1973 Processing helix chain 'B' and resid 1986 through 1996 Processing helix chain 'B' and resid 2001 through 2011 Processing helix chain 'B' and resid 2029 through 2038 Processing helix chain 'B' and resid 2042 through 2051 removed outlier: 3.618A pdb=" N VAL B2047 " --> pdb=" O GLY B2043 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2070 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 2075 through 2087 Processing helix chain 'B' and resid 2093 through 2105 Processing helix chain 'B' and resid 2124 through 2136 Processing helix chain 'B' and resid 2140 through 2160 Processing helix chain 'B' and resid 2167 through 2190 Proline residue: B2171 - end of helix Processing helix chain 'B' and resid 2195 through 2212 Processing helix chain 'B' and resid 2217 through 2236 Proline residue: B2222 - end of helix Processing helix chain 'B' and resid 2242 through 2265 removed outlier: 3.741A pdb=" N PHE B2265 " --> pdb=" O LEU B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2269 through 2281 Processing helix chain 'B' and resid 2291 through 2301 Processing helix chain 'B' and resid 2305 through 2321 removed outlier: 3.549A pdb=" N ALA B2321 " --> pdb=" O LYS B2317 " (cutoff:3.500A) Processing helix chain 'B' and resid 2328 through 2348 Processing helix chain 'B' and resid 2353 through 2371 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 2377 through 2405 removed outlier: 4.146A pdb=" N GLY B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) Processing helix chain 'B' and resid 2408 through 2429 Processing helix chain 'B' and resid 2436 through 2475 Processing helix chain 'B' and resid 2481 through 2493 removed outlier: 3.742A pdb=" N VAL B2484 " --> pdb=" O ASP B2481 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE B2485 " --> pdb=" O MET B2482 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B2492 " --> pdb=" O SER B2489 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B2493 " --> pdb=" O LEU B2490 " (cutoff:3.500A) Processing helix chain 'B' and resid 2498 through 2506 Processing helix chain 'B' and resid 2508 through 2510 No H-bonds generated for 'chain 'B' and resid 2508 through 2510' Processing helix chain 'B' and resid 2513 through 2515 No H-bonds generated for 'chain 'B' and resid 2513 through 2515' Processing helix chain 'B' and resid 2520 through 2525 Processing helix chain 'B' and resid 2535 through 2551 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 2557 through 2564 Processing helix chain 'B' and resid 2568 through 2572 Processing helix chain 'B' and resid 2593 through 2612 removed outlier: 3.822A pdb=" N ARG B2612 " --> pdb=" O THR B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2614 through 2632 Processing helix chain 'B' and resid 2636 through 2638 No H-bonds generated for 'chain 'B' and resid 2636 through 2638' Processing helix chain 'B' and resid 2652 through 2655 No H-bonds generated for 'chain 'B' and resid 2652 through 2655' Processing helix chain 'B' and resid 2723 through 2741 Processing helix chain 'B' and resid 2743 through 2748 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) No H-bonds generated for 'chain 'B' and resid 2743 through 2748' Processing helix chain 'B' and resid 2776 through 2780 Processing helix chain 'B' and resid 2787 through 2791 Processing helix chain 'B' and resid 2798 through 2808 Processing helix chain 'B' and resid 2813 through 2825 Processing helix chain 'B' and resid 2831 through 2838 removed outlier: 4.421A pdb=" N CYS B2835 " --> pdb=" O ARG B2832 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B2838 " --> pdb=" O CYS B2835 " (cutoff:3.500A) Processing helix chain 'B' and resid 2842 through 2866 Processing helix chain 'B' and resid 2873 through 2875 No H-bonds generated for 'chain 'B' and resid 2873 through 2875' Processing helix chain 'B' and resid 2912 through 2918 removed outlier: 3.514A pdb=" N MET B2918 " --> pdb=" O ILE B2914 " (cutoff:3.500A) Processing helix chain 'B' and resid 2922 through 2924 No H-bonds generated for 'chain 'B' and resid 2922 through 2924' Processing helix chain 'B' and resid 2926 through 2951 removed outlier: 3.615A pdb=" N GLN B2942 " --> pdb=" O MET B2938 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU B2943 " --> pdb=" O ARG B2939 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B2944 " --> pdb=" O ASN B2940 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B2951 " --> pdb=" O THR B2947 " (cutoff:3.500A) Processing helix chain 'B' and resid 3004 through 3018 Processing helix chain 'B' and resid 3028 through 3040 Processing helix chain 'B' and resid 3042 through 3046 Processing helix chain 'B' and resid 3050 through 3052 No H-bonds generated for 'chain 'B' and resid 3050 through 3052' Processing sheet with id= A, first strand: chain 'A' and resid 2757 through 2759 removed outlier: 3.650A pdb=" N GLY A2765 " --> pdb=" O LYS A2717 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id= C, first strand: chain 'B' and resid 2757 through 2759 removed outlier: 3.679A pdb=" N GLY B2765 " --> pdb=" O LYS B2717 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 2773 through 2775 1301 hydrogen bonds defined for protein. 3717 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: 9.40 Time building geometry restraints manager: 10.51 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: 100.00 - 107.63: 741 107.63 - 115.26: 14916 115.26 - 122.89: 15952 122.89 - 130.52: 1259 130.52 - 138.16: 114 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: 22932 3.21 - 3.77: 38469 3.77 - 4.34: 50060 4.34 - 4.90: 82286 Nonbonded interactions: 193978 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 193973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.470 Check model and map are aligned: 0.330 Set scattering table: 0.230 Process input model: 67.850 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.140 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.080 ------------------------------------------------------------------------------- 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= 0.167 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 : 2.764 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: 1.3743 time to fit residues: 920.1561 Evaluate side-chains 305 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 2.944 ------------------------------------------------------------------------------- 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: 5.9990 chunk 223 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 231 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2070 ASN A2101 GLN A2106 ASN A2658 ASN A3038 GLN B1802 HIS ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2070 ASN B2101 GLN ** B2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2658 ASN B3038 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24420 Z= 0.188 Angle : 0.578 9.469 32982 Z= 0.278 Chirality : 0.039 0.315 3736 Planarity : 0.004 0.047 4176 Dihedral : 6.013 108.332 3274 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.47 % Allowed : 12.23 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.16), residues: 2930 helix: 2.18 (0.12), residues: 2006 sheet: 0.89 (0.75), residues: 36 loop : -0.03 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B2638 HIS 0.014 0.001 HIS B2208 PHE 0.021 0.001 PHE A1712 TYR 0.027 0.001 TYR B1844 ARG 0.007 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 407 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 341 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1556 TYR cc_start: 0.7224 (m-80) cc_final: 0.6965 (m-80) REVERT: A 1575 ARG cc_start: 0.8955 (mtt180) cc_final: 0.8204 (mmm160) REVERT: A 1619 ARG cc_start: 0.8139 (mpp80) cc_final: 0.7840 (mpp80) REVERT: A 1682 ASP cc_start: 0.8760 (t70) cc_final: 0.8396 (t0) REVERT: A 1720 ASN cc_start: 0.8598 (m110) cc_final: 0.8393 (m110) REVERT: A 1793 ASN cc_start: 0.8848 (m-40) cc_final: 0.8553 (p0) REVERT: A 1844 TYR cc_start: 0.8901 (m-80) cc_final: 0.8578 (m-80) REVERT: A 2016 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7281 (p0) REVERT: A 2411 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8899 (mm-30) REVERT: A 2446 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 2450 LEU cc_start: 0.9193 (tt) cc_final: 0.8642 (mm) REVERT: A 2503 MET cc_start: 0.8759 (ttm) cc_final: 0.8296 (ttm) REVERT: A 2507 ASP cc_start: 0.8529 (t0) cc_final: 0.7824 (m-30) REVERT: A 2597 ASP cc_start: 0.8942 (t0) cc_final: 0.8691 (OUTLIER) REVERT: A 2670 LYS cc_start: 0.9228 (tppp) cc_final: 0.8761 (tmtt) REVERT: A 2896 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6319 (tm-30) REVERT: A 3018 LYS cc_start: 0.9387 (mttt) cc_final: 0.9139 (mttp) REVERT: B 1556 TYR cc_start: 0.7253 (m-80) cc_final: 0.6968 (m-80) REVERT: B 1575 ARG cc_start: 0.8821 (mtt180) cc_final: 0.8447 (mtp85) REVERT: B 1714 MET cc_start: 0.9479 (tpp) cc_final: 0.9263 (tpp) REVERT: B 1793 ASN cc_start: 0.8838 (m-40) cc_final: 0.8426 (p0) REVERT: B 1844 TYR cc_start: 0.8916 (m-80) cc_final: 0.8547 (m-80) REVERT: B 1907 ARG cc_start: 0.8549 (ptp-170) cc_final: 0.8201 (mtt90) REVERT: B 2016 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7189 (p0) REVERT: B 2156 GLU cc_start: 0.8030 (pp20) cc_final: 0.7244 (pp20) REVERT: B 2411 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8921 (mm-30) REVERT: B 2446 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 2450 LEU cc_start: 0.9222 (tt) cc_final: 0.8660 (mm) REVERT: B 2475 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8883 (mm) REVERT: B 2507 ASP cc_start: 0.8544 (t0) cc_final: 0.7887 (m-30) REVERT: B 2597 ASP cc_start: 0.8936 (t0) cc_final: 0.8685 (m-30) REVERT: B 2670 LYS cc_start: 0.9219 (tppp) cc_final: 0.8782 (tmtt) REVERT: B 2751 THR cc_start: 0.9214 (p) cc_final: 0.8853 (t) REVERT: B 2962 MET cc_start: 0.7892 (mtm) cc_final: 0.7634 (mmm) REVERT: B 3018 LYS cc_start: 0.9395 (mttt) cc_final: 0.9116 (mttp) outliers start: 66 outliers final: 18 residues processed: 382 average time/residue: 1.3289 time to fit residues: 591.8224 Evaluate side-chains 306 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 285 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2003 ASP Chi-restraints excluded: chain A residue 2016 ASP Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2697 ASN Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1823 ILE Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1932 PHE Chi-restraints excluded: chain B residue 2003 ASP Chi-restraints excluded: chain B residue 2016 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 2606 ILE Chi-restraints excluded: chain B residue 2697 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 268 optimal weight: 0.4980 chunk 289 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 215 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1650 ASN A1802 HIS A1946 GLN A2002 GLN A2593 GLN B1650 ASN B1802 HIS ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2002 GLN B2106 ASN B2593 GLN B2632 ASN B2736 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2445 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= 0.198 Angle : 0.574 9.571 32982 Z= 0.273 Chirality : 0.039 0.351 3736 Planarity : 0.003 0.044 4176 Dihedral : 4.674 91.577 3270 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.28 % Allowed : 14.17 % Favored : 83.55 % 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: 2.35 (0.16), residues: 2930 helix: 2.24 (0.12), residues: 2006 sheet: 0.90 (0.80), residues: 36 loop : 0.04 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1805 HIS 0.012 0.001 HIS B1802 PHE 0.017 0.001 PHE A1712 TYR 0.015 0.001 TYR B1696 ARG 0.007 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 364 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 303 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 TYR cc_start: 0.9396 (m-80) cc_final: 0.8726 (t80) REVERT: A 1556 TYR cc_start: 0.7308 (m-80) cc_final: 0.7099 (m-80) REVERT: A 1575 ARG cc_start: 0.8831 (mtt180) cc_final: 0.8219 (mmm160) REVERT: A 1616 ASP cc_start: 0.9365 (t0) cc_final: 0.9130 (t0) REVERT: A 1714 MET cc_start: 0.9439 (tpp) cc_final: 0.9237 (tpp) REVERT: A 1720 ASN cc_start: 0.8712 (m110) cc_final: 0.8466 (m110) REVERT: A 1793 ASN cc_start: 0.8871 (m-40) cc_final: 0.8571 (p0) REVERT: A 2051 LEU cc_start: 0.8977 (tm) cc_final: 0.8729 (tm) REVERT: A 2126 GLU cc_start: 0.9338 (tt0) cc_final: 0.9000 (tt0) REVERT: A 2196 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8472 (ppp80) REVERT: A 2235 MET cc_start: 0.8975 (tpt) cc_final: 0.8730 (tpt) REVERT: A 2239 MET cc_start: 0.7001 (ppp) cc_final: 0.6599 (mmp) REVERT: A 2304 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: A 2411 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8908 (mm-30) REVERT: A 2446 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8361 (tm-30) REVERT: A 2450 LEU cc_start: 0.9212 (tt) cc_final: 0.8651 (mm) REVERT: A 2507 ASP cc_start: 0.8608 (t0) cc_final: 0.7902 (m-30) REVERT: A 2670 LYS cc_start: 0.9212 (tppp) cc_final: 0.8731 (tmtt) REVERT: A 2896 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6666 (tm-30) REVERT: A 3018 LYS cc_start: 0.9409 (mttt) cc_final: 0.9120 (mttp) REVERT: B 1475 TYR cc_start: 0.8633 (m-80) cc_final: 0.8315 (m-80) REVERT: B 1575 ARG cc_start: 0.8936 (mtt180) cc_final: 0.8215 (mmm160) REVERT: B 1793 ASN cc_start: 0.8831 (m-40) cc_final: 0.8438 (p0) REVERT: B 1844 TYR cc_start: 0.9018 (m-80) cc_final: 0.8645 (m-80) REVERT: B 2008 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8996 (mp) REVERT: B 2156 GLU cc_start: 0.7696 (pp20) cc_final: 0.7284 (pp20) REVERT: B 2157 GLU cc_start: 0.8184 (tp30) cc_final: 0.7656 (tp30) REVERT: B 2160 LYS cc_start: 0.8247 (mtmt) cc_final: 0.8002 (mtpt) REVERT: B 2177 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: B 2239 MET cc_start: 0.7002 (ppp) cc_final: 0.6595 (mmp) REVERT: B 2304 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: B 2411 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8919 (mm-30) REVERT: B 2446 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 2450 LEU cc_start: 0.9218 (tt) cc_final: 0.8655 (mm) REVERT: B 2475 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8922 (mm) REVERT: B 2503 MET cc_start: 0.8782 (ttm) cc_final: 0.8531 (ttm) REVERT: B 2507 ASP cc_start: 0.8644 (t0) cc_final: 0.7941 (m-30) REVERT: B 2670 LYS cc_start: 0.9235 (tppp) cc_final: 0.8784 (tmtt) REVERT: B 2736 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8443 (m-40) REVERT: B 2751 THR cc_start: 0.9328 (p) cc_final: 0.9104 (t) REVERT: B 2896 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: B 3018 LYS cc_start: 0.9427 (mttt) cc_final: 0.9139 (mttp) outliers start: 61 outliers final: 16 residues processed: 339 average time/residue: 1.2524 time to fit residues: 496.3159 Evaluate side-chains 289 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 264 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2196 ARG Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2697 ASN Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain B residue 1801 ASN Chi-restraints excluded: chain B residue 1823 ILE Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1935 ASP Chi-restraints excluded: chain B residue 2008 ILE Chi-restraints excluded: chain B residue 2026 MET Chi-restraints excluded: chain B residue 2027 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2177 GLN Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2304 GLU Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2697 ASN 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: 7.9990 chunk 201 optimal weight: 0.2980 chunk 139 optimal weight: 0.5980 chunk 29 optimal weight: 0.0010 chunk 128 optimal weight: 0.5980 chunk 180 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 255 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1650 ASN B1802 HIS ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24420 Z= 0.143 Angle : 0.559 10.504 32982 Z= 0.263 Chirality : 0.038 0.395 3736 Planarity : 0.003 0.043 4176 Dihedral : 4.306 79.669 3270 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.24 % Allowed : 15.97 % Favored : 81.79 % 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: 2.32 (0.16), residues: 2930 helix: 2.23 (0.12), residues: 2010 sheet: 0.99 (0.67), residues: 58 loop : -0.06 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1805 HIS 0.011 0.001 HIS B1802 PHE 0.022 0.001 PHE A1712 TYR 0.018 0.001 TYR B1470 ARG 0.004 0.000 ARG B1633 *********************** 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 350 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 290 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1475 TYR cc_start: 0.8698 (m-80) cc_final: 0.8384 (m-80) REVERT: A 1556 TYR cc_start: 0.7317 (m-80) cc_final: 0.7015 (m-80) REVERT: A 1575 ARG cc_start: 0.8881 (mtt180) cc_final: 0.8364 (mmm160) REVERT: A 1664 GLU cc_start: 0.8677 (pt0) cc_final: 0.8236 (pt0) REVERT: A 1720 ASN cc_start: 0.8738 (m110) cc_final: 0.8449 (m110) REVERT: A 1793 ASN cc_start: 0.8880 (m-40) cc_final: 0.8577 (p0) REVERT: A 2126 GLU cc_start: 0.9323 (tt0) cc_final: 0.8983 (tt0) REVERT: A 2156 GLU cc_start: 0.8200 (pp20) cc_final: 0.7313 (pp20) REVERT: A 2196 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8507 (ppp80) REVERT: A 2235 MET cc_start: 0.8944 (tpt) cc_final: 0.8714 (tpt) REVERT: A 2304 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: A 2411 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8909 (mm-30) REVERT: A 2446 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 2450 LEU cc_start: 0.9210 (tt) cc_final: 0.8654 (mm) REVERT: A 2503 MET cc_start: 0.8534 (ttm) cc_final: 0.8314 (ttt) REVERT: A 2507 ASP cc_start: 0.8620 (t0) cc_final: 0.7914 (m-30) REVERT: A 2527 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7173 (mpt) REVERT: A 2667 MET cc_start: 0.8791 (ttp) cc_final: 0.7793 (ptm) REVERT: A 2670 LYS cc_start: 0.9193 (tppp) cc_final: 0.8719 (tmtt) REVERT: A 2806 MET cc_start: 0.9345 (mmp) cc_final: 0.9143 (mmm) REVERT: A 2896 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: A 2938 MET cc_start: 0.9436 (mmm) cc_final: 0.8899 (mtm) REVERT: A 3018 LYS cc_start: 0.9411 (mttt) cc_final: 0.9044 (mttm) REVERT: B 1470 TYR cc_start: 0.9303 (m-80) cc_final: 0.8743 (t80) REVERT: B 1475 TYR cc_start: 0.8615 (m-80) cc_final: 0.8317 (m-80) REVERT: B 1556 TYR cc_start: 0.7230 (m-80) cc_final: 0.6941 (m-80) REVERT: B 1575 ARG cc_start: 0.8933 (mtt180) cc_final: 0.8230 (mmm160) REVERT: B 1706 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8597 (tmmm) REVERT: B 1844 TYR cc_start: 0.8989 (m-80) cc_final: 0.8672 (m-80) REVERT: B 2008 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8989 (mp) REVERT: B 2126 GLU cc_start: 0.9339 (tt0) cc_final: 0.8997 (tt0) REVERT: B 2156 GLU cc_start: 0.7670 (pp20) cc_final: 0.7252 (pp20) REVERT: B 2157 GLU cc_start: 0.8225 (tp30) cc_final: 0.7715 (tp30) REVERT: B 2160 LYS cc_start: 0.8331 (mtmt) cc_final: 0.7917 (mtpt) REVERT: B 2177 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: B 2196 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8554 (ppp80) REVERT: B 2304 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: B 2411 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8931 (mm-30) REVERT: B 2446 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8431 (tm-30) REVERT: B 2450 LEU cc_start: 0.9215 (tt) cc_final: 0.8643 (mm) REVERT: B 2503 MET cc_start: 0.8823 (ttm) cc_final: 0.8604 (ttm) REVERT: B 2507 ASP cc_start: 0.8623 (t0) cc_final: 0.7930 (m-30) REVERT: B 2667 MET cc_start: 0.8795 (ttp) cc_final: 0.7778 (ptm) REVERT: B 2670 LYS cc_start: 0.9227 (tppp) cc_final: 0.8760 (tmtt) REVERT: B 2752 ILE cc_start: 0.8668 (mm) cc_final: 0.8436 (mm) REVERT: B 2896 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: B 3018 LYS cc_start: 0.9424 (mttt) cc_final: 0.9128 (mttp) outliers start: 60 outliers final: 23 residues processed: 329 average time/residue: 1.2791 time to fit residues: 492.2647 Evaluate side-chains 296 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 263 time to evaluate : 2.784 ------------------------------------------------------------------------------- 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 1678 VAL Chi-restraints excluded: chain A residue 1807 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 1935 ASP Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2196 ARG Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2527 MET Chi-restraints excluded: chain A residue 2697 ASN Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1706 LYS Chi-restraints excluded: chain B residue 1803 ASP 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 2177 GLN Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2196 ARG Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2304 GLU Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2697 ASN Chi-restraints excluded: chain B residue 2896 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 243 optimal weight: 0.0770 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1518 HIS A1578 GLN ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8593 moved from start: 0.2913 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= 0.184 Angle : 0.570 11.076 32982 Z= 0.269 Chirality : 0.039 0.356 3736 Planarity : 0.003 0.044 4176 Dihedral : 4.219 72.169 3270 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.92 % Allowed : 16.31 % Favored : 80.78 % 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: 2.37 (0.16), residues: 2930 helix: 2.28 (0.12), residues: 2008 sheet: 0.92 (0.65), residues: 58 loop : -0.06 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1805 HIS 0.008 0.001 HIS B1802 PHE 0.019 0.001 PHE A1712 TYR 0.020 0.001 TYR B1529 ARG 0.012 0.000 ARG A1633 *********************** 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 361 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 283 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1475 TYR cc_start: 0.8730 (m-80) cc_final: 0.8406 (m-80) REVERT: A 1556 TYR cc_start: 0.7376 (m-80) cc_final: 0.7052 (m-80) REVERT: A 1575 ARG cc_start: 0.8782 (mtt180) cc_final: 0.8478 (mmm160) REVERT: A 1664 GLU cc_start: 0.8715 (pt0) cc_final: 0.8294 (pt0) REVERT: A 1701 LYS cc_start: 0.9253 (pttm) cc_final: 0.8955 (pttp) REVERT: A 1706 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8444 (tmmm) REVERT: A 2051 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8938 (tm) REVERT: A 2126 GLU cc_start: 0.9341 (tt0) cc_final: 0.9006 (tt0) REVERT: A 2158 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8936 (ttp) REVERT: A 2239 MET cc_start: 0.6924 (ppp) cc_final: 0.6574 (mmp) REVERT: A 2304 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: A 2411 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8903 (mm-30) REVERT: A 2670 LYS cc_start: 0.9173 (tppp) cc_final: 0.8667 (tmtt) REVERT: A 2896 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: A 3018 LYS cc_start: 0.9418 (mttt) cc_final: 0.9160 (mttp) REVERT: B 1475 TYR cc_start: 0.8667 (m-80) cc_final: 0.8346 (m-80) REVERT: B 1556 TYR cc_start: 0.7319 (m-80) cc_final: 0.7084 (m-80) REVERT: B 1575 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8248 (mmm160) REVERT: B 1706 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8595 (tmmm) REVERT: B 1844 TYR cc_start: 0.9032 (m-80) cc_final: 0.8775 (m-80) REVERT: B 2008 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8982 (mp) REVERT: B 2126 GLU cc_start: 0.9362 (tt0) cc_final: 0.9011 (tt0) REVERT: B 2239 MET cc_start: 0.6900 (ppp) cc_final: 0.6582 (mmp) REVERT: B 2304 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: B 2411 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8909 (mm-30) REVERT: B 2667 MET cc_start: 0.8795 (ttp) cc_final: 0.7863 (ptm) REVERT: B 2670 LYS cc_start: 0.9213 (tppp) cc_final: 0.8699 (tmtt) REVERT: B 2736 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8501 (m-40) REVERT: B 2752 ILE cc_start: 0.8409 (mm) cc_final: 0.8208 (mm) REVERT: B 2896 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: B 3018 LYS cc_start: 0.9444 (mttt) cc_final: 0.9176 (mttp) outliers start: 78 outliers final: 23 residues processed: 339 average time/residue: 1.2324 time to fit residues: 491.0219 Evaluate side-chains 286 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 253 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 1935 ASP Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2158 MET Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2597 ASP Chi-restraints excluded: chain A residue 2697 ASN Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain B residue 1559 ILE 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 1803 ASP 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 2597 ASP Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2697 ASN Chi-restraints excluded: chain B residue 2736 ASN Chi-restraints excluded: chain B residue 2896 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 chunk 285 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 0.0970 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1552 ASN ** B1802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 24420 Z= 0.153 Angle : 0.587 12.073 32982 Z= 0.270 Chirality : 0.038 0.298 3736 Planarity : 0.003 0.047 4176 Dihedral : 4.144 66.249 3270 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.28 % Allowed : 18.06 % 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: 2.34 (0.16), residues: 2930 helix: 2.28 (0.12), residues: 2002 sheet: 0.89 (0.65), residues: 58 loop : -0.09 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1805 HIS 0.008 0.001 HIS B1802 PHE 0.023 0.001 PHE A1712 TYR 0.011 0.001 TYR B1753 ARG 0.013 0.000 ARG B1633 *********************** 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 341 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 280 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1470 TYR cc_start: 0.9409 (m-80) cc_final: 0.8738 (t80) REVERT: A 1475 TYR cc_start: 0.8690 (m-80) cc_final: 0.8363 (m-80) REVERT: A 1556 TYR cc_start: 0.7387 (m-80) cc_final: 0.7136 (m-80) REVERT: A 1575 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8437 (mmm160) REVERT: A 1664 GLU cc_start: 0.8712 (pt0) cc_final: 0.8317 (pt0) REVERT: A 1706 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8533 (tmmm) REVERT: A 2051 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8961 (tm) REVERT: A 2126 GLU cc_start: 0.9334 (tt0) cc_final: 0.9002 (tt0) REVERT: A 2304 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: A 2411 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8903 (mm-30) REVERT: A 2448 ASP cc_start: 0.8774 (m-30) cc_final: 0.8423 (m-30) REVERT: A 2450 LEU cc_start: 0.9211 (tt) cc_final: 0.8791 (mm) REVERT: A 2670 LYS cc_start: 0.9177 (tppp) cc_final: 0.8635 (tmtt) REVERT: A 2896 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: A 3018 LYS cc_start: 0.9423 (mttt) cc_final: 0.9164 (mttp) REVERT: B 1556 TYR cc_start: 0.7348 (m-80) cc_final: 0.7052 (m-80) REVERT: B 1575 ARG cc_start: 0.8917 (mtt180) cc_final: 0.8264 (mmm160) REVERT: B 1632 MET cc_start: 0.8963 (mtp) cc_final: 0.8653 (mtp) REVERT: B 1664 GLU cc_start: 0.8685 (pt0) cc_final: 0.8321 (pt0) REVERT: B 1701 LYS cc_start: 0.9255 (pttm) cc_final: 0.8960 (pttp) REVERT: B 1706 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8600 (tmmm) REVERT: B 1717 TYR cc_start: 0.9279 (t80) cc_final: 0.9074 (t80) REVERT: B 1836 ASP cc_start: 0.9445 (m-30) cc_final: 0.8894 (t0) REVERT: B 2008 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8973 (mp) REVERT: B 2126 GLU cc_start: 0.9347 (tt0) cc_final: 0.8992 (tt0) REVERT: B 2177 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: B 2304 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: B 2411 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8911 (mm-30) REVERT: B 2448 ASP cc_start: 0.8744 (m-30) cc_final: 0.8459 (m-30) REVERT: B 2450 LEU cc_start: 0.9223 (tt) cc_final: 0.8790 (mm) REVERT: B 2667 MET cc_start: 0.8773 (ttp) cc_final: 0.7786 (ptm) REVERT: B 2670 LYS cc_start: 0.9206 (tppp) cc_final: 0.8672 (tmtt) REVERT: B 3018 LYS cc_start: 0.9417 (mttt) cc_final: 0.9166 (mttp) outliers start: 61 outliers final: 28 residues processed: 320 average time/residue: 1.2772 time to fit residues: 477.1878 Evaluate side-chains 298 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 262 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1652 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2026 MET Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2051 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2270 LEU Chi-restraints excluded: chain A residue 2304 GLU Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2697 ASN Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1706 LYS Chi-restraints excluded: chain B residue 1803 ASP 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 2051 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2177 GLN Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2304 GLU Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2697 ASN Chi-restraints excluded: chain B residue 2896 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 162 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 284 optimal weight: 0.0980 chunk 177 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24420 Z= 0.153 Angle : 0.592 12.186 32982 Z= 0.272 Chirality : 0.038 0.296 3736 Planarity : 0.003 0.042 4176 Dihedral : 4.101 62.159 3270 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.36 % Allowed : 18.62 % Favored : 79.02 % 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: 2.30 (0.16), residues: 2930 helix: 2.24 (0.12), residues: 2004 sheet: 0.88 (0.63), residues: 58 loop : -0.11 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1805 HIS 0.008 0.001 HIS B2208 PHE 0.027 0.001 PHE B1749 TYR 0.023 0.001 TYR A1529 ARG 0.006 0.000 ARG B1633 *********************** 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 344 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 281 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1475 TYR cc_start: 0.8687 (m-80) cc_final: 0.8370 (m-80) REVERT: A 1539 LEU cc_start: 0.9331 (mm) cc_final: 0.9039 (pp) REVERT: A 1556 TYR cc_start: 0.7382 (m-80) cc_final: 0.7040 (m-80) REVERT: A 1575 ARG cc_start: 0.8744 (mtt180) cc_final: 0.8429 (mmm160) REVERT: A 1664 GLU cc_start: 0.8676 (pt0) cc_final: 0.8339 (pt0) REVERT: A 1701 LYS cc_start: 0.9267 (pttm) cc_final: 0.8991 (pttp) REVERT: A 1706 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8593 (tmmm) REVERT: A 2126 GLU cc_start: 0.9335 (tt0) cc_final: 0.9003 (tt0) REVERT: A 2239 MET cc_start: 0.6822 (ppp) cc_final: 0.6448 (mmp) REVERT: A 2304 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 2411 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8907 (mm-30) REVERT: A 2448 ASP cc_start: 0.8769 (m-30) cc_final: 0.8411 (m-30) REVERT: A 2468 GLU cc_start: 0.8249 (tm-30) cc_final: 0.8008 (tm-30) REVERT: A 2475 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8498 (mm) REVERT: A 2670 LYS cc_start: 0.9186 (tppp) cc_final: 0.8644 (tmtt) REVERT: A 3018 LYS cc_start: 0.9412 (mttt) cc_final: 0.9121 (mttm) REVERT: B 1470 TYR cc_start: 0.9395 (m-80) cc_final: 0.8378 (t80) REVERT: B 1474 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.7924 (m-70) REVERT: B 1475 TYR cc_start: 0.8689 (m-80) cc_final: 0.8350 (m-80) REVERT: B 1539 LEU cc_start: 0.9276 (mm) cc_final: 0.8989 (pp) REVERT: B 1556 TYR cc_start: 0.7337 (m-80) cc_final: 0.7103 (m-80) REVERT: B 1575 ARG cc_start: 0.8914 (mtt180) cc_final: 0.8258 (mmm160) REVERT: B 1664 GLU cc_start: 0.8710 (pt0) cc_final: 0.8350 (pt0) REVERT: B 1706 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8604 (tmmm) REVERT: B 1730 ARG cc_start: 0.9296 (mtm180) cc_final: 0.9093 (mtm-85) REVERT: B 1836 ASP cc_start: 0.9429 (m-30) cc_final: 0.8904 (t0) REVERT: B 1844 TYR cc_start: 0.9007 (m-80) cc_final: 0.8726 (m-80) REVERT: B 2008 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8963 (mp) REVERT: B 2126 GLU cc_start: 0.9346 (tt0) cc_final: 0.8998 (tt0) REVERT: B 2177 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.8572 (tt0) REVERT: B 2237 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8277 (ttmm) REVERT: B 2239 MET cc_start: 0.6800 (ppp) cc_final: 0.6448 (mmp) REVERT: B 2304 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: B 2411 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8906 (mm-30) REVERT: B 2448 ASP cc_start: 0.8736 (m-30) cc_final: 0.8437 (m-30) REVERT: B 2475 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8621 (mm) REVERT: B 2667 MET cc_start: 0.8759 (ttp) cc_final: 0.8151 (ptm) REVERT: B 2670 LYS cc_start: 0.9198 (tppp) cc_final: 0.8666 (tmtt) REVERT: B 3018 LYS cc_start: 0.9432 (mttt) cc_final: 0.9165 (mttp) outliers start: 63 outliers final: 27 residues processed: 324 average time/residue: 1.2192 time to fit residues: 463.2882 Evaluate side-chains 299 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 263 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1565 PHE Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 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 2475 LEU Chi-restraints excluded: chain A residue 2557 LEU Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2697 ASN Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain B residue 1474 HIS Chi-restraints excluded: chain B residue 1559 ILE 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 1803 ASP 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 2177 GLN Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2304 GLU Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2697 ASN Chi-restraints excluded: chain B residue 2896 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 169 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 140 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2002 GLN ** A2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1946 GLN B2632 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3399 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= 0.201 Angle : 0.625 12.962 32982 Z= 0.290 Chirality : 0.040 0.347 3736 Planarity : 0.003 0.042 4176 Dihedral : 4.154 60.392 3270 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.13 % Allowed : 19.04 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.16), residues: 2930 helix: 2.23 (0.12), residues: 2006 sheet: 0.93 (0.62), residues: 58 loop : -0.01 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1805 HIS 0.008 0.001 HIS B2208 PHE 0.035 0.001 PHE B1749 TYR 0.013 0.001 TYR A2049 ARG 0.022 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 330 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 273 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 LEU cc_start: 0.9337 (mm) cc_final: 0.9048 (pp) REVERT: A 1556 TYR cc_start: 0.7421 (m-80) cc_final: 0.7187 (m-80) REVERT: A 1575 ARG cc_start: 0.8740 (mtt180) cc_final: 0.8447 (mmm160) REVERT: A 1664 GLU cc_start: 0.8693 (pt0) cc_final: 0.8353 (pt0) REVERT: A 1701 LYS cc_start: 0.9290 (pttm) cc_final: 0.8993 (pttp) REVERT: A 1706 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8600 (tmmm) REVERT: A 1830 MET cc_start: 0.8422 (tmm) cc_final: 0.7615 (ppp) REVERT: A 1999 ILE cc_start: 0.9190 (mp) cc_final: 0.8967 (mm) REVERT: A 2126 GLU cc_start: 0.9356 (tt0) cc_final: 0.9017 (tt0) REVERT: A 2239 MET cc_start: 0.6869 (ppp) cc_final: 0.6330 (mmp) REVERT: A 2304 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 2411 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8912 (mm-30) REVERT: A 2448 ASP cc_start: 0.8777 (m-30) cc_final: 0.8394 (m-30) REVERT: A 2475 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8479 (mm) REVERT: A 2507 ASP cc_start: 0.8818 (t0) cc_final: 0.8429 (t0) REVERT: A 2670 LYS cc_start: 0.9182 (tppp) cc_final: 0.8618 (tmtt) REVERT: A 3018 LYS cc_start: 0.9429 (mttt) cc_final: 0.9115 (mttm) REVERT: B 1470 TYR cc_start: 0.9395 (m-80) cc_final: 0.8692 (t80) REVERT: B 1475 TYR cc_start: 0.8735 (m-80) cc_final: 0.8403 (m-80) REVERT: B 1556 TYR cc_start: 0.7367 (m-80) cc_final: 0.7155 (m-80) REVERT: B 1575 ARG cc_start: 0.8890 (mtt180) cc_final: 0.8251 (mmm160) REVERT: B 1664 GLU cc_start: 0.8705 (pt0) cc_final: 0.8350 (pt0) REVERT: B 1701 LYS cc_start: 0.9303 (pttm) cc_final: 0.9015 (pttp) REVERT: B 1706 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8606 (tmmm) REVERT: B 1793 ASN cc_start: 0.8894 (m-40) cc_final: 0.8519 (p0) REVERT: B 1836 ASP cc_start: 0.9381 (m-30) cc_final: 0.8871 (t0) REVERT: B 2008 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8968 (mp) REVERT: B 2126 GLU cc_start: 0.9371 (tt0) cc_final: 0.9024 (tt0) REVERT: B 2177 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: B 2239 MET cc_start: 0.6847 (ppp) cc_final: 0.6323 (mmp) REVERT: B 2304 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: B 2411 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8922 (mm-30) REVERT: B 2426 LEU cc_start: 0.9351 (tm) cc_final: 0.9129 (mt) REVERT: B 2429 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8221 (mm-30) REVERT: B 2448 ASP cc_start: 0.8754 (m-30) cc_final: 0.8414 (m-30) REVERT: B 2450 LEU cc_start: 0.9211 (tt) cc_final: 0.8789 (mm) REVERT: B 2670 LYS cc_start: 0.9199 (tppp) cc_final: 0.8661 (tmtt) REVERT: B 3018 LYS cc_start: 0.9451 (mttt) cc_final: 0.9141 (mttm) outliers start: 57 outliers final: 27 residues processed: 309 average time/residue: 1.2782 time to fit residues: 465.2808 Evaluate side-chains 290 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 256 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 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 2475 LEU Chi-restraints excluded: chain A residue 2597 ASP Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2697 ASN Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain A residue 3011 MET 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 1803 ASP 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 2051 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2177 GLN Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2304 GLU Chi-restraints excluded: chain B residue 2597 ASP Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2697 ASN Chi-restraints excluded: chain B residue 2896 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 264 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 250 optimal weight: 0.0980 chunk 173 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24420 Z= 0.195 Angle : 0.631 14.286 32982 Z= 0.291 Chirality : 0.040 0.324 3736 Planarity : 0.003 0.042 4176 Dihedral : 4.167 58.851 3270 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.83 % Allowed : 19.63 % Favored : 78.53 % 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: 2.26 (0.16), residues: 2930 helix: 2.17 (0.12), residues: 2008 sheet: 0.90 (0.61), residues: 58 loop : -0.03 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1805 HIS 0.008 0.001 HIS B2208 PHE 0.042 0.001 PHE B1749 TYR 0.011 0.001 TYR B1753 ARG 0.004 0.000 ARG B1633 *********************** 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 324 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 275 time to evaluate : 2.838 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: 0.8753 (m-80) cc_final: 0.8404 (m-80) REVERT: A 1539 LEU cc_start: 0.9322 (mm) cc_final: 0.9071 (pp) REVERT: A 1556 TYR cc_start: 0.7450 (m-80) cc_final: 0.7174 (m-80) REVERT: A 1575 ARG cc_start: 0.8743 (mtt180) cc_final: 0.8395 (mmm160) REVERT: A 1664 GLU cc_start: 0.8676 (pt0) cc_final: 0.8315 (pt0) REVERT: A 1701 LYS cc_start: 0.9328 (pttm) cc_final: 0.9032 (pttp) REVERT: A 1706 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8603 (tmmm) REVERT: A 1830 MET cc_start: 0.8361 (tmm) cc_final: 0.7626 (ppp) REVERT: A 2126 GLU cc_start: 0.9352 (tt0) cc_final: 0.9001 (tt0) REVERT: A 2239 MET cc_start: 0.6865 (ppp) cc_final: 0.6381 (mmp) REVERT: A 2304 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: A 2411 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8921 (mm-30) REVERT: A 2475 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8512 (mm) REVERT: A 2507 ASP cc_start: 0.8885 (t0) cc_final: 0.8499 (t0) REVERT: A 2670 LYS cc_start: 0.9163 (tppp) cc_final: 0.8600 (tmtt) REVERT: A 3018 LYS cc_start: 0.9431 (mttt) cc_final: 0.9107 (mttm) REVERT: B 1470 TYR cc_start: 0.9401 (m-80) cc_final: 0.8732 (t80) REVERT: B 1475 TYR cc_start: 0.8701 (m-80) cc_final: 0.8381 (m-80) REVERT: B 1556 TYR cc_start: 0.7291 (m-80) cc_final: 0.6986 (m-80) REVERT: B 1565 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: B 1575 ARG cc_start: 0.8891 (mtt180) cc_final: 0.8248 (mmm160) REVERT: B 1664 GLU cc_start: 0.8690 (pt0) cc_final: 0.8324 (pt0) REVERT: B 1701 LYS cc_start: 0.9335 (pttm) cc_final: 0.9030 (pttp) REVERT: B 1706 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8598 (tmmm) REVERT: B 1793 ASN cc_start: 0.8902 (m-40) cc_final: 0.8522 (p0) REVERT: B 1830 MET cc_start: 0.8452 (tmm) cc_final: 0.7677 (ppp) REVERT: B 2008 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8996 (mp) REVERT: B 2126 GLU cc_start: 0.9367 (tt0) cc_final: 0.8988 (tt0) REVERT: B 2177 GLN cc_start: 0.9387 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: B 2216 ASP cc_start: 0.8945 (t0) cc_final: 0.8703 (t0) REVERT: B 2239 MET cc_start: 0.6850 (ppp) cc_final: 0.6361 (mmp) REVERT: B 2304 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: B 2411 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8919 (mm-30) REVERT: B 2450 LEU cc_start: 0.9226 (tt) cc_final: 0.8758 (mm) REVERT: B 2612 ARG cc_start: 0.8671 (ttt-90) cc_final: 0.8436 (tmt90) REVERT: B 2670 LYS cc_start: 0.9186 (tppp) cc_final: 0.8627 (tmtt) REVERT: B 3018 LYS cc_start: 0.9448 (mttt) cc_final: 0.9119 (mttm) outliers start: 49 outliers final: 31 residues processed: 307 average time/residue: 1.2773 time to fit residues: 458.2485 Evaluate side-chains 298 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 259 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 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 2475 LEU Chi-restraints excluded: chain A residue 2597 ASP Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2697 ASN Chi-restraints excluded: chain A residue 2805 MET Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1706 LYS Chi-restraints excluded: chain B residue 1803 ASP 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 2051 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2177 GLN Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2304 GLU Chi-restraints excluded: chain B residue 2597 ASP Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2697 ASN Chi-restraints excluded: chain B residue 2896 GLN Chi-restraints excluded: chain B residue 2945 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 234 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 249 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN B2809 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3597 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= 0.179 Angle : 0.656 15.085 32982 Z= 0.299 Chirality : 0.040 0.373 3736 Planarity : 0.003 0.043 4176 Dihedral : 4.194 59.403 3270 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.57 % Allowed : 20.01 % Favored : 78.42 % 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: 2.21 (0.16), residues: 2930 helix: 2.13 (0.12), residues: 2010 sheet: 0.84 (0.61), residues: 58 loop : -0.03 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1805 HIS 0.006 0.001 HIS B2208 PHE 0.050 0.001 PHE B1749 TYR 0.016 0.001 TYR A1529 ARG 0.004 0.000 ARG B1633 ********************** 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 314 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 272 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1475 TYR cc_start: 0.8760 (m-80) cc_final: 0.8407 (m-80) REVERT: A 1539 LEU cc_start: 0.9321 (mm) cc_final: 0.9048 (pp) REVERT: A 1556 TYR cc_start: 0.7437 (m-80) cc_final: 0.7158 (m-80) REVERT: A 1575 ARG cc_start: 0.8727 (mtt180) cc_final: 0.8412 (mmm160) REVERT: A 1664 GLU cc_start: 0.8642 (pt0) cc_final: 0.8281 (pt0) REVERT: A 1701 LYS cc_start: 0.9328 (pttm) cc_final: 0.9033 (pttp) REVERT: A 1706 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8642 (tmmm) REVERT: A 1717 TYR cc_start: 0.9273 (t80) cc_final: 0.8774 (t80) REVERT: A 1830 MET cc_start: 0.8357 (tmm) cc_final: 0.7691 (ppp) REVERT: A 1836 ASP cc_start: 0.9471 (m-30) cc_final: 0.8816 (t0) REVERT: A 1844 TYR cc_start: 0.9006 (m-80) cc_final: 0.8712 (m-80) REVERT: A 2126 GLU cc_start: 0.9347 (tt0) cc_final: 0.8996 (tt0) REVERT: A 2196 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8639 (ppp80) REVERT: A 2304 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: A 2411 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8923 (mm-30) REVERT: A 2475 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8451 (mm) REVERT: A 2507 ASP cc_start: 0.8860 (t0) cc_final: 0.8461 (t0) REVERT: A 2670 LYS cc_start: 0.9162 (tppp) cc_final: 0.8583 (tmtt) REVERT: A 3018 LYS cc_start: 0.9423 (mttt) cc_final: 0.9091 (mttm) REVERT: B 1470 TYR cc_start: 0.9405 (m-80) cc_final: 0.8751 (t80) REVERT: B 1556 TYR cc_start: 0.7335 (m-80) cc_final: 0.7016 (m-80) REVERT: B 1565 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: B 1575 ARG cc_start: 0.8884 (mtt180) cc_final: 0.8242 (mmm160) REVERT: B 1664 GLU cc_start: 0.8623 (pt0) cc_final: 0.8313 (pt0) REVERT: B 1701 LYS cc_start: 0.9332 (pttm) cc_final: 0.9037 (pttp) REVERT: B 1706 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8621 (tmmm) REVERT: B 1793 ASN cc_start: 0.8904 (m-40) cc_final: 0.8521 (p0) REVERT: B 1830 MET cc_start: 0.8370 (tmm) cc_final: 0.7640 (ppp) REVERT: B 1836 ASP cc_start: 0.9373 (m-30) cc_final: 0.8965 (t0) REVERT: B 1844 TYR cc_start: 0.9049 (m-80) cc_final: 0.8656 (m-80) REVERT: B 2008 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8971 (mp) REVERT: B 2126 GLU cc_start: 0.9359 (tt0) cc_final: 0.9000 (tt0) REVERT: B 2177 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: B 2304 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: B 2411 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8925 (mm-30) REVERT: B 2450 LEU cc_start: 0.9229 (tt) cc_final: 0.8795 (mm) REVERT: B 2532 MET cc_start: 0.6943 (tpt) cc_final: 0.6718 (tpp) REVERT: B 2612 ARG cc_start: 0.8660 (ttt-90) cc_final: 0.8413 (tmt90) REVERT: B 2670 LYS cc_start: 0.9176 (tppp) cc_final: 0.8603 (tmtt) REVERT: B 3018 LYS cc_start: 0.9443 (mttt) cc_final: 0.9180 (mttp) outliers start: 42 outliers final: 31 residues processed: 301 average time/residue: 1.2764 time to fit residues: 450.8754 Evaluate side-chains 302 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 262 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1567 ASP Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1706 LYS Chi-restraints excluded: chain A residue 1823 ILE Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2185 ILE Chi-restraints excluded: chain A residue 2196 ARG 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 2357 MET Chi-restraints excluded: chain A residue 2475 LEU Chi-restraints excluded: chain A residue 2597 ASP Chi-restraints excluded: chain A residue 2606 ILE Chi-restraints excluded: chain A residue 2697 ASN Chi-restraints excluded: chain A residue 2896 GLN Chi-restraints excluded: chain A residue 2945 LEU Chi-restraints excluded: chain B residue 1565 PHE Chi-restraints excluded: chain B residue 1588 PHE Chi-restraints excluded: chain B residue 1652 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1706 LYS Chi-restraints excluded: chain B residue 1803 ASP 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 2051 LEU Chi-restraints excluded: chain B residue 2176 LEU Chi-restraints excluded: chain B residue 2177 GLN Chi-restraints excluded: chain B residue 2185 ILE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2304 GLU Chi-restraints excluded: chain B residue 2475 LEU Chi-restraints excluded: chain B residue 2597 ASP Chi-restraints excluded: chain B residue 2606 ILE Chi-restraints excluded: chain B residue 2697 ASN Chi-restraints excluded: chain B residue 2896 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: 0.8980 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 205 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2206 GLN ** B1867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2632 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.068013 restraints weight = 55136.052| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.78 r_work: 0.2896 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24420 Z= 0.170 Angle : 0.659 15.129 32982 Z= 0.299 Chirality : 0.041 0.416 3736 Planarity : 0.003 0.044 4176 Dihedral : 4.191 59.540 3270 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.94 % Allowed : 19.71 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.16), residues: 2930 helix: 2.13 (0.12), residues: 2002 sheet: 0.84 (0.60), residues: 58 loop : -0.00 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1805 HIS 0.006 0.001 HIS B1802 PHE 0.047 0.001 PHE A1749 TYR 0.023 0.001 TYR B1475 ARG 0.004 0.000 ARG B1633 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8459.78 seconds wall clock time: 157 minutes 50.33 seconds (9470.33 seconds total)