Starting phenix.real_space_refine on Sun Sep 13 10:31:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6sky_10231/09_2026/6sky_10231.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sky_10231/09_2026/6sky_10231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sky_10231/09_2026/6sky_10231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sky_10231/09_2026/6sky_10231.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6sky_10231/09_2026/6sky_10231.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6sky_10231/09_2026/6sky_10231.cif" model { file = "/net/cci-nas-00/data/ceres_data/6sky_10231/09_2026/6sky_10231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sky_10231/09_2026/6sky_10231.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 14064 2.51 5 N 3942 2.21 5 O 4242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22348 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 11142 Classifications: {'peptide': 1412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1359} Chain breaks: 7 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 16.61, per 1000 atoms: 0.74 Number of scatterers: 22348 At special positions: 0 Unit cell: (189.561, 104.841, 115.431, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 6 15.00 Mg 2 11.99 O 4242 8.00 N 3942 7.00 C 14064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 959.1 milliseconds 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5388 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 6 sheets defined 73.2% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 1428 through 1442 removed outlier: 3.749A pdb=" N GLU A1432 " --> pdb=" O GLY A1428 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL A1440 " --> pdb=" O HIS A1436 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A1441 " --> pdb=" O SER A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1462 removed outlier: 3.965A pdb=" N ALA A1451 " --> pdb=" O CYS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1467 Processing helix chain 'A' and resid 1469 through 1488 removed outlier: 3.645A pdb=" N GLY A1475 " --> pdb=" O SER A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1522 Processing helix chain 'A' and resid 1529 through 1544 removed outlier: 3.616A pdb=" N LYS A1533 " --> pdb=" O ASP A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1570 Processing helix chain 'A' and resid 1577 through 1589 Processing helix chain 'A' and resid 1605 through 1620 removed outlier: 5.111A pdb=" N ALA A1614 " --> pdb=" O ILE A1610 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A1615 " --> pdb=" O LYS A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1645 Processing helix chain 'A' and resid 1648 through 1652 Processing helix chain 'A' and resid 1656 through 1664 Processing helix chain 'A' and resid 1669 through 1685 removed outlier: 3.753A pdb=" N LEU A1681 " --> pdb=" O LEU A1677 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A1682 " --> pdb=" O ILE A1678 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A1683 " --> pdb=" O LYS A1679 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A1684 " --> pdb=" O SER A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1707 removed outlier: 3.549A pdb=" N ASP A1707 " --> pdb=" O ASP A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1720 removed outlier: 3.595A pdb=" N GLU A1718 " --> pdb=" O SER A1714 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1727 Processing helix chain 'A' and resid 1755 through 1759 removed outlier: 3.781A pdb=" N GLU A1758 " --> pdb=" O ARG A1755 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A1759 " --> pdb=" O ALA A1756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1755 through 1759' Processing helix chain 'A' and resid 1761 through 1772 Processing helix chain 'A' and resid 1777 through 1782 removed outlier: 3.770A pdb=" N VAL A1782 " --> pdb=" O VAL A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1790 removed outlier: 4.459A pdb=" N ILE A1786 " --> pdb=" O VAL A1782 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1809 removed outlier: 3.750A pdb=" N ARG A1796 " --> pdb=" O GLY A1792 " (cutoff:3.500A) Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1814 through 1828 removed outlier: 3.653A pdb=" N ARG A1818 " --> pdb=" O GLN A1814 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN A1825 " --> pdb=" O SER A1821 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1850 removed outlier: 3.774A pdb=" N LEU A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1866 removed outlier: 3.655A pdb=" N ASP A1862 " --> pdb=" O SER A1859 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A1864 " --> pdb=" O ALA A1861 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP A1866 " --> pdb=" O ARG A1863 " (cutoff:3.500A) Processing helix chain 'A' and resid 1870 through 1881 Processing helix chain 'A' and resid 1883 through 1899 Processing helix chain 'A' and resid 1915 through 1924 removed outlier: 4.034A pdb=" N GLU A1919 " --> pdb=" O ASP A1915 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A1923 " --> pdb=" O GLU A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1933 Processing helix chain 'A' and resid 1938 through 1949 Processing helix chain 'A' and resid 1952 through 1969 removed outlier: 3.805A pdb=" N PHE A1958 " --> pdb=" O LYS A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1973 through 1989 removed outlier: 3.768A pdb=" N GLY A1989 " --> pdb=" O LEU A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2000 removed outlier: 3.514A pdb=" N SER A1994 " --> pdb=" O LEU A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2011 through 2022 Processing helix chain 'A' and resid 2034 through 2048 removed outlier: 3.507A pdb=" N THR A2038 " --> pdb=" O SER A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2051 through 2071 removed outlier: 3.743A pdb=" N VAL A2055 " --> pdb=" O GLU A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2098 Processing helix chain 'A' and resid 2101 through 2120 Processing helix chain 'A' and resid 2123 through 2144 Processing helix chain 'A' and resid 2145 through 2148 removed outlier: 3.703A pdb=" N ARG A2148 " --> pdb=" O HIS A2145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2145 through 2148' Processing helix chain 'A' and resid 2153 through 2175 Processing helix chain 'A' and resid 2177 through 2190 Processing helix chain 'A' and resid 2192 through 2197 removed outlier: 3.674A pdb=" N SER A2197 " --> pdb=" O PRO A2193 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2217 Processing helix chain 'A' and resid 2219 through 2233 Processing helix chain 'A' and resid 2244 through 2259 Processing helix chain 'A' and resid 2263 through 2271 removed outlier: 3.829A pdb=" N GLN A2268 " --> pdb=" O PRO A2264 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A2269 " --> pdb=" O ASP A2265 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2280 removed outlier: 4.049A pdb=" N LYS A2280 " --> pdb=" O LEU A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2285 through 2304 Processing helix chain 'A' and resid 2305 through 2329 Processing helix chain 'A' and resid 2348 through 2388 removed outlier: 3.740A pdb=" N SER A2388 " --> pdb=" O SER A2384 " (cutoff:3.500A) Processing helix chain 'A' and resid 2393 through 2405 Processing helix chain 'A' and resid 2408 through 2419 Processing helix chain 'A' and resid 2420 through 2422 No H-bonds generated for 'chain 'A' and resid 2420 through 2422' Processing helix chain 'A' and resid 2423 through 2427 Processing helix chain 'A' and resid 2430 through 2435 Processing helix chain 'A' and resid 2443 through 2460 removed outlier: 3.620A pdb=" N ASP A2451 " --> pdb=" O LYS A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2460 through 2473 removed outlier: 5.859A pdb=" N TYR A2466 " --> pdb=" O TYR A2462 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS A2467 " --> pdb=" O HIS A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2483 through 2498 Processing helix chain 'A' and resid 2506 through 2523 Processing helix chain 'A' and resid 2540 through 2553 Processing helix chain 'A' and resid 2615 through 2633 removed outlier: 4.136A pdb=" N ASP A2619 " --> pdb=" O ASP A2615 " (cutoff:3.500A) Processing helix chain 'A' and resid 2636 through 2642 removed outlier: 3.636A pdb=" N ARG A2642 " --> pdb=" O GLU A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2670 through 2682 Proline residue: A2676 - end of helix removed outlier: 3.897A pdb=" N GLU A2679 " --> pdb=" O MET A2675 " (cutoff:3.500A) Processing helix chain 'A' and resid 2687 through 2698 removed outlier: 3.740A pdb=" N ALA A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) Processing helix chain 'A' and resid 2702 through 2715 Processing helix chain 'A' and resid 2721 through 2727 removed outlier: 4.321A pdb=" N PHE A2725 " --> pdb=" O MET A2721 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET A2726 " --> pdb=" O ARG A2722 " (cutoff:3.500A) Processing helix chain 'A' and resid 2731 through 2756 Processing helix chain 'A' and resid 2785 through 2790 removed outlier: 3.678A pdb=" N VAL A2789 " --> pdb=" O MET A2786 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A2790 " --> pdb=" O GLY A2787 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2807 removed outlier: 3.501A pdb=" N GLY A2807 " --> pdb=" O ASP A2803 " (cutoff:3.500A) Processing helix chain 'A' and resid 2815 through 2829 Processing helix chain 'A' and resid 2831 through 2844 Processing helix chain 'A' and resid 2853 through 2861 removed outlier: 3.678A pdb=" N GLN A2861 " --> pdb=" O MET A2857 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2909 Processing helix chain 'A' and resid 2915 through 2928 Processing helix chain 'A' and resid 2929 through 2934 Processing helix chain 'B' and resid 1429 through 1442 removed outlier: 4.670A pdb=" N VAL B1440 " --> pdb=" O HIS B1436 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE B1441 " --> pdb=" O SER B1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1462 removed outlier: 3.965A pdb=" N ALA B1451 " --> pdb=" O CYS B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1467 Processing helix chain 'B' and resid 1469 through 1488 removed outlier: 3.645A pdb=" N GLY B1475 " --> pdb=" O SER B1471 " (cutoff:3.500A) Processing helix chain 'B' and resid 1502 through 1522 Processing helix chain 'B' and resid 1529 through 1544 removed outlier: 3.616A pdb=" N LYS B1533 " --> pdb=" O ASP B1529 " (cutoff:3.500A) Processing helix chain 'B' and resid 1556 through 1570 Processing helix chain 'B' and resid 1577 through 1589 Processing helix chain 'B' and resid 1605 through 1620 removed outlier: 5.111A pdb=" N ALA B1614 " --> pdb=" O ILE B1610 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL B1615 " --> pdb=" O LYS B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1626 through 1645 Processing helix chain 'B' and resid 1648 through 1652 Processing helix chain 'B' and resid 1656 through 1664 Processing helix chain 'B' and resid 1669 through 1685 removed outlier: 3.753A pdb=" N LEU B1681 " --> pdb=" O LEU B1677 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR B1682 " --> pdb=" O ILE B1678 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE B1683 " --> pdb=" O LYS B1679 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B1684 " --> pdb=" O SER B1680 " (cutoff:3.500A) Processing helix chain 'B' and resid 1686 through 1707 removed outlier: 3.549A pdb=" N ASP B1707 " --> pdb=" O ASP B1703 " (cutoff:3.500A) Processing helix chain 'B' and resid 1709 through 1720 removed outlier: 3.595A pdb=" N GLU B1718 " --> pdb=" O SER B1714 " (cutoff:3.500A) Processing helix chain 'B' and resid 1721 through 1727 Processing helix chain 'B' and resid 1755 through 1759 removed outlier: 3.781A pdb=" N GLU B1758 " --> pdb=" O ARG B1755 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B1759 " --> pdb=" O ALA B1756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1755 through 1759' Processing helix chain 'B' and resid 1761 through 1772 Processing helix chain 'B' and resid 1777 through 1782 removed outlier: 3.770A pdb=" N VAL B1782 " --> pdb=" O VAL B1778 " (cutoff:3.500A) Processing helix chain 'B' and resid 1782 through 1790 removed outlier: 4.459A pdb=" N ILE B1786 " --> pdb=" O VAL B1782 " (cutoff:3.500A) Processing helix chain 'B' and resid 1792 through 1809 removed outlier: 3.750A pdb=" N ARG B1796 " --> pdb=" O GLY B1792 " (cutoff:3.500A) Proline residue: B1799 - end of helix Processing helix chain 'B' and resid 1814 through 1828 removed outlier: 3.653A pdb=" N ARG B1818 " --> pdb=" O GLN B1814 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN B1825 " --> pdb=" O SER B1821 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU B1826 " --> pdb=" O GLU B1822 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1850 removed outlier: 3.774A pdb=" N LEU B1841 " --> pdb=" O GLU B1837 " (cutoff:3.500A) Processing helix chain 'B' and resid 1859 through 1866 removed outlier: 3.655A pdb=" N ASP B1862 " --> pdb=" O SER B1859 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B1864 " --> pdb=" O ALA B1861 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP B1866 " --> pdb=" O ARG B1863 " (cutoff:3.500A) Processing helix chain 'B' and resid 1870 through 1881 Processing helix chain 'B' and resid 1883 through 1899 Processing helix chain 'B' and resid 1915 through 1924 removed outlier: 4.034A pdb=" N GLU B1919 " --> pdb=" O ASP B1915 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B1923 " --> pdb=" O GLU B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1928 through 1933 Processing helix chain 'B' and resid 1938 through 1949 Processing helix chain 'B' and resid 1952 through 1969 removed outlier: 3.805A pdb=" N PHE B1958 " --> pdb=" O LYS B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1973 through 1989 removed outlier: 3.768A pdb=" N GLY B1989 " --> pdb=" O LEU B1985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1990 through 2000 removed outlier: 3.514A pdb=" N SER B1994 " --> pdb=" O LEU B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 2011 through 2022 Processing helix chain 'B' and resid 2034 through 2048 removed outlier: 3.507A pdb=" N THR B2038 " --> pdb=" O SER B2034 " (cutoff:3.500A) Processing helix chain 'B' and resid 2051 through 2071 removed outlier: 3.743A pdb=" N VAL B2055 " --> pdb=" O GLU B2051 " (cutoff:3.500A) Processing helix chain 'B' and resid 2076 through 2098 Processing helix chain 'B' and resid 2101 through 2120 Processing helix chain 'B' and resid 2123 through 2144 Processing helix chain 'B' and resid 2145 through 2148 removed outlier: 3.703A pdb=" N ARG B2148 " --> pdb=" O HIS B2145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2145 through 2148' Processing helix chain 'B' and resid 2153 through 2175 Processing helix chain 'B' and resid 2177 through 2190 Processing helix chain 'B' and resid 2192 through 2197 removed outlier: 3.674A pdb=" N SER B2197 " --> pdb=" O PRO B2193 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2217 Processing helix chain 'B' and resid 2219 through 2233 Processing helix chain 'B' and resid 2244 through 2259 Processing helix chain 'B' and resid 2263 through 2271 removed outlier: 3.829A pdb=" N GLN B2268 " --> pdb=" O PRO B2264 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B2269 " --> pdb=" O ASP B2265 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2280 removed outlier: 4.049A pdb=" N LYS B2280 " --> pdb=" O LEU B2276 " (cutoff:3.500A) Processing helix chain 'B' and resid 2285 through 2304 Processing helix chain 'B' and resid 2305 through 2329 Processing helix chain 'B' and resid 2348 through 2388 removed outlier: 3.740A pdb=" N SER B2388 " --> pdb=" O SER B2384 " (cutoff:3.500A) Processing helix chain 'B' and resid 2393 through 2405 Processing helix chain 'B' and resid 2408 through 2419 Processing helix chain 'B' and resid 2420 through 2422 No H-bonds generated for 'chain 'B' and resid 2420 through 2422' Processing helix chain 'B' and resid 2423 through 2427 Processing helix chain 'B' and resid 2430 through 2435 Processing helix chain 'B' and resid 2443 through 2460 removed outlier: 3.620A pdb=" N ASP B2451 " --> pdb=" O LYS B2447 " (cutoff:3.500A) Processing helix chain 'B' and resid 2460 through 2473 removed outlier: 5.859A pdb=" N TYR B2466 " --> pdb=" O TYR B2462 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS B2467 " --> pdb=" O HIS B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2483 through 2498 Processing helix chain 'B' and resid 2506 through 2523 Processing helix chain 'B' and resid 2540 through 2553 Processing helix chain 'B' and resid 2615 through 2633 removed outlier: 4.136A pdb=" N ASP B2619 " --> pdb=" O ASP B2615 " (cutoff:3.500A) Processing helix chain 'B' and resid 2636 through 2642 removed outlier: 3.636A pdb=" N ARG B2642 " --> pdb=" O GLU B2638 " (cutoff:3.500A) Processing helix chain 'B' and resid 2670 through 2682 Proline residue: B2676 - end of helix removed outlier: 3.897A pdb=" N GLU B2679 " --> pdb=" O MET B2675 " (cutoff:3.500A) Processing helix chain 'B' and resid 2687 through 2698 removed outlier: 3.740A pdb=" N ALA B2698 " --> pdb=" O GLU B2694 " (cutoff:3.500A) Processing helix chain 'B' and resid 2702 through 2715 Processing helix chain 'B' and resid 2721 through 2727 removed outlier: 4.321A pdb=" N PHE B2725 " --> pdb=" O MET B2721 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET B2726 " --> pdb=" O ARG B2722 " (cutoff:3.500A) Processing helix chain 'B' and resid 2731 through 2756 Processing helix chain 'B' and resid 2785 through 2790 removed outlier: 3.678A pdb=" N VAL B2789 " --> pdb=" O MET B2786 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B2790 " --> pdb=" O GLY B2787 " (cutoff:3.500A) Processing helix chain 'B' and resid 2801 through 2807 removed outlier: 3.501A pdb=" N GLY B2807 " --> pdb=" O ASP B2803 " (cutoff:3.500A) Processing helix chain 'B' and resid 2815 through 2829 Processing helix chain 'B' and resid 2831 through 2844 Processing helix chain 'B' and resid 2853 through 2861 removed outlier: 3.678A pdb=" N GLN B2861 " --> pdb=" O MET B2857 " (cutoff:3.500A) Processing helix chain 'B' and resid 2898 through 2909 Processing helix chain 'B' and resid 2915 through 2928 Processing helix chain 'B' and resid 2929 through 2934 Processing sheet with id=AA1, first strand: chain 'A' and resid 2534 through 2536 removed outlier: 7.017A pdb=" N GLU A2582 " --> pdb=" O THR A2596 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR A2596 " --> pdb=" O GLU A2582 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2534 through 2536 removed outlier: 7.017A pdb=" N GLU A2582 " --> pdb=" O THR A2596 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR A2596 " --> pdb=" O GLU A2582 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A2593 " --> pdb=" O VAL A2609 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER A2658 " --> pdb=" O LEU A2654 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2667 through 2669 Processing sheet with id=AA4, first strand: chain 'B' and resid 2534 through 2536 removed outlier: 7.017A pdb=" N GLU B2582 " --> pdb=" O THR B2596 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR B2596 " --> pdb=" O GLU B2582 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2534 through 2536 removed outlier: 7.017A pdb=" N GLU B2582 " --> pdb=" O THR B2596 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR B2596 " --> pdb=" O GLU B2582 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B2593 " --> pdb=" O VAL B2609 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER B2658 " --> pdb=" O LEU B2654 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2667 through 2669 1420 hydrogen bonds defined for protein. 4200 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: 4.76 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7968 1.36 - 1.51: 7774 1.51 - 1.66: 6866 1.66 - 1.80: 142 1.80 - 1.95: 8 Bond restraints: 22758 Sorted by residual: bond pdb=" C ASN B2539 " pdb=" N SER B2540 " ideal model delta sigma weight residual 1.333 1.249 0.083 2.74e-02 1.33e+03 9.21e+00 bond pdb=" C ASN A2539 " pdb=" N SER A2540 " ideal model delta sigma weight residual 1.333 1.249 0.083 2.74e-02 1.33e+03 9.21e+00 bond pdb=" C GLN A2304 " pdb=" N ASN A2305 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.61e-02 3.86e+03 4.68e+00 bond pdb=" C GLN B2304 " pdb=" N ASN B2305 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.61e-02 3.86e+03 4.68e+00 bond pdb=" CB GLU A2774 " pdb=" CG GLU A2774 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.16e+00 ... (remaining 22753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 30588 2.85 - 5.71: 202 5.71 - 8.56: 10 8.56 - 11.41: 2 11.41 - 14.27: 2 Bond angle restraints: 30804 Sorted by residual: angle pdb=" CA TRP A2118 " pdb=" CB TRP A2118 " pdb=" CG TRP A2118 " ideal model delta sigma weight residual 113.60 119.56 -5.96 1.90e+00 2.77e-01 9.83e+00 angle pdb=" CA TRP B2118 " pdb=" CB TRP B2118 " pdb=" CG TRP B2118 " ideal model delta sigma weight residual 113.60 119.56 -5.96 1.90e+00 2.77e-01 9.83e+00 angle pdb=" CA TRP B2940 " pdb=" CB TRP B2940 " pdb=" CG TRP B2940 " ideal model delta sigma weight residual 113.60 118.75 -5.15 1.90e+00 2.77e-01 7.33e+00 angle pdb=" CA TRP A2940 " pdb=" CB TRP A2940 " pdb=" CG TRP A2940 " ideal model delta sigma weight residual 113.60 118.75 -5.15 1.90e+00 2.77e-01 7.33e+00 angle pdb=" C LEU A2674 " pdb=" N MET A2675 " pdb=" CA MET A2675 " ideal model delta sigma weight residual 121.80 115.33 6.47 2.44e+00 1.68e-01 7.03e+00 ... (remaining 30799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.92: 12766 18.92 - 37.84: 904 37.84 - 56.76: 188 56.76 - 75.68: 28 75.68 - 94.60: 8 Dihedral angle restraints: 13894 sinusoidal: 5616 harmonic: 8278 Sorted by residual: dihedral pdb=" CA VAL B2664 " pdb=" C VAL B2664 " pdb=" N SER B2665 " pdb=" CA SER B2665 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA VAL A2664 " pdb=" C VAL A2664 " pdb=" N SER A2665 " pdb=" CA SER A2665 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA THR A2811 " pdb=" C THR A2811 " pdb=" N LYS A2812 " pdb=" CA LYS A2812 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 13891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1764 0.033 - 0.067: 1266 0.067 - 0.100: 328 0.100 - 0.134: 114 0.134 - 0.167: 18 Chirality restraints: 3490 Sorted by residual: chirality pdb=" CB ILE B2852 " pdb=" CA ILE B2852 " pdb=" CG1 ILE B2852 " pdb=" CG2 ILE B2852 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CB ILE A2852 " pdb=" CA ILE A2852 " pdb=" CG1 ILE A2852 " pdb=" CG2 ILE A2852 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA PHE A2015 " pdb=" N PHE A2015 " pdb=" C PHE A2015 " pdb=" CB PHE A2015 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 3487 not shown) Planarity restraints: 3958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B2675 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B2676 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B2676 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B2676 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A2675 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO A2676 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A2676 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2676 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A2731 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO A2732 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A2732 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2732 " 0.027 5.00e-02 4.00e+02 ... (remaining 3955 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 256 2.64 - 3.21: 20150 3.21 - 3.77: 33239 3.77 - 4.34: 48079 4.34 - 4.90: 80189 Nonbonded interactions: 181913 Sorted by model distance: nonbonded pdb=" OD1 ASP A2012 " pdb=" OG SER A2034 " model vdw 2.077 3.040 nonbonded pdb=" OD1 ASP B2012 " pdb=" OG SER B2034 " model vdw 2.077 3.040 nonbonded pdb=" OD2 ASP A2190 " pdb=" OG SER B1965 " model vdw 2.126 3.040 nonbonded pdb=" OG SER A1965 " pdb=" OD2 ASP B2190 " model vdw 2.126 3.040 nonbonded pdb=" OG SER A2244 " pdb=" OD2 ASP A2247 " model vdw 2.173 3.040 ... (remaining 181908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 33.860 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 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 : 0.009 0.083 22758 Z= 0.391 Angle : 0.685 14.267 30804 Z= 0.372 Chirality : 0.047 0.167 3490 Planarity : 0.004 0.056 3958 Dihedral : 13.795 94.596 8506 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.63 % Allowed : 7.18 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.14), residues: 2792 helix: -0.77 (0.10), residues: 1948 sheet: -0.85 (0.65), residues: 72 loop : -2.86 (0.18), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B2019 TYR 0.018 0.002 TYR B2673 PHE 0.022 0.002 PHE A2015 TRP 0.020 0.002 TRP A2940 HIS 0.006 0.001 HIS B1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00944 / 0.39 (22758) covalent geometry : angle 0.68512 / 0.37 (30804) hydrogen bonds : bond 0.14556 / 9.59 ( 1412) hydrogen bonds : angle 5.35262 / 3.79 ( 4200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 378 time to evaluate : 0.892 Fit side-chains REVERT: A 1433 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8097 (tmm) REVERT: A 1463 ASP cc_start: 0.7320 (m-30) cc_final: 0.7088 (m-30) REVERT: A 1507 LYS cc_start: 0.8020 (mttt) cc_final: 0.7731 (mtpt) REVERT: A 1818 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7644 (ttp80) REVERT: A 1883 MET cc_start: 0.8764 (mtp) cc_final: 0.8552 (mtm) REVERT: A 1899 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6609 (ptp-170) REVERT: A 2068 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7490 (mtm110) REVERT: A 2176 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7655 (mmp80) REVERT: A 2191 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 2247 ASP cc_start: 0.7601 (p0) cc_final: 0.7103 (p0) REVERT: A 2304 GLN cc_start: 0.7926 (pt0) cc_final: 0.7406 (mp10) REVERT: A 2317 ASN cc_start: 0.6612 (m-40) cc_final: 0.6303 (m110) REVERT: A 2365 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7298 (ttp80) REVERT: A 2368 GLN cc_start: 0.7944 (tp40) cc_final: 0.7640 (mm-40) REVERT: A 2393 ASN cc_start: 0.8286 (m-40) cc_final: 0.8051 (m110) REVERT: A 2487 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: A 2502 LYS cc_start: 0.8336 (mttt) cc_final: 0.7958 (tttp) REVERT: A 2522 MET cc_start: 0.8713 (mmp) cc_final: 0.8362 (mmm) REVERT: A 2561 GLN cc_start: 0.8910 (mt0) cc_final: 0.8638 (mt0) REVERT: A 2613 ASN cc_start: 0.6815 (OUTLIER) cc_final: 0.6525 (p0) REVERT: A 2637 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8165 (tpt90) REVERT: A 2693 LYS cc_start: 0.8222 (tttt) cc_final: 0.7936 (ttpt) REVERT: A 2752 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8738 (tt) REVERT: A 2808 MET cc_start: 0.9164 (mtt) cc_final: 0.8728 (mtt) REVERT: B 1433 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8091 (tmm) REVERT: B 1463 ASP cc_start: 0.7323 (m-30) cc_final: 0.7089 (m-30) REVERT: B 1507 LYS cc_start: 0.8021 (mttt) cc_final: 0.7730 (mtpt) REVERT: B 1818 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7641 (ttp80) REVERT: B 1883 MET cc_start: 0.8766 (mtp) cc_final: 0.8552 (mtm) REVERT: B 1899 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6600 (ptp-170) REVERT: B 2068 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7490 (mtm110) REVERT: B 2176 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7654 (mmp80) REVERT: B 2191 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8300 (mp) REVERT: B 2247 ASP cc_start: 0.7599 (p0) cc_final: 0.7098 (p0) REVERT: B 2304 GLN cc_start: 0.7925 (pt0) cc_final: 0.7410 (mp10) REVERT: B 2317 ASN cc_start: 0.6618 (m-40) cc_final: 0.6307 (m110) REVERT: B 2365 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7298 (ttp80) REVERT: B 2368 GLN cc_start: 0.7943 (tp40) cc_final: 0.7638 (mm-40) REVERT: B 2393 ASN cc_start: 0.8286 (m-40) cc_final: 0.8048 (m110) REVERT: B 2487 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: B 2502 LYS cc_start: 0.8338 (mttt) cc_final: 0.7958 (tttp) REVERT: B 2522 MET cc_start: 0.8712 (mmp) cc_final: 0.8363 (mmm) REVERT: B 2561 GLN cc_start: 0.8912 (mt0) cc_final: 0.8642 (mt0) REVERT: B 2613 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6533 (p0) REVERT: B 2637 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8163 (tpt90) REVERT: B 2693 LYS cc_start: 0.8221 (tttt) cc_final: 0.7938 (ttpt) REVERT: B 2752 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8734 (tt) REVERT: B 2808 MET cc_start: 0.9181 (mtt) cc_final: 0.8750 (mtt) outliers start: 88 outliers final: 34 residues processed: 452 average time/residue: 0.7780 time to fit residues: 391.7925 Evaluate side-chains 332 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1650 ASP Chi-restraints excluded: chain A residue 1658 GLN Chi-restraints excluded: chain A residue 1899 ARG Chi-restraints excluded: chain A residue 1935 GLN Chi-restraints excluded: chain A residue 1936 ASP Chi-restraints excluded: chain A residue 2076 ASN Chi-restraints excluded: chain A residue 2077 THR Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2126 ASP Chi-restraints excluded: chain A residue 2160 VAL Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2369 THR Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2485 SER Chi-restraints excluded: chain A residue 2487 GLN Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2600 THR Chi-restraints excluded: chain A residue 2613 ASN Chi-restraints excluded: chain A residue 2637 ARG Chi-restraints excluded: chain A residue 2713 VAL Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain B residue 1433 MET Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1650 ASP Chi-restraints excluded: chain B residue 1658 GLN Chi-restraints excluded: chain B residue 1899 ARG Chi-restraints excluded: chain B residue 1935 GLN Chi-restraints excluded: chain B residue 1936 ASP Chi-restraints excluded: chain B residue 2076 ASN Chi-restraints excluded: chain B residue 2077 THR Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2126 ASP Chi-restraints excluded: chain B residue 2160 VAL Chi-restraints excluded: chain B residue 2191 LEU Chi-restraints excluded: chain B residue 2369 THR Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2485 SER Chi-restraints excluded: chain B residue 2487 GLN Chi-restraints excluded: chain B residue 2573 VAL Chi-restraints excluded: chain B residue 2600 THR Chi-restraints excluded: chain B residue 2613 ASN Chi-restraints excluded: chain B residue 2637 ARG Chi-restraints excluded: chain B residue 2713 VAL Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2813 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 0.7980 chunk 244 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.0932 > 50:) chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1560 ASN A1612 ASN A1656 GLN A1844 ASN A1950 ASN A2179 GLN A2255 GLN A2294 GLN A2317 ASN A2354 GLN A2360 GLN A2446 GLN A2518 HIS A2567 ASN A2577 HIS A2624 GLN A2641 GLN A2702 ASN A2754 HIS A2849 GLN A2925 ASN B1560 ASN B1612 ASN B1656 GLN B1844 ASN B1950 ASN B2179 GLN B2255 GLN B2294 GLN B2317 ASN B2354 GLN B2360 GLN B2446 GLN B2518 HIS B2567 ASN B2577 HIS B2624 GLN B2641 GLN B2702 ASN B2754 HIS B2849 GLN B2925 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108331 restraints weight = 25853.133| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.73 r_work: 0.2925 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22758 Z= 0.135 Angle : 0.530 11.076 30804 Z= 0.276 Chirality : 0.039 0.139 3490 Planarity : 0.004 0.045 3958 Dihedral : 7.505 87.763 3180 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.30 % Allowed : 12.71 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 2792 helix: 0.82 (0.11), residues: 1974 sheet: -0.69 (0.67), residues: 66 loop : -2.49 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2515 TYR 0.018 0.001 TYR A1457 PHE 0.017 0.001 PHE A2174 TRP 0.014 0.001 TRP B2940 HIS 0.004 0.001 HIS A1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (22758) covalent geometry : angle 0.52990 / 0.28 (30804) hydrogen bonds : bond 0.05077 / 3.38 ( 1412) hydrogen bonds : angle 3.93942 / 2.83 ( 4200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 320 time to evaluate : 0.814 Fit side-chains REVERT: A 1433 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7922 (tmm) REVERT: A 1460 LYS cc_start: 0.7965 (tttt) cc_final: 0.7320 (ttpt) REVERT: A 1461 ARG cc_start: 0.7060 (mmm160) cc_final: 0.6825 (mmm160) REVERT: A 1469 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7534 (p) REVERT: A 1537 ARG cc_start: 0.7240 (mpt90) cc_final: 0.6802 (tpp80) REVERT: A 1671 GLU cc_start: 0.7624 (mp0) cc_final: 0.6909 (mp0) REVERT: A 1755 ARG cc_start: 0.7783 (mmt90) cc_final: 0.7455 (ppt90) REVERT: A 1776 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8382 (mmpt) REVERT: A 1819 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7418 (mt-10) REVERT: A 1883 MET cc_start: 0.9035 (mtp) cc_final: 0.8758 (mtm) REVERT: A 2051 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: A 2068 ARG cc_start: 0.8297 (mtt90) cc_final: 0.7825 (mtm110) REVERT: A 2121 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7676 (t) REVERT: A 2247 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7524 (p0) REVERT: A 2278 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7947 (mm-30) REVERT: A 2304 GLN cc_start: 0.7696 (pt0) cc_final: 0.6868 (mp-120) REVERT: A 2317 ASN cc_start: 0.6604 (m110) cc_final: 0.6280 (m110) REVERT: A 2358 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6292 (mp) REVERT: A 2365 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7253 (ttp80) REVERT: A 2367 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 2368 GLN cc_start: 0.8050 (tp40) cc_final: 0.7742 (mm-40) REVERT: A 2487 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: A 2502 LYS cc_start: 0.8453 (mttt) cc_final: 0.7718 (tttp) REVERT: A 2522 MET cc_start: 0.8323 (mmp) cc_final: 0.7969 (mmm) REVERT: A 2524 ARG cc_start: 0.6921 (ptp-170) cc_final: 0.6314 (ptp-110) REVERT: A 2561 GLN cc_start: 0.9046 (mt0) cc_final: 0.8695 (mt0) REVERT: A 2693 LYS cc_start: 0.8367 (tttt) cc_final: 0.7732 (ttpt) REVERT: A 2904 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7318 (pt0) REVERT: B 1433 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7865 (tmm) REVERT: B 1460 LYS cc_start: 0.7972 (tttt) cc_final: 0.7329 (ttpt) REVERT: B 1461 ARG cc_start: 0.7068 (mmm160) cc_final: 0.6832 (mmm160) REVERT: B 1469 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7539 (p) REVERT: B 1537 ARG cc_start: 0.7244 (mpt90) cc_final: 0.6805 (tpp80) REVERT: B 1671 GLU cc_start: 0.7645 (mp0) cc_final: 0.6931 (mp0) REVERT: B 1755 ARG cc_start: 0.7777 (mmt90) cc_final: 0.7454 (ppt90) REVERT: B 1776 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8380 (mmpt) REVERT: B 1819 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7437 (mt-10) REVERT: B 1883 MET cc_start: 0.9027 (mtp) cc_final: 0.8755 (mtm) REVERT: B 2051 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: B 2068 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7822 (mtm110) REVERT: B 2121 SER cc_start: 0.8039 (OUTLIER) cc_final: 0.7681 (t) REVERT: B 2247 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7532 (p0) REVERT: B 2278 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7946 (mm-30) REVERT: B 2304 GLN cc_start: 0.7695 (pt0) cc_final: 0.6867 (mp-120) REVERT: B 2317 ASN cc_start: 0.6600 (m110) cc_final: 0.6277 (m110) REVERT: B 2358 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6296 (mp) REVERT: B 2365 ARG cc_start: 0.7627 (ttp80) cc_final: 0.7243 (ttp80) REVERT: B 2367 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7376 (mt-10) REVERT: B 2368 GLN cc_start: 0.8034 (tp40) cc_final: 0.7726 (mm-40) REVERT: B 2487 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: B 2502 LYS cc_start: 0.8452 (mttt) cc_final: 0.7723 (tttp) REVERT: B 2522 MET cc_start: 0.8330 (mmp) cc_final: 0.7975 (mmm) REVERT: B 2524 ARG cc_start: 0.6922 (ptp-170) cc_final: 0.6318 (ptp-110) REVERT: B 2561 GLN cc_start: 0.9040 (mt0) cc_final: 0.8682 (mt0) REVERT: B 2693 LYS cc_start: 0.8350 (tttt) cc_final: 0.7718 (ttpt) REVERT: B 2904 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7306 (pt0) outliers start: 80 outliers final: 36 residues processed: 368 average time/residue: 0.8577 time to fit residues: 349.3638 Evaluate side-chains 330 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1650 ASP Chi-restraints excluded: chain A residue 1658 GLN Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1935 GLN Chi-restraints excluded: chain A residue 2051 GLU Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2121 SER Chi-restraints excluded: chain A residue 2160 VAL Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2265 ASP Chi-restraints excluded: chain A residue 2358 LEU Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2465 MET Chi-restraints excluded: chain A residue 2487 GLN Chi-restraints excluded: chain A residue 2713 VAL Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2830 GLU Chi-restraints excluded: chain B residue 1433 MET Chi-restraints excluded: chain B residue 1442 VAL Chi-restraints excluded: chain B residue 1469 THR Chi-restraints excluded: chain B residue 1650 ASP Chi-restraints excluded: chain B residue 1658 GLN Chi-restraints excluded: chain B residue 1683 ILE Chi-restraints excluded: chain B residue 1719 SER Chi-restraints excluded: chain B residue 1935 GLN Chi-restraints excluded: chain B residue 2051 GLU Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2121 SER Chi-restraints excluded: chain B residue 2160 VAL Chi-restraints excluded: chain B residue 2240 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2265 ASP Chi-restraints excluded: chain B residue 2358 LEU Chi-restraints excluded: chain B residue 2384 SER Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2465 MET Chi-restraints excluded: chain B residue 2487 GLN Chi-restraints excluded: chain B residue 2713 VAL Chi-restraints excluded: chain B residue 2733 ASP Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2813 THR Chi-restraints excluded: chain B residue 2830 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 30 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 135 optimal weight: 0.0060 chunk 246 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 221 optimal weight: 0.0770 chunk 94 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2567 ASN A2577 HIS B2567 ASN B2577 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.111155 restraints weight = 25908.508| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.71 r_work: 0.3018 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22758 Z= 0.106 Angle : 0.468 9.088 30804 Z= 0.242 Chirality : 0.037 0.143 3490 Planarity : 0.003 0.043 3958 Dihedral : 6.640 82.103 3130 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.05 % Allowed : 13.20 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.16), residues: 2792 helix: 1.55 (0.12), residues: 1986 sheet: -0.17 (0.65), residues: 76 loop : -2.22 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1755 TYR 0.013 0.001 TYR A1457 PHE 0.013 0.001 PHE A2015 TRP 0.014 0.001 TRP A2118 HIS 0.005 0.001 HIS A1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (22758) covalent geometry : angle 0.46836 / 0.24 (30804) hydrogen bonds : bond 0.04066 / 2.70 ( 1412) hydrogen bonds : angle 3.60826 / 2.59 ( 4200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 308 time to evaluate : 0.841 Fit side-chains REVERT: A 1433 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7881 (tmm) REVERT: A 1460 LYS cc_start: 0.7985 (tttt) cc_final: 0.7347 (ttpt) REVERT: A 1469 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7528 (p) REVERT: A 1546 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8223 (pp) REVERT: A 1571 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6853 (tpp80) REVERT: A 1650 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8230 (m-30) REVERT: A 1659 GLU cc_start: 0.8246 (tp30) cc_final: 0.7932 (tp30) REVERT: A 1671 GLU cc_start: 0.7776 (mp0) cc_final: 0.7094 (mp0) REVERT: A 1755 ARG cc_start: 0.7680 (mmt90) cc_final: 0.7400 (ppt90) REVERT: A 1776 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8389 (mmpt) REVERT: A 1883 MET cc_start: 0.9083 (mtp) cc_final: 0.8822 (mtm) REVERT: A 2051 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: A 2068 ARG cc_start: 0.8250 (mtt90) cc_final: 0.7792 (mtm110) REVERT: A 2176 ARG cc_start: 0.8052 (mpt-90) cc_final: 0.7653 (mpt180) REVERT: A 2216 ASP cc_start: 0.7915 (m-30) cc_final: 0.7713 (m-30) REVERT: A 2247 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7513 (p0) REVERT: A 2276 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8303 (mt) REVERT: A 2277 LYS cc_start: 0.8275 (mppt) cc_final: 0.7679 (mtmt) REVERT: A 2278 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 2304 GLN cc_start: 0.7651 (pt0) cc_final: 0.6914 (mp10) REVERT: A 2317 ASN cc_start: 0.6795 (m110) cc_final: 0.6480 (m110) REVERT: A 2365 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7334 (ttp80) REVERT: A 2368 GLN cc_start: 0.8131 (tp40) cc_final: 0.7821 (mm-40) REVERT: A 2487 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: A 2502 LYS cc_start: 0.8443 (mttt) cc_final: 0.7904 (tmtt) REVERT: A 2522 MET cc_start: 0.8303 (mmp) cc_final: 0.7977 (mmm) REVERT: A 2524 ARG cc_start: 0.6826 (ptp-170) cc_final: 0.6477 (ptp-110) REVERT: A 2561 GLN cc_start: 0.9030 (mt0) cc_final: 0.8677 (mt0) REVERT: A 2577 HIS cc_start: 0.8440 (t-90) cc_final: 0.8225 (t70) REVERT: A 2693 LYS cc_start: 0.8448 (tttt) cc_final: 0.7847 (ttpt) REVERT: A 2904 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7296 (pt0) REVERT: A 2908 LYS cc_start: 0.8396 (pttt) cc_final: 0.8057 (tmmt) REVERT: B 1433 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7857 (tmm) REVERT: B 1460 LYS cc_start: 0.7985 (tttt) cc_final: 0.7347 (ttpt) REVERT: B 1469 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7526 (p) REVERT: B 1546 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8229 (pp) REVERT: B 1571 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6851 (tpp80) REVERT: B 1650 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8221 (m-30) REVERT: B 1659 GLU cc_start: 0.8241 (tp30) cc_final: 0.7929 (tp30) REVERT: B 1671 GLU cc_start: 0.7787 (mp0) cc_final: 0.7105 (mp0) REVERT: B 1755 ARG cc_start: 0.7686 (mmt90) cc_final: 0.7398 (ppt90) REVERT: B 1776 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8389 (mmpt) REVERT: B 1883 MET cc_start: 0.9084 (mtp) cc_final: 0.8826 (mtm) REVERT: B 2051 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: B 2068 ARG cc_start: 0.8262 (mtt90) cc_final: 0.7804 (mtm110) REVERT: B 2176 ARG cc_start: 0.8040 (mpt-90) cc_final: 0.7638 (mpt180) REVERT: B 2247 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7511 (p0) REVERT: B 2276 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8303 (mt) REVERT: B 2277 LYS cc_start: 0.8276 (mppt) cc_final: 0.7680 (mtmt) REVERT: B 2278 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 2304 GLN cc_start: 0.7649 (pt0) cc_final: 0.6913 (mp10) REVERT: B 2317 ASN cc_start: 0.6788 (m110) cc_final: 0.6471 (m110) REVERT: B 2365 ARG cc_start: 0.7691 (ttp80) cc_final: 0.7318 (ttp80) REVERT: B 2368 GLN cc_start: 0.8123 (tp40) cc_final: 0.7813 (mm-40) REVERT: B 2487 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: B 2502 LYS cc_start: 0.8463 (mttt) cc_final: 0.7912 (tmtt) REVERT: B 2522 MET cc_start: 0.8307 (mmp) cc_final: 0.7983 (mmm) REVERT: B 2524 ARG cc_start: 0.6830 (ptp-170) cc_final: 0.6481 (ptp-110) REVERT: B 2561 GLN cc_start: 0.9022 (mt0) cc_final: 0.8667 (mt0) REVERT: B 2577 HIS cc_start: 0.8441 (t-90) cc_final: 0.8227 (t70) REVERT: B 2693 LYS cc_start: 0.8437 (tttt) cc_final: 0.7838 (ttpt) REVERT: B 2904 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7289 (pt0) REVERT: B 2908 LYS cc_start: 0.8398 (pttt) cc_final: 0.8063 (tmmt) outliers start: 74 outliers final: 30 residues processed: 354 average time/residue: 0.8122 time to fit residues: 320.7765 Evaluate side-chains 334 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1650 ASP Chi-restraints excluded: chain A residue 1658 GLN Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1935 GLN Chi-restraints excluded: chain A residue 2051 GLU Chi-restraints excluded: chain A residue 2103 SER Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2160 VAL Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2265 ASP Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2487 GLN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2830 GLU Chi-restraints excluded: chain B residue 1433 MET Chi-restraints excluded: chain B residue 1442 VAL Chi-restraints excluded: chain B residue 1469 THR Chi-restraints excluded: chain B residue 1546 ILE Chi-restraints excluded: chain B residue 1650 ASP Chi-restraints excluded: chain B residue 1658 GLN Chi-restraints excluded: chain B residue 1719 SER Chi-restraints excluded: chain B residue 1935 GLN Chi-restraints excluded: chain B residue 2051 GLU Chi-restraints excluded: chain B residue 2103 SER Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2160 VAL Chi-restraints excluded: chain B residue 2240 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2265 ASP Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2384 SER Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2487 GLN Chi-restraints excluded: chain B residue 2733 ASP Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2813 THR Chi-restraints excluded: chain B residue 2830 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 208 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 182 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 chunk 215 optimal weight: 0.0070 chunk 128 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2567 ASN B2567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.111522 restraints weight = 25888.951| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.70 r_work: 0.3011 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22758 Z= 0.114 Angle : 0.468 8.285 30804 Z= 0.241 Chirality : 0.037 0.141 3490 Planarity : 0.003 0.041 3958 Dihedral : 6.382 75.904 3126 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.97 % Allowed : 14.19 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.16), residues: 2792 helix: 1.85 (0.12), residues: 1980 sheet: -0.04 (0.66), residues: 76 loop : -2.05 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B2515 TYR 0.011 0.001 TYR B1629 PHE 0.015 0.001 PHE A2015 TRP 0.014 0.001 TRP A2118 HIS 0.004 0.001 HIS A1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (22758) covalent geometry : angle 0.46789 / 0.24 (30804) hydrogen bonds : bond 0.04101 / 2.73 ( 1412) hydrogen bonds : angle 3.51315 / 2.53 ( 4200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 310 time to evaluate : 0.561 Fit side-chains REVERT: A 1433 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7942 (tmm) REVERT: A 1450 ASP cc_start: 0.6043 (OUTLIER) cc_final: 0.5666 (t0) REVERT: A 1460 LYS cc_start: 0.7972 (tttt) cc_final: 0.7335 (ttpt) REVERT: A 1469 THR cc_start: 0.7744 (OUTLIER) cc_final: 0.7509 (p) REVERT: A 1547 ARG cc_start: 0.8181 (mtp-110) cc_final: 0.7289 (mtm180) REVERT: A 1650 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8262 (m-30) REVERT: A 1659 GLU cc_start: 0.8206 (tp30) cc_final: 0.7852 (tp30) REVERT: A 1671 GLU cc_start: 0.7766 (mp0) cc_final: 0.7082 (mp0) REVERT: A 1755 ARG cc_start: 0.7671 (mmt90) cc_final: 0.7397 (ppt90) REVERT: A 1776 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8380 (mmpt) REVERT: A 1819 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 1883 MET cc_start: 0.9097 (mtp) cc_final: 0.8815 (mtm) REVERT: A 2051 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: A 2068 ARG cc_start: 0.8220 (mtt90) cc_final: 0.7775 (mtm110) REVERT: A 2176 ARG cc_start: 0.8119 (mpt-90) cc_final: 0.7729 (mpt180) REVERT: A 2247 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7561 (p0) REVERT: A 2276 LEU cc_start: 0.8511 (mp) cc_final: 0.8298 (mt) REVERT: A 2277 LYS cc_start: 0.8303 (mppt) cc_final: 0.7689 (mtmt) REVERT: A 2278 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 2304 GLN cc_start: 0.7650 (pt0) cc_final: 0.6926 (mp10) REVERT: A 2317 ASN cc_start: 0.6846 (m110) cc_final: 0.6542 (m110) REVERT: A 2358 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6384 (mp) REVERT: A 2364 ARG cc_start: 0.6576 (mtm110) cc_final: 0.6227 (mtm-85) REVERT: A 2365 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7360 (ttp80) REVERT: A 2368 GLN cc_start: 0.8126 (tp40) cc_final: 0.7816 (mm-40) REVERT: A 2487 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: A 2502 LYS cc_start: 0.8393 (mttt) cc_final: 0.7808 (tmtt) REVERT: A 2522 MET cc_start: 0.8294 (mmp) cc_final: 0.7974 (mmm) REVERT: A 2524 ARG cc_start: 0.6772 (ptp-170) cc_final: 0.6385 (ptp-110) REVERT: A 2561 GLN cc_start: 0.8951 (mt0) cc_final: 0.8613 (mt0) REVERT: A 2577 HIS cc_start: 0.8480 (t-90) cc_final: 0.8262 (t70) REVERT: A 2693 LYS cc_start: 0.8434 (tttt) cc_final: 0.7880 (ttpt) REVERT: A 2904 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7361 (pt0) REVERT: A 2908 LYS cc_start: 0.8401 (pttt) cc_final: 0.8064 (tmmt) REVERT: B 1433 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7920 (tmm) REVERT: B 1450 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5664 (t0) REVERT: B 1460 LYS cc_start: 0.7979 (tttt) cc_final: 0.7342 (ttpt) REVERT: B 1469 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7509 (p) REVERT: B 1547 ARG cc_start: 0.8203 (mtp-110) cc_final: 0.7308 (mtm180) REVERT: B 1650 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: B 1659 GLU cc_start: 0.8212 (tp30) cc_final: 0.7857 (tp30) REVERT: B 1671 GLU cc_start: 0.7774 (mp0) cc_final: 0.7090 (mp0) REVERT: B 1755 ARG cc_start: 0.7687 (mmt90) cc_final: 0.7400 (ppt90) REVERT: B 1776 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8386 (mmpt) REVERT: B 1819 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 1883 MET cc_start: 0.9097 (mtp) cc_final: 0.8817 (mtm) REVERT: B 2051 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: B 2068 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7762 (mtm110) REVERT: B 2176 ARG cc_start: 0.8102 (mpt-90) cc_final: 0.7714 (mpt180) REVERT: B 2247 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7564 (p0) REVERT: B 2276 LEU cc_start: 0.8515 (mp) cc_final: 0.8304 (mt) REVERT: B 2277 LYS cc_start: 0.8308 (mppt) cc_final: 0.7697 (mtmt) REVERT: B 2278 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7913 (mm-30) REVERT: B 2304 GLN cc_start: 0.7638 (pt0) cc_final: 0.6924 (mp10) REVERT: B 2317 ASN cc_start: 0.6843 (m110) cc_final: 0.6539 (m110) REVERT: B 2358 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6386 (mp) REVERT: B 2364 ARG cc_start: 0.6577 (mtm110) cc_final: 0.6230 (mtm-85) REVERT: B 2365 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7343 (ttp80) REVERT: B 2368 GLN cc_start: 0.8110 (tp40) cc_final: 0.7801 (mm-40) REVERT: B 2487 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: B 2502 LYS cc_start: 0.8409 (mttt) cc_final: 0.7809 (tmtt) REVERT: B 2522 MET cc_start: 0.8297 (mmp) cc_final: 0.7982 (mmm) REVERT: B 2524 ARG cc_start: 0.6773 (ptp-170) cc_final: 0.6385 (ptp-110) REVERT: B 2561 GLN cc_start: 0.8951 (mt0) cc_final: 0.8613 (mt0) REVERT: B 2577 HIS cc_start: 0.8471 (t-90) cc_final: 0.8249 (t70) REVERT: B 2693 LYS cc_start: 0.8428 (tttt) cc_final: 0.7872 (ttpt) REVERT: B 2904 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7361 (pt0) REVERT: B 2908 LYS cc_start: 0.8403 (pttt) cc_final: 0.8067 (tmmt) outliers start: 72 outliers final: 26 residues processed: 354 average time/residue: 0.8302 time to fit residues: 326.1567 Evaluate side-chains 335 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1650 ASP Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1868 ASP Chi-restraints excluded: chain A residue 2051 GLU Chi-restraints excluded: chain A residue 2160 VAL Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2265 ASP Chi-restraints excluded: chain A residue 2358 LEU Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2487 GLN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2830 GLU Chi-restraints excluded: chain B residue 1433 MET Chi-restraints excluded: chain B residue 1442 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1469 THR Chi-restraints excluded: chain B residue 1650 ASP Chi-restraints excluded: chain B residue 1719 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1868 ASP Chi-restraints excluded: chain B residue 2051 GLU Chi-restraints excluded: chain B residue 2160 VAL Chi-restraints excluded: chain B residue 2191 LEU Chi-restraints excluded: chain B residue 2240 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2265 ASP Chi-restraints excluded: chain B residue 2358 LEU Chi-restraints excluded: chain B residue 2384 SER Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2487 GLN Chi-restraints excluded: chain B residue 2733 ASP Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2830 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 184 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 231 optimal weight: 0.0270 chunk 203 optimal weight: 0.5980 chunk 208 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2552 ASN A2567 ASN B2567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.110434 restraints weight = 25673.182| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.68 r_work: 0.2996 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22758 Z= 0.120 Angle : 0.476 7.957 30804 Z= 0.244 Chirality : 0.037 0.144 3490 Planarity : 0.003 0.041 3958 Dihedral : 5.986 71.217 3112 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.76 % Allowed : 14.48 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.16), residues: 2792 helix: 1.95 (0.12), residues: 1984 sheet: 0.06 (0.67), residues: 76 loop : -1.98 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2515 TYR 0.011 0.001 TYR B1629 PHE 0.015 0.001 PHE B2015 TRP 0.012 0.001 TRP B2118 HIS 0.004 0.001 HIS A1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (22758) covalent geometry : angle 0.47589 / 0.24 (30804) hydrogen bonds : bond 0.04135 / 2.75 ( 1412) hydrogen bonds : angle 3.49159 / 2.51 ( 4200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 302 time to evaluate : 0.933 Fit side-chains REVERT: A 1433 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7828 (tmm) REVERT: A 1450 ASP cc_start: 0.6023 (OUTLIER) cc_final: 0.5679 (t0) REVERT: A 1469 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7478 (p) REVERT: A 1547 ARG cc_start: 0.8280 (mtp-110) cc_final: 0.7405 (mtm180) REVERT: A 1650 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: A 1659 GLU cc_start: 0.8191 (tp30) cc_final: 0.7862 (tp30) REVERT: A 1671 GLU cc_start: 0.7786 (mp0) cc_final: 0.7092 (mp0) REVERT: A 1755 ARG cc_start: 0.7690 (mmt90) cc_final: 0.7395 (ppt90) REVERT: A 1776 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8369 (mmpt) REVERT: A 1819 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 1883 MET cc_start: 0.9086 (mtp) cc_final: 0.8799 (mtm) REVERT: A 2051 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: A 2068 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7716 (mtm110) REVERT: A 2176 ARG cc_start: 0.8135 (mpt-90) cc_final: 0.7736 (mpt180) REVERT: A 2247 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7501 (p0) REVERT: A 2276 LEU cc_start: 0.8491 (mp) cc_final: 0.8282 (mt) REVERT: A 2277 LYS cc_start: 0.8288 (mppt) cc_final: 0.7668 (mtmt) REVERT: A 2278 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7878 (mm-30) REVERT: A 2304 GLN cc_start: 0.7651 (pt0) cc_final: 0.6893 (mp10) REVERT: A 2317 ASN cc_start: 0.6830 (m110) cc_final: 0.6518 (m110) REVERT: A 2358 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6411 (mp) REVERT: A 2364 ARG cc_start: 0.6519 (mtm110) cc_final: 0.6249 (mtm110) REVERT: A 2365 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7349 (ttp80) REVERT: A 2368 GLN cc_start: 0.8027 (tp40) cc_final: 0.7716 (mm-40) REVERT: A 2487 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: A 2502 LYS cc_start: 0.8374 (mttt) cc_final: 0.7785 (tmtt) REVERT: A 2522 MET cc_start: 0.8286 (mmp) cc_final: 0.8012 (mmm) REVERT: A 2524 ARG cc_start: 0.6737 (ptp-170) cc_final: 0.6334 (ptp-110) REVERT: A 2561 GLN cc_start: 0.8993 (mt0) cc_final: 0.8662 (mt0) REVERT: A 2577 HIS cc_start: 0.8413 (t-90) cc_final: 0.8185 (t70) REVERT: A 2693 LYS cc_start: 0.8413 (tttt) cc_final: 0.7845 (ttpt) REVERT: A 2908 LYS cc_start: 0.8415 (pttt) cc_final: 0.8034 (tmmt) REVERT: B 1450 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5678 (t0) REVERT: B 1469 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7478 (p) REVERT: B 1547 ARG cc_start: 0.8291 (mtp-110) cc_final: 0.7410 (mtm180) REVERT: B 1650 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8265 (m-30) REVERT: B 1659 GLU cc_start: 0.8187 (tp30) cc_final: 0.7858 (tp30) REVERT: B 1671 GLU cc_start: 0.7790 (mp0) cc_final: 0.7094 (mp0) REVERT: B 1755 ARG cc_start: 0.7704 (mmt90) cc_final: 0.7397 (ppt90) REVERT: B 1776 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8372 (mmpt) REVERT: B 1819 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7570 (mt-10) REVERT: B 1883 MET cc_start: 0.9088 (mtp) cc_final: 0.8802 (mtm) REVERT: B 2051 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: B 2068 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7709 (mtm110) REVERT: B 2176 ARG cc_start: 0.8127 (mpt-90) cc_final: 0.7726 (mpt180) REVERT: B 2247 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7498 (p0) REVERT: B 2276 LEU cc_start: 0.8496 (mp) cc_final: 0.8286 (mt) REVERT: B 2277 LYS cc_start: 0.8293 (mppt) cc_final: 0.7675 (mtmt) REVERT: B 2278 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7894 (mm-30) REVERT: B 2304 GLN cc_start: 0.7648 (pt0) cc_final: 0.6894 (mp10) REVERT: B 2317 ASN cc_start: 0.6829 (m110) cc_final: 0.6517 (m110) REVERT: B 2358 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6414 (mp) REVERT: B 2364 ARG cc_start: 0.6519 (mtm110) cc_final: 0.6250 (mtm110) REVERT: B 2365 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7334 (ttp80) REVERT: B 2368 GLN cc_start: 0.8018 (tp40) cc_final: 0.7708 (mm-40) REVERT: B 2487 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: B 2502 LYS cc_start: 0.8379 (mttt) cc_final: 0.7793 (tmtt) REVERT: B 2522 MET cc_start: 0.8287 (mmp) cc_final: 0.8018 (mmm) REVERT: B 2524 ARG cc_start: 0.6741 (ptp-170) cc_final: 0.6337 (ptp-110) REVERT: B 2561 GLN cc_start: 0.8990 (mt0) cc_final: 0.8658 (mt0) REVERT: B 2577 HIS cc_start: 0.8407 (t-90) cc_final: 0.8177 (t70) REVERT: B 2693 LYS cc_start: 0.8403 (tttt) cc_final: 0.7831 (ttpt) REVERT: B 2908 LYS cc_start: 0.8419 (pttt) cc_final: 0.8042 (tmmt) outliers start: 67 outliers final: 36 residues processed: 342 average time/residue: 0.8579 time to fit residues: 325.6050 Evaluate side-chains 343 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1649 GLU Chi-restraints excluded: chain A residue 1650 ASP Chi-restraints excluded: chain A residue 1658 GLN Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1936 ASP Chi-restraints excluded: chain A residue 2051 GLU Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2160 VAL Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2265 ASP Chi-restraints excluded: chain A residue 2358 LEU Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2487 GLN Chi-restraints excluded: chain A residue 2501 ASN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2830 GLU Chi-restraints excluded: chain B residue 1442 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1469 THR Chi-restraints excluded: chain B residue 1649 GLU Chi-restraints excluded: chain B residue 1650 ASP Chi-restraints excluded: chain B residue 1658 GLN Chi-restraints excluded: chain B residue 1719 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1936 ASP Chi-restraints excluded: chain B residue 2051 GLU Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2160 VAL Chi-restraints excluded: chain B residue 2191 LEU Chi-restraints excluded: chain B residue 2240 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2265 ASP Chi-restraints excluded: chain B residue 2358 LEU Chi-restraints excluded: chain B residue 2384 SER Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2487 GLN Chi-restraints excluded: chain B residue 2501 ASN Chi-restraints excluded: chain B residue 2733 ASP Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2830 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 211 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 146 optimal weight: 0.9990 chunk 223 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 255 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1612 ASN A2567 ASN B2552 ASN B2567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111616 restraints weight = 25728.128| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.69 r_work: 0.3003 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22758 Z= 0.104 Angle : 0.455 7.626 30804 Z= 0.235 Chirality : 0.037 0.147 3490 Planarity : 0.003 0.040 3958 Dihedral : 5.792 67.176 3109 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.93 % Allowed : 14.65 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.16), residues: 2792 helix: 2.11 (0.12), residues: 1984 sheet: 0.19 (0.68), residues: 76 loop : -1.93 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B2515 TYR 0.010 0.001 TYR A1629 PHE 0.014 0.001 PHE B2015 TRP 0.012 0.001 TRP B2118 HIS 0.004 0.001 HIS A1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (22758) covalent geometry : angle 0.45547 / 0.23 (30804) hydrogen bonds : bond 0.03831 / 2.55 ( 1412) hydrogen bonds : angle 3.42391 / 2.47 ( 4200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 311 time to evaluate : 0.924 Fit side-chains REVERT: A 1450 ASP cc_start: 0.5988 (OUTLIER) cc_final: 0.5663 (t0) REVERT: A 1469 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7457 (p) REVERT: A 1547 ARG cc_start: 0.8234 (mtp-110) cc_final: 0.7336 (mtm180) REVERT: A 1650 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8237 (m-30) REVERT: A 1659 GLU cc_start: 0.8161 (tp30) cc_final: 0.7812 (tp30) REVERT: A 1671 GLU cc_start: 0.7784 (mp0) cc_final: 0.7068 (mp0) REVERT: A 1755 ARG cc_start: 0.7648 (mmt90) cc_final: 0.7375 (ppt90) REVERT: A 1776 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8429 (mmpt) REVERT: A 1819 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 1883 MET cc_start: 0.9083 (mtp) cc_final: 0.8788 (mtm) REVERT: A 2051 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: A 2068 ARG cc_start: 0.8087 (mtt90) cc_final: 0.7640 (mtm110) REVERT: A 2176 ARG cc_start: 0.8014 (mpt-90) cc_final: 0.7615 (mpt180) REVERT: A 2247 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7498 (p0) REVERT: A 2276 LEU cc_start: 0.8442 (mp) cc_final: 0.8224 (mt) REVERT: A 2277 LYS cc_start: 0.8299 (mppt) cc_final: 0.7736 (mtmt) REVERT: A 2278 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 2304 GLN cc_start: 0.7604 (pt0) cc_final: 0.6845 (mp-120) REVERT: A 2317 ASN cc_start: 0.6796 (m110) cc_final: 0.6491 (m110) REVERT: A 2364 ARG cc_start: 0.6465 (mtm110) cc_final: 0.6181 (mtm110) REVERT: A 2365 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7273 (ttp80) REVERT: A 2368 GLN cc_start: 0.8014 (tp40) cc_final: 0.7713 (mm-40) REVERT: A 2487 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: A 2502 LYS cc_start: 0.8359 (mttt) cc_final: 0.7781 (tmtt) REVERT: A 2522 MET cc_start: 0.8159 (mmp) cc_final: 0.7908 (mmm) REVERT: A 2524 ARG cc_start: 0.6710 (ptp-170) cc_final: 0.6307 (ptp-110) REVERT: A 2561 GLN cc_start: 0.8936 (mt0) cc_final: 0.8609 (mt0) REVERT: A 2577 HIS cc_start: 0.8385 (t-90) cc_final: 0.8159 (t70) REVERT: A 2693 LYS cc_start: 0.8366 (tttt) cc_final: 0.7795 (ttpt) REVERT: A 2908 LYS cc_start: 0.8354 (pttt) cc_final: 0.7983 (tmmt) REVERT: B 1433 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7822 (tmm) REVERT: B 1450 ASP cc_start: 0.5993 (OUTLIER) cc_final: 0.5662 (t0) REVERT: B 1469 THR cc_start: 0.7694 (OUTLIER) cc_final: 0.7452 (p) REVERT: B 1547 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.7338 (mtm180) REVERT: B 1659 GLU cc_start: 0.8160 (tp30) cc_final: 0.7810 (tp30) REVERT: B 1671 GLU cc_start: 0.7788 (mp0) cc_final: 0.7069 (mp0) REVERT: B 1755 ARG cc_start: 0.7662 (mmt90) cc_final: 0.7376 (ppt90) REVERT: B 1776 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8433 (mmpt) REVERT: B 1819 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 1883 MET cc_start: 0.9081 (mtp) cc_final: 0.8788 (mtm) REVERT: B 2051 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: B 2068 ARG cc_start: 0.8082 (mtt90) cc_final: 0.7633 (mtm110) REVERT: B 2176 ARG cc_start: 0.8003 (mpt-90) cc_final: 0.7604 (mpt180) REVERT: B 2247 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7491 (p0) REVERT: B 2276 LEU cc_start: 0.8445 (mp) cc_final: 0.8228 (mt) REVERT: B 2277 LYS cc_start: 0.8298 (mppt) cc_final: 0.7740 (mtmt) REVERT: B 2278 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7851 (mm-30) REVERT: B 2304 GLN cc_start: 0.7604 (pt0) cc_final: 0.6849 (mp-120) REVERT: B 2317 ASN cc_start: 0.6800 (m110) cc_final: 0.6491 (m110) REVERT: B 2364 ARG cc_start: 0.6470 (mtm110) cc_final: 0.6185 (mtm110) REVERT: B 2365 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7261 (ttp80) REVERT: B 2368 GLN cc_start: 0.8008 (tp40) cc_final: 0.7708 (mm-40) REVERT: B 2487 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: B 2502 LYS cc_start: 0.8353 (mttt) cc_final: 0.7773 (tmtt) REVERT: B 2522 MET cc_start: 0.8164 (mmp) cc_final: 0.7919 (mmm) REVERT: B 2524 ARG cc_start: 0.6712 (ptp-170) cc_final: 0.6314 (ptp-110) REVERT: B 2561 GLN cc_start: 0.8941 (mt0) cc_final: 0.8612 (mt0) REVERT: B 2577 HIS cc_start: 0.8374 (t-90) cc_final: 0.8144 (t70) REVERT: B 2693 LYS cc_start: 0.8370 (tttt) cc_final: 0.7799 (ttpt) REVERT: B 2908 LYS cc_start: 0.8358 (pttt) cc_final: 0.7991 (tmmt) outliers start: 71 outliers final: 36 residues processed: 355 average time/residue: 0.8102 time to fit residues: 320.8402 Evaluate side-chains 336 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1650 ASP Chi-restraints excluded: chain A residue 1658 GLN Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1868 ASP Chi-restraints excluded: chain A residue 2051 GLU Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2160 VAL Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2265 ASP Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2487 GLN Chi-restraints excluded: chain A residue 2501 ASN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2830 GLU Chi-restraints excluded: chain B residue 1433 MET Chi-restraints excluded: chain B residue 1442 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1469 THR Chi-restraints excluded: chain B residue 1658 GLN Chi-restraints excluded: chain B residue 1719 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1868 ASP Chi-restraints excluded: chain B residue 2051 GLU Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2160 VAL Chi-restraints excluded: chain B residue 2191 LEU Chi-restraints excluded: chain B residue 2240 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2265 ASP Chi-restraints excluded: chain B residue 2384 SER Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2487 GLN Chi-restraints excluded: chain B residue 2501 ASN Chi-restraints excluded: chain B residue 2733 ASP Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2813 THR Chi-restraints excluded: chain B residue 2830 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 143 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 255 optimal weight: 0.0570 chunk 129 optimal weight: 0.8980 chunk 80 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 268 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2567 ASN A2702 ASN B2567 ASN B2702 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111674 restraints weight = 25731.699| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.72 r_work: 0.3005 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22758 Z= 0.107 Angle : 0.458 7.288 30804 Z= 0.235 Chirality : 0.037 0.141 3490 Planarity : 0.003 0.040 3958 Dihedral : 5.599 67.369 3104 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.85 % Allowed : 14.98 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.16), residues: 2792 helix: 2.21 (0.12), residues: 1978 sheet: 0.17 (0.67), residues: 76 loop : -1.82 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2515 TYR 0.010 0.001 TYR A1629 PHE 0.015 0.001 PHE B2174 TRP 0.012 0.001 TRP A2118 HIS 0.004 0.001 HIS B1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (22758) covalent geometry : angle 0.45759 / 0.24 (30804) hydrogen bonds : bond 0.03808 / 2.53 ( 1412) hydrogen bonds : angle 3.38792 / 2.45 ( 4200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 308 time to evaluate : 0.864 Fit side-chains REVERT: A 1450 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5671 (t0) REVERT: A 1469 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7470 (p) REVERT: A 1507 LYS cc_start: 0.7999 (mttt) cc_final: 0.7571 (mtpt) REVERT: A 1547 ARG cc_start: 0.8239 (mtp-110) cc_final: 0.7337 (mtm180) REVERT: A 1659 GLU cc_start: 0.8162 (tp30) cc_final: 0.7839 (tp30) REVERT: A 1755 ARG cc_start: 0.7665 (mmt90) cc_final: 0.7378 (ppt90) REVERT: A 1776 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8456 (mmpt) REVERT: A 1819 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 1883 MET cc_start: 0.9083 (mtp) cc_final: 0.8792 (mtm) REVERT: A 2051 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: A 2068 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7632 (mtm110) REVERT: A 2176 ARG cc_start: 0.8005 (mpt-90) cc_final: 0.7608 (mpt180) REVERT: A 2247 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7403 (p0) REVERT: A 2276 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 2277 LYS cc_start: 0.8293 (mppt) cc_final: 0.7727 (mtmt) REVERT: A 2278 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7815 (mm-30) REVERT: A 2304 GLN cc_start: 0.7599 (pt0) cc_final: 0.6836 (mp-120) REVERT: A 2317 ASN cc_start: 0.6788 (m110) cc_final: 0.6473 (m110) REVERT: A 2368 GLN cc_start: 0.8013 (tp40) cc_final: 0.7702 (mm-40) REVERT: A 2502 LYS cc_start: 0.8406 (mttt) cc_final: 0.7799 (tmtt) REVERT: A 2522 MET cc_start: 0.8117 (mmp) cc_final: 0.7879 (mmm) REVERT: A 2524 ARG cc_start: 0.6709 (ptp-170) cc_final: 0.6295 (ptp-110) REVERT: A 2561 GLN cc_start: 0.8946 (mt0) cc_final: 0.8655 (mt0) REVERT: A 2577 HIS cc_start: 0.8382 (t-90) cc_final: 0.8179 (t70) REVERT: A 2693 LYS cc_start: 0.8360 (tttt) cc_final: 0.7791 (ttpt) REVERT: A 2752 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8614 (tt) REVERT: A 2908 LYS cc_start: 0.8366 (pttt) cc_final: 0.7989 (tmmt) REVERT: B 1433 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7816 (tmm) REVERT: B 1450 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5675 (t0) REVERT: B 1469 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7461 (p) REVERT: B 1507 LYS cc_start: 0.7996 (mttt) cc_final: 0.7566 (mtpt) REVERT: B 1547 ARG cc_start: 0.8255 (mtp-110) cc_final: 0.7341 (mtm180) REVERT: B 1659 GLU cc_start: 0.8164 (tp30) cc_final: 0.7839 (tp30) REVERT: B 1755 ARG cc_start: 0.7667 (mmt90) cc_final: 0.7378 (ppt90) REVERT: B 1776 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8462 (mmpt) REVERT: B 1819 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7446 (mt-10) REVERT: B 1883 MET cc_start: 0.9083 (mtp) cc_final: 0.8793 (mtm) REVERT: B 2051 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: B 2068 ARG cc_start: 0.8072 (mtt90) cc_final: 0.7620 (mtm110) REVERT: B 2176 ARG cc_start: 0.7984 (mpt-90) cc_final: 0.7586 (mpt180) REVERT: B 2247 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7400 (p0) REVERT: B 2276 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8193 (mt) REVERT: B 2277 LYS cc_start: 0.8304 (mppt) cc_final: 0.7741 (mtmt) REVERT: B 2278 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7854 (mm-30) REVERT: B 2304 GLN cc_start: 0.7601 (pt0) cc_final: 0.6847 (mp-120) REVERT: B 2317 ASN cc_start: 0.6790 (m110) cc_final: 0.6475 (m110) REVERT: B 2364 ARG cc_start: 0.6462 (mtm110) cc_final: 0.6261 (mtm110) REVERT: B 2368 GLN cc_start: 0.7990 (tp40) cc_final: 0.7677 (mm-40) REVERT: B 2502 LYS cc_start: 0.8401 (mttt) cc_final: 0.7799 (tmtt) REVERT: B 2522 MET cc_start: 0.8130 (mmp) cc_final: 0.7896 (mmm) REVERT: B 2524 ARG cc_start: 0.6721 (ptp-170) cc_final: 0.6309 (ptp-110) REVERT: B 2561 GLN cc_start: 0.8947 (mt0) cc_final: 0.8652 (mt0) REVERT: B 2577 HIS cc_start: 0.8379 (t-90) cc_final: 0.8173 (t70) REVERT: B 2693 LYS cc_start: 0.8363 (tttt) cc_final: 0.7792 (ttpt) REVERT: B 2752 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8611 (tt) REVERT: B 2908 LYS cc_start: 0.8368 (pttt) cc_final: 0.7991 (tmmt) outliers start: 69 outliers final: 32 residues processed: 348 average time/residue: 0.8042 time to fit residues: 312.4897 Evaluate side-chains 345 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1649 GLU Chi-restraints excluded: chain A residue 1658 GLN Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1868 ASP Chi-restraints excluded: chain A residue 2051 GLU Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2160 VAL Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2265 ASP Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2830 GLU Chi-restraints excluded: chain B residue 1433 MET Chi-restraints excluded: chain B residue 1442 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1469 THR Chi-restraints excluded: chain B residue 1649 GLU Chi-restraints excluded: chain B residue 1658 GLN Chi-restraints excluded: chain B residue 1719 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1868 ASP Chi-restraints excluded: chain B residue 2051 GLU Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2160 VAL Chi-restraints excluded: chain B residue 2191 LEU Chi-restraints excluded: chain B residue 2240 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2265 ASP Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2384 SER Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2733 ASP Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2813 THR Chi-restraints excluded: chain B residue 2830 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 196 optimal weight: 0.0010 chunk 225 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2567 ASN B1612 ASN B2567 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111728 restraints weight = 25608.978| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.72 r_work: 0.2993 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22758 Z= 0.111 Angle : 0.462 6.988 30804 Z= 0.239 Chirality : 0.037 0.140 3490 Planarity : 0.004 0.061 3958 Dihedral : 5.158 67.695 3096 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.43 % Allowed : 15.68 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.16), residues: 2792 helix: 2.25 (0.12), residues: 1978 sheet: 0.23 (0.67), residues: 76 loop : -1.75 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2515 TYR 0.011 0.001 TYR B1629 PHE 0.014 0.001 PHE B2015 TRP 0.011 0.001 TRP B2118 HIS 0.004 0.001 HIS B1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (22758) covalent geometry : angle 0.46182 / 0.24 (30804) hydrogen bonds : bond 0.03847 / 2.56 ( 1412) hydrogen bonds : angle 3.37569 / 2.44 ( 4200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 300 time to evaluate : 0.901 Fit side-chains REVERT: A 1433 MET cc_start: 0.8077 (ttt) cc_final: 0.7855 (tmm) REVERT: A 1450 ASP cc_start: 0.5908 (OUTLIER) cc_final: 0.5636 (t0) REVERT: A 1469 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7496 (p) REVERT: A 1507 LYS cc_start: 0.8010 (mttt) cc_final: 0.7581 (mtpt) REVERT: A 1547 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7347 (mtm180) REVERT: A 1659 GLU cc_start: 0.8183 (tp30) cc_final: 0.7889 (tp30) REVERT: A 1755 ARG cc_start: 0.7682 (mmt90) cc_final: 0.7457 (ppt90) REVERT: A 1776 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8465 (mmpt) REVERT: A 1819 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 1883 MET cc_start: 0.9097 (mtp) cc_final: 0.8807 (mtm) REVERT: A 1936 ASP cc_start: 0.7773 (p0) cc_final: 0.7491 (m-30) REVERT: A 2051 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: A 2068 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7619 (mtm110) REVERT: A 2176 ARG cc_start: 0.8039 (mpt-90) cc_final: 0.7648 (mpt180) REVERT: A 2247 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7433 (p0) REVERT: A 2276 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8215 (mt) REVERT: A 2277 LYS cc_start: 0.8305 (mppt) cc_final: 0.7773 (mtmt) REVERT: A 2278 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7878 (mm-30) REVERT: A 2304 GLN cc_start: 0.7609 (pt0) cc_final: 0.6862 (mp-120) REVERT: A 2317 ASN cc_start: 0.6813 (m110) cc_final: 0.6493 (m110) REVERT: A 2364 ARG cc_start: 0.6463 (mtm110) cc_final: 0.6224 (mtm-85) REVERT: A 2368 GLN cc_start: 0.8033 (tp40) cc_final: 0.7718 (mm-40) REVERT: A 2502 LYS cc_start: 0.8415 (mttt) cc_final: 0.7817 (tmtt) REVERT: A 2522 MET cc_start: 0.8147 (mmp) cc_final: 0.7923 (mmm) REVERT: A 2524 ARG cc_start: 0.6722 (ptp-170) cc_final: 0.6254 (ptp-110) REVERT: A 2561 GLN cc_start: 0.8949 (mt0) cc_final: 0.8479 (mt0) REVERT: A 2693 LYS cc_start: 0.8404 (tttt) cc_final: 0.7864 (ttpt) REVERT: A 2752 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 2908 LYS cc_start: 0.8401 (pttt) cc_final: 0.8027 (tmmt) REVERT: B 1433 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7828 (tmm) REVERT: B 1450 ASP cc_start: 0.5913 (OUTLIER) cc_final: 0.5639 (t0) REVERT: B 1469 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7499 (p) REVERT: B 1507 LYS cc_start: 0.8008 (mttt) cc_final: 0.7577 (mtpt) REVERT: B 1547 ARG cc_start: 0.8285 (mtp-110) cc_final: 0.7358 (mtm180) REVERT: B 1659 GLU cc_start: 0.8176 (tp30) cc_final: 0.7881 (tp30) REVERT: B 1755 ARG cc_start: 0.7681 (mmt90) cc_final: 0.7457 (ppt90) REVERT: B 1776 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8471 (mmpt) REVERT: B 1819 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7490 (mt-10) REVERT: B 1883 MET cc_start: 0.9104 (mtp) cc_final: 0.8814 (mtm) REVERT: B 1936 ASP cc_start: 0.7785 (p0) cc_final: 0.7496 (m-30) REVERT: B 2051 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: B 2068 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7612 (mtm110) REVERT: B 2176 ARG cc_start: 0.8024 (mpt-90) cc_final: 0.7633 (mpt180) REVERT: B 2247 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7419 (p0) REVERT: B 2276 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8231 (mt) REVERT: B 2277 LYS cc_start: 0.8312 (mppt) cc_final: 0.7783 (mtmt) REVERT: B 2278 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7888 (mm-30) REVERT: B 2304 GLN cc_start: 0.7609 (pt0) cc_final: 0.6869 (mp-120) REVERT: B 2317 ASN cc_start: 0.6817 (m110) cc_final: 0.6498 (m110) REVERT: B 2368 GLN cc_start: 0.8007 (tp40) cc_final: 0.7695 (mm-40) REVERT: B 2502 LYS cc_start: 0.8415 (mttt) cc_final: 0.7822 (tmtt) REVERT: B 2522 MET cc_start: 0.8152 (mmp) cc_final: 0.7931 (mmm) REVERT: B 2524 ARG cc_start: 0.6725 (ptp-170) cc_final: 0.6260 (ptp-110) REVERT: B 2561 GLN cc_start: 0.8948 (mt0) cc_final: 0.8477 (mt0) REVERT: B 2577 HIS cc_start: 0.8387 (t-90) cc_final: 0.8187 (t70) REVERT: B 2693 LYS cc_start: 0.8401 (tttt) cc_final: 0.7861 (ttpt) REVERT: B 2752 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8631 (tt) REVERT: B 2908 LYS cc_start: 0.8401 (pttt) cc_final: 0.8026 (tmmt) outliers start: 59 outliers final: 35 residues processed: 338 average time/residue: 0.7892 time to fit residues: 298.5626 Evaluate side-chains 343 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1649 GLU Chi-restraints excluded: chain A residue 1658 GLN Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1868 ASP Chi-restraints excluded: chain A residue 2051 GLU Chi-restraints excluded: chain A residue 2055 VAL Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2118 TRP Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2265 ASP Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2501 ASN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2830 GLU Chi-restraints excluded: chain B residue 1433 MET Chi-restraints excluded: chain B residue 1442 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1469 THR Chi-restraints excluded: chain B residue 1658 GLN Chi-restraints excluded: chain B residue 1719 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1868 ASP Chi-restraints excluded: chain B residue 2051 GLU Chi-restraints excluded: chain B residue 2055 VAL Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2118 TRP Chi-restraints excluded: chain B residue 2191 LEU Chi-restraints excluded: chain B residue 2240 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2265 ASP Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2384 SER Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2501 ASN Chi-restraints excluded: chain B residue 2733 ASP Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2813 THR Chi-restraints excluded: chain B residue 2830 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1560 ASN A2567 ASN B1560 ASN B2567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110708 restraints weight = 25631.810| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.71 r_work: 0.3001 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22758 Z= 0.125 Angle : 0.473 6.819 30804 Z= 0.245 Chirality : 0.038 0.140 3490 Planarity : 0.004 0.061 3958 Dihedral : 5.128 68.650 3094 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.23 % Allowed : 15.88 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.16), residues: 2792 helix: 2.24 (0.12), residues: 1978 sheet: 0.22 (0.67), residues: 76 loop : -1.74 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2515 TYR 0.011 0.001 TYR B1629 PHE 0.016 0.001 PHE A2015 TRP 0.012 0.001 TRP A2940 HIS 0.004 0.001 HIS B1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (22758) covalent geometry : angle 0.47292 / 0.24 (30804) hydrogen bonds : bond 0.04113 / 2.74 ( 1412) hydrogen bonds : angle 3.42107 / 2.47 ( 4200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 301 time to evaluate : 0.896 Fit side-chains REVERT: A 1450 ASP cc_start: 0.5911 (OUTLIER) cc_final: 0.5632 (t0) REVERT: A 1469 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7490 (p) REVERT: A 1507 LYS cc_start: 0.8010 (mttt) cc_final: 0.7603 (mtpt) REVERT: A 1547 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.7344 (mtm180) REVERT: A 1659 GLU cc_start: 0.8186 (tp30) cc_final: 0.7882 (tp30) REVERT: A 1717 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7739 (mp10) REVERT: A 1755 ARG cc_start: 0.7712 (mmt90) cc_final: 0.7491 (ppt90) REVERT: A 1776 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8436 (mmpt) REVERT: A 1883 MET cc_start: 0.9093 (mtp) cc_final: 0.8804 (mtm) REVERT: A 2051 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: A 2068 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7613 (mtm110) REVERT: A 2176 ARG cc_start: 0.8096 (mpt-90) cc_final: 0.7655 (mpt180) REVERT: A 2247 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7443 (p0) REVERT: A 2276 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8244 (mt) REVERT: A 2277 LYS cc_start: 0.8330 (mppt) cc_final: 0.7761 (mttt) REVERT: A 2278 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 2304 GLN cc_start: 0.7667 (pt0) cc_final: 0.6860 (mp10) REVERT: A 2317 ASN cc_start: 0.6804 (m110) cc_final: 0.6497 (m110) REVERT: A 2364 ARG cc_start: 0.6381 (mtm110) cc_final: 0.6125 (mtm-85) REVERT: A 2368 GLN cc_start: 0.8014 (tp40) cc_final: 0.7703 (mm-40) REVERT: A 2502 LYS cc_start: 0.8444 (mttt) cc_final: 0.7842 (tmtt) REVERT: A 2522 MET cc_start: 0.8145 (mmp) cc_final: 0.7915 (mmm) REVERT: A 2524 ARG cc_start: 0.6751 (ptp-170) cc_final: 0.6273 (ptp-110) REVERT: A 2561 GLN cc_start: 0.8955 (mt0) cc_final: 0.8483 (mt0) REVERT: A 2693 LYS cc_start: 0.8400 (tttt) cc_final: 0.7863 (ttpt) REVERT: A 2752 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 2771 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8740 (mptt) REVERT: A 2908 LYS cc_start: 0.8434 (pttt) cc_final: 0.8032 (tmmt) REVERT: B 1433 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7837 (tmm) REVERT: B 1450 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.5636 (t0) REVERT: B 1469 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7489 (p) REVERT: B 1507 LYS cc_start: 0.8009 (mttt) cc_final: 0.7598 (mtpt) REVERT: B 1547 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.7350 (mtm180) REVERT: B 1659 GLU cc_start: 0.8185 (tp30) cc_final: 0.7881 (tp30) REVERT: B 1717 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7742 (mp10) REVERT: B 1755 ARG cc_start: 0.7716 (mmt90) cc_final: 0.7489 (ppt90) REVERT: B 1776 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8439 (mmpt) REVERT: B 1883 MET cc_start: 0.9100 (mtp) cc_final: 0.8811 (mtm) REVERT: B 2051 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: B 2068 ARG cc_start: 0.8071 (mtt90) cc_final: 0.7611 (mtm110) REVERT: B 2176 ARG cc_start: 0.8079 (mpt-90) cc_final: 0.7636 (mpt180) REVERT: B 2247 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7474 (p0) REVERT: B 2276 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8255 (mt) REVERT: B 2277 LYS cc_start: 0.8338 (mppt) cc_final: 0.7769 (mttt) REVERT: B 2278 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 2304 GLN cc_start: 0.7667 (pt0) cc_final: 0.6864 (mp10) REVERT: B 2317 ASN cc_start: 0.6803 (m110) cc_final: 0.6497 (m110) REVERT: B 2364 ARG cc_start: 0.6498 (mtm110) cc_final: 0.6142 (mtm-85) REVERT: B 2368 GLN cc_start: 0.7996 (tp40) cc_final: 0.7683 (mm-40) REVERT: B 2502 LYS cc_start: 0.8425 (mttt) cc_final: 0.7843 (tmtt) REVERT: B 2522 MET cc_start: 0.8149 (mmp) cc_final: 0.7920 (mmm) REVERT: B 2524 ARG cc_start: 0.6751 (ptp-170) cc_final: 0.6274 (ptp-110) REVERT: B 2561 GLN cc_start: 0.8950 (mt0) cc_final: 0.8477 (mt0) REVERT: B 2577 HIS cc_start: 0.8381 (t-90) cc_final: 0.8181 (t70) REVERT: B 2693 LYS cc_start: 0.8392 (tttt) cc_final: 0.7858 (ttpt) REVERT: B 2752 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8669 (tt) REVERT: B 2771 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8740 (mptt) REVERT: B 2908 LYS cc_start: 0.8432 (pttt) cc_final: 0.8027 (tmmt) outliers start: 54 outliers final: 32 residues processed: 335 average time/residue: 0.8084 time to fit residues: 301.7359 Evaluate side-chains 339 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 294 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1658 GLN Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1868 ASP Chi-restraints excluded: chain A residue 2051 GLU Chi-restraints excluded: chain A residue 2055 VAL Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2265 ASP Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2501 ASN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2830 GLU Chi-restraints excluded: chain B residue 1433 MET Chi-restraints excluded: chain B residue 1442 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1469 THR Chi-restraints excluded: chain B residue 1658 GLN Chi-restraints excluded: chain B residue 1719 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1868 ASP Chi-restraints excluded: chain B residue 2051 GLU Chi-restraints excluded: chain B residue 2055 VAL Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2191 LEU Chi-restraints excluded: chain B residue 2240 SER Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2265 ASP Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2384 SER Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2501 ASN Chi-restraints excluded: chain B residue 2733 ASP Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2813 THR Chi-restraints excluded: chain B residue 2830 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 261 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 229 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2567 ASN B2567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111150 restraints weight = 25822.094| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.71 r_work: 0.2975 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22758 Z= 0.138 Angle : 0.487 7.012 30804 Z= 0.253 Chirality : 0.038 0.130 3490 Planarity : 0.004 0.058 3958 Dihedral : 5.152 69.358 3094 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.39 % Allowed : 15.92 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.16), residues: 2792 helix: 2.17 (0.12), residues: 1984 sheet: 0.17 (0.67), residues: 76 loop : -1.73 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2515 TYR 0.010 0.001 TYR A1629 PHE 0.018 0.001 PHE A2015 TRP 0.016 0.001 TRP B2118 HIS 0.005 0.001 HIS A1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (22758) covalent geometry : angle 0.48744 / 0.25 (30804) hydrogen bonds : bond 0.04348 / 2.89 ( 1412) hydrogen bonds : angle 3.47760 / 2.51 ( 4200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 0.916 Fit side-chains REVERT: A 1450 ASP cc_start: 0.5937 (OUTLIER) cc_final: 0.5643 (t0) REVERT: A 1469 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7536 (p) REVERT: A 1507 LYS cc_start: 0.8012 (mttt) cc_final: 0.7652 (mtpt) REVERT: A 1547 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.7222 (mtm180) REVERT: A 1659 GLU cc_start: 0.8189 (tp30) cc_final: 0.7877 (tp30) REVERT: A 1717 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7764 (mp10) REVERT: A 1755 ARG cc_start: 0.7730 (mmt90) cc_final: 0.7498 (ppt90) REVERT: A 1776 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8420 (mmpt) REVERT: A 1883 MET cc_start: 0.9094 (mtp) cc_final: 0.8807 (mtm) REVERT: A 2051 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 2068 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7632 (mtm110) REVERT: A 2176 ARG cc_start: 0.8179 (mpt-90) cc_final: 0.7715 (mpt180) REVERT: A 2276 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8227 (mt) REVERT: A 2277 LYS cc_start: 0.8318 (mppt) cc_final: 0.7727 (mttt) REVERT: A 2278 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 2304 GLN cc_start: 0.7688 (pt0) cc_final: 0.6877 (mp10) REVERT: A 2317 ASN cc_start: 0.6770 (m110) cc_final: 0.6460 (m110) REVERT: A 2364 ARG cc_start: 0.6401 (mtm110) cc_final: 0.6133 (mtm-85) REVERT: A 2368 GLN cc_start: 0.7997 (tp40) cc_final: 0.7691 (mm-40) REVERT: A 2502 LYS cc_start: 0.8449 (mttt) cc_final: 0.7828 (tmtt) REVERT: A 2522 MET cc_start: 0.8130 (mmp) cc_final: 0.7881 (mmm) REVERT: A 2524 ARG cc_start: 0.6769 (ptp-170) cc_final: 0.6276 (ptp-110) REVERT: A 2561 GLN cc_start: 0.8959 (mt0) cc_final: 0.8485 (mt0) REVERT: A 2693 LYS cc_start: 0.8386 (tttt) cc_final: 0.7832 (ttpt) REVERT: A 2752 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8715 (tt) REVERT: A 2771 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8732 (mptt) REVERT: A 2908 LYS cc_start: 0.8430 (pttt) cc_final: 0.8004 (tmmt) REVERT: B 1433 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7815 (tmm) REVERT: B 1450 ASP cc_start: 0.5941 (OUTLIER) cc_final: 0.5644 (t0) REVERT: B 1469 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7526 (p) REVERT: B 1507 LYS cc_start: 0.8011 (mttt) cc_final: 0.7648 (mtpt) REVERT: B 1547 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.7226 (mtm180) REVERT: B 1659 GLU cc_start: 0.8192 (tp30) cc_final: 0.7880 (tp30) REVERT: B 1717 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7766 (mp10) REVERT: B 1755 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7498 (ppt90) REVERT: B 1776 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8426 (mmpt) REVERT: B 1883 MET cc_start: 0.9096 (mtp) cc_final: 0.8811 (mtm) REVERT: B 2051 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: B 2068 ARG cc_start: 0.8083 (mtt90) cc_final: 0.7622 (mtm110) REVERT: B 2176 ARG cc_start: 0.8165 (mpt-90) cc_final: 0.7698 (mpt180) REVERT: B 2247 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7533 (p0) REVERT: B 2276 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8232 (mt) REVERT: B 2277 LYS cc_start: 0.8312 (mppt) cc_final: 0.7727 (mttt) REVERT: B 2278 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 2304 GLN cc_start: 0.7680 (pt0) cc_final: 0.6868 (mp10) REVERT: B 2317 ASN cc_start: 0.6781 (m110) cc_final: 0.6473 (m110) REVERT: B 2364 ARG cc_start: 0.6318 (mtm110) cc_final: 0.6094 (mtm-85) REVERT: B 2368 GLN cc_start: 0.7985 (tp40) cc_final: 0.7675 (mm-40) REVERT: B 2502 LYS cc_start: 0.8450 (mttt) cc_final: 0.7832 (tmtt) REVERT: B 2522 MET cc_start: 0.8133 (mmp) cc_final: 0.7887 (mmm) REVERT: B 2524 ARG cc_start: 0.6768 (ptp-170) cc_final: 0.6277 (ptp-110) REVERT: B 2561 GLN cc_start: 0.8957 (mt0) cc_final: 0.8484 (mt0) REVERT: B 2693 LYS cc_start: 0.8379 (tttt) cc_final: 0.7827 (ttpt) REVERT: B 2752 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8707 (tt) REVERT: B 2771 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8732 (mptt) REVERT: B 2908 LYS cc_start: 0.8428 (pttt) cc_final: 0.8004 (tmmt) outliers start: 58 outliers final: 36 residues processed: 332 average time/residue: 0.8142 time to fit residues: 301.2569 Evaluate side-chains 331 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1658 GLN Chi-restraints excluded: chain A residue 1719 SER Chi-restraints excluded: chain A residue 1779 THR Chi-restraints excluded: chain A residue 1868 ASP Chi-restraints excluded: chain A residue 1935 GLN Chi-restraints excluded: chain A residue 2051 GLU Chi-restraints excluded: chain A residue 2055 VAL Chi-restraints excluded: chain A residue 2096 ILE Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2240 SER Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2265 ASP Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain A residue 2501 ASN Chi-restraints excluded: chain A residue 2733 ASP Chi-restraints excluded: chain A residue 2752 LEU Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2830 GLU Chi-restraints excluded: chain B residue 1433 MET Chi-restraints excluded: chain B residue 1442 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1469 THR Chi-restraints excluded: chain B residue 1658 GLN Chi-restraints excluded: chain B residue 1719 SER Chi-restraints excluded: chain B residue 1779 THR Chi-restraints excluded: chain B residue 1868 ASP Chi-restraints excluded: chain B residue 1935 GLN Chi-restraints excluded: chain B residue 2051 GLU Chi-restraints excluded: chain B residue 2055 VAL Chi-restraints excluded: chain B residue 2096 ILE Chi-restraints excluded: chain B residue 2191 LEU Chi-restraints excluded: chain B residue 2240 SER Chi-restraints excluded: chain B residue 2243 LEU Chi-restraints excluded: chain B residue 2247 ASP Chi-restraints excluded: chain B residue 2265 ASP Chi-restraints excluded: chain B residue 2276 LEU Chi-restraints excluded: chain B residue 2384 SER Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2501 ASN Chi-restraints excluded: chain B residue 2733 ASP Chi-restraints excluded: chain B residue 2752 LEU Chi-restraints excluded: chain B residue 2813 THR Chi-restraints excluded: chain B residue 2830 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 242 optimal weight: 0.5980 chunk 221 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1560 ASN A2567 ASN B1560 ASN B2567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111070 restraints weight = 25761.280| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.70 r_work: 0.2978 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22758 Z= 0.125 Angle : 0.481 6.979 30804 Z= 0.249 Chirality : 0.038 0.129 3490 Planarity : 0.004 0.053 3958 Dihedral : 5.130 68.943 3094 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.06 % Allowed : 16.34 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.16), residues: 2792 helix: 2.22 (0.12), residues: 1984 sheet: 0.16 (0.67), residues: 76 loop : -1.71 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B2515 TYR 0.011 0.001 TYR B1629 PHE 0.016 0.001 PHE A2015 TRP 0.015 0.001 TRP B2118 HIS 0.004 0.001 HIS B1512 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (22758) covalent geometry : angle 0.48071 / 0.25 (30804) hydrogen bonds : bond 0.04151 / 2.76 ( 1412) hydrogen bonds : angle 3.45985 / 2.50 ( 4200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8741.66 seconds wall clock time: 149 minutes 32.21 seconds (8972.21 seconds total)