Starting phenix.real_space_refine on Sat Jan 18 11:53:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cv6_45956/01_2025/9cv6_45956.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cv6_45956/01_2025/9cv6_45956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cv6_45956/01_2025/9cv6_45956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cv6_45956/01_2025/9cv6_45956.map" model { file = "/net/cci-nas-00/data/ceres_data/9cv6_45956/01_2025/9cv6_45956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cv6_45956/01_2025/9cv6_45956.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 7586 2.51 5 N 2146 2.21 5 O 2254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12030 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6015 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 36, 'TRANS': 723} Chain breaks: 1 Chain: "B" Number of atoms: 6015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6015 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 36, 'TRANS': 723} Chain breaks: 1 Time building chain proxies: 8.58, per 1000 atoms: 0.71 Number of scatterers: 12030 At special positions: 0 Unit cell: (123.061, 172.64, 112.437, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2254 8.00 N 2146 7.00 C 7586 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: 2.54 Conformation dependent library (CDL) restraints added in 1.7 seconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 14 sheets defined 53.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 1624 through 1635 Processing helix chain 'A' and resid 1638 through 1640 No H-bonds generated for 'chain 'A' and resid 1638 through 1640' Processing helix chain 'A' and resid 1641 through 1661 removed outlier: 4.129A pdb=" N MET A1645 " --> pdb=" O ASP A1641 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A1646 " --> pdb=" O ILE A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1732 Processing helix chain 'A' and resid 1734 through 1751 removed outlier: 3.754A pdb=" N VAL A1740 " --> pdb=" O GLN A1736 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A1741 " --> pdb=" O GLU A1737 " (cutoff:3.500A) Processing helix chain 'A' and resid 1769 through 1774 removed outlier: 3.788A pdb=" N LYS A1773 " --> pdb=" O ALA A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1796 through 1804 removed outlier: 3.636A pdb=" N LYS A1802 " --> pdb=" O GLU A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1856 removed outlier: 4.153A pdb=" N LEU A1839 " --> pdb=" O GLY A1835 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A1841 " --> pdb=" O GLU A1837 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A1843 " --> pdb=" O LEU A1839 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1844 " --> pdb=" O ARG A1840 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1878 removed outlier: 3.545A pdb=" N TYR A1872 " --> pdb=" O GLY A1868 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A1878 " --> pdb=" O VAL A1874 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1901 Processing helix chain 'A' and resid 1907 through 1913 removed outlier: 4.167A pdb=" N LEU A1911 " --> pdb=" O SER A1907 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1921 removed outlier: 4.316A pdb=" N HIS A1919 " --> pdb=" O GLN A1915 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1944 removed outlier: 3.912A pdb=" N PHE A1943 " --> pdb=" O ARG A1939 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A1944 " --> pdb=" O TRP A1940 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1981 removed outlier: 4.068A pdb=" N MET A1979 " --> pdb=" O ASP A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2071 removed outlier: 3.645A pdb=" N GLU A2071 " --> pdb=" O ASP A2067 " (cutoff:3.500A) Processing helix chain 'A' and resid 2087 through 2093 Processing helix chain 'A' and resid 2094 through 2108 removed outlier: 3.674A pdb=" N PHE A2098 " --> pdb=" O GLN A2094 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A2102 " --> pdb=" O PHE A2098 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A2103 " --> pdb=" O GLY A2099 " (cutoff:3.500A) Processing helix chain 'A' and resid 2125 through 2132 removed outlier: 4.006A pdb=" N ALA A2129 " --> pdb=" O GLY A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2133 through 2136 Processing helix chain 'A' and resid 2154 through 2163 Processing helix chain 'A' and resid 2164 through 2176 Processing helix chain 'A' and resid 2176 through 2196 Processing helix chain 'A' and resid 2220 through 2235 removed outlier: 3.567A pdb=" N ARG A2224 " --> pdb=" O GLU A2220 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A2235 " --> pdb=" O LEU A2231 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2244 Processing helix chain 'A' and resid 2244 through 2258 Processing helix chain 'A' and resid 2261 through 2268 removed outlier: 3.642A pdb=" N MET A2265 " --> pdb=" O THR A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2305 removed outlier: 3.725A pdb=" N LEU A2283 " --> pdb=" O ASP A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2312 through 2328 removed outlier: 3.668A pdb=" N ALA A2316 " --> pdb=" O GLN A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2334 through 2339 Processing helix chain 'A' and resid 2341 through 2353 removed outlier: 3.934A pdb=" N GLY A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP A2353 " --> pdb=" O ALA A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2380 removed outlier: 3.634A pdb=" N ARG A2360 " --> pdb=" O SER A2356 " (cutoff:3.500A) Processing helix chain 'A' and resid 2382 through 2396 removed outlier: 3.612A pdb=" N SER A2387 " --> pdb=" O PRO A2383 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A2388 " --> pdb=" O SER A2384 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A2396 " --> pdb=" O LYS A2392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1624 through 1635 Processing helix chain 'B' and resid 1638 through 1640 No H-bonds generated for 'chain 'B' and resid 1638 through 1640' Processing helix chain 'B' and resid 1641 through 1661 removed outlier: 4.112A pdb=" N MET B1645 " --> pdb=" O ASP B1641 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE B1646 " --> pdb=" O ILE B1642 " (cutoff:3.500A) Processing helix chain 'B' and resid 1728 through 1732 Processing helix chain 'B' and resid 1734 through 1751 Processing helix chain 'B' and resid 1769 through 1776 removed outlier: 3.635A pdb=" N LYS B1773 " --> pdb=" O ALA B1769 " (cutoff:3.500A) Processing helix chain 'B' and resid 1796 through 1804 removed outlier: 3.579A pdb=" N LYS B1802 " --> pdb=" O GLU B1798 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1856 removed outlier: 4.146A pdb=" N LEU B1839 " --> pdb=" O GLY B1835 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B1843 " --> pdb=" O LEU B1839 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B1844 " --> pdb=" O ARG B1840 " (cutoff:3.500A) Processing helix chain 'B' and resid 1868 through 1878 removed outlier: 3.532A pdb=" N TYR B1872 " --> pdb=" O GLY B1868 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B1878 " --> pdb=" O VAL B1874 " (cutoff:3.500A) Processing helix chain 'B' and resid 1892 through 1901 Processing helix chain 'B' and resid 1908 through 1913 Processing helix chain 'B' and resid 1913 through 1921 removed outlier: 4.377A pdb=" N HIS B1919 " --> pdb=" O GLN B1915 " (cutoff:3.500A) Processing helix chain 'B' and resid 1929 through 1944 removed outlier: 3.941A pdb=" N PHE B1943 " --> pdb=" O ARG B1939 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B1944 " --> pdb=" O TRP B1940 " (cutoff:3.500A) Processing helix chain 'B' and resid 1975 through 1981 removed outlier: 4.157A pdb=" N MET B1979 " --> pdb=" O ASP B1975 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B1980 " --> pdb=" O PRO B1976 " (cutoff:3.500A) Processing helix chain 'B' and resid 2054 through 2071 removed outlier: 3.619A pdb=" N GLU B2071 " --> pdb=" O ASP B2067 " (cutoff:3.500A) Processing helix chain 'B' and resid 2087 through 2093 Processing helix chain 'B' and resid 2094 through 2108 removed outlier: 3.610A pdb=" N PHE B2098 " --> pdb=" O GLN B2094 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B2101 " --> pdb=" O LYS B2097 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B2102 " --> pdb=" O PHE B2098 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B2103 " --> pdb=" O GLY B2099 " (cutoff:3.500A) Processing helix chain 'B' and resid 2125 through 2132 removed outlier: 3.998A pdb=" N ALA B2129 " --> pdb=" O GLY B2125 " (cutoff:3.500A) Processing helix chain 'B' and resid 2133 through 2136 Processing helix chain 'B' and resid 2154 through 2163 Processing helix chain 'B' and resid 2164 through 2176 Processing helix chain 'B' and resid 2176 through 2196 Processing helix chain 'B' and resid 2217 through 2219 No H-bonds generated for 'chain 'B' and resid 2217 through 2219' Processing helix chain 'B' and resid 2220 through 2235 removed outlier: 3.774A pdb=" N ARG B2224 " --> pdb=" O GLU B2220 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B2225 " --> pdb=" O THR B2221 " (cutoff:3.500A) Processing helix chain 'B' and resid 2238 through 2244 Processing helix chain 'B' and resid 2244 through 2258 Processing helix chain 'B' and resid 2261 through 2268 removed outlier: 3.699A pdb=" N MET B2265 " --> pdb=" O THR B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2279 through 2306 removed outlier: 3.659A pdb=" N LEU B2283 " --> pdb=" O ASP B2279 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B2296 " --> pdb=" O LEU B2292 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B2306 " --> pdb=" O GLN B2302 " (cutoff:3.500A) Processing helix chain 'B' and resid 2312 through 2328 removed outlier: 3.674A pdb=" N ALA B2316 " --> pdb=" O GLN B2312 " (cutoff:3.500A) Processing helix chain 'B' and resid 2333 through 2337 removed outlier: 3.772A pdb=" N TRP B2336 " --> pdb=" O SER B2333 " (cutoff:3.500A) Processing helix chain 'B' and resid 2339 through 2353 removed outlier: 3.622A pdb=" N VAL B2343 " --> pdb=" O ASP B2339 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP B2353 " --> pdb=" O ALA B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2356 through 2380 removed outlier: 3.660A pdb=" N ARG B2360 " --> pdb=" O SER B2356 " (cutoff:3.500A) Processing helix chain 'B' and resid 2382 through 2396 removed outlier: 3.542A pdb=" N SER B2387 " --> pdb=" O PRO B2383 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B2388 " --> pdb=" O SER B2384 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B2396 " --> pdb=" O LYS B2392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1687 through 1690 removed outlier: 4.525A pdb=" N ALA A1703 " --> pdb=" O LEU A1677 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL A1679 " --> pdb=" O MET A1701 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N MET A1701 " --> pdb=" O VAL A1679 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE A1756 " --> pdb=" O ASP A1718 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A1720 " --> pdb=" O ILE A1756 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A1758 " --> pdb=" O VAL A1720 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A1722 " --> pdb=" O ILE A1758 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A1880 " --> pdb=" O ALA A1925 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ALA A1927 " --> pdb=" O VAL A1880 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN A1882 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1777 through 1780 removed outlier: 6.480A pdb=" N ASN A1777 " --> pdb=" O LEU A1793 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A1793 " --> pdb=" O ASN A1777 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A1779 " --> pdb=" O LYS A1791 " (cutoff:3.500A) removed outlier: 16.388A pdb=" N LYS A1791 " --> pdb=" O ASP A1826 " (cutoff:3.500A) removed outlier: 12.225A pdb=" N ASP A1826 " --> pdb=" O LYS A1791 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU A1793 " --> pdb=" O ILE A1824 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A1816 " --> pdb=" O GLU A1819 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS A1810 " --> pdb=" O THR A1825 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1866 through 1867 removed outlier: 5.940A pdb=" N ALA A1866 " --> pdb=" O ILE A1889 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1996 through 1997 removed outlier: 7.587A pdb=" N MET A2076 " --> pdb=" O PRO A2017 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLY A2019 " --> pdb=" O MET A2076 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N PHE A2078 " --> pdb=" O GLY A2019 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A2021 " --> pdb=" O PHE A2078 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A2075 " --> pdb=" O LEU A2114 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR A2116 " --> pdb=" O ILE A2075 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A2077 " --> pdb=" O TYR A2116 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A2273 " --> pdb=" O MET A2142 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A2144 " --> pdb=" O GLU A2273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2028 through 2032 Processing sheet with id=AA6, first strand: chain 'A' and resid 2052 through 2053 removed outlier: 3.703A pdb=" N TRP A2053 " --> pdb=" O GLY A2083 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 2122 through 2124 removed outlier: 3.537A pdb=" N GLY A2151 " --> pdb=" O LEU A2123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1687 through 1690 removed outlier: 4.544A pdb=" N ALA B1703 " --> pdb=" O LEU B1677 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL B1679 " --> pdb=" O MET B1701 " (cutoff:3.500A) removed outlier: 11.176A pdb=" N MET B1701 " --> pdb=" O VAL B1679 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ILE B1756 " --> pdb=" O ASP B1718 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B1720 " --> pdb=" O ILE B1756 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE B1758 " --> pdb=" O VAL B1720 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B1722 " --> pdb=" O ILE B1758 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B1880 " --> pdb=" O ALA B1925 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA B1927 " --> pdb=" O VAL B1880 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN B1882 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1777 through 1780 removed outlier: 6.633A pdb=" N ASN B1777 " --> pdb=" O LEU B1793 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU B1793 " --> pdb=" O ASN B1777 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA B1779 " --> pdb=" O LYS B1791 " (cutoff:3.500A) removed outlier: 16.272A pdb=" N LYS B1791 " --> pdb=" O ASP B1826 " (cutoff:3.500A) removed outlier: 12.266A pdb=" N ASP B1826 " --> pdb=" O LYS B1791 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU B1793 " --> pdb=" O ILE B1824 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B1816 " --> pdb=" O GLU B1819 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS B1810 " --> pdb=" O THR B1825 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1866 through 1867 removed outlier: 5.987A pdb=" N ALA B1866 " --> pdb=" O ILE B1889 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 1996 through 1997 removed outlier: 7.578A pdb=" N MET B2076 " --> pdb=" O PRO B2017 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY B2019 " --> pdb=" O MET B2076 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE B2078 " --> pdb=" O GLY B2019 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B2021 " --> pdb=" O PHE B2078 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B2075 " --> pdb=" O LEU B2114 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N TYR B2116 " --> pdb=" O ILE B2075 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE B2077 " --> pdb=" O TYR B2116 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B2273 " --> pdb=" O MET B2142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B2144 " --> pdb=" O GLU B2273 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2028 through 2032 Processing sheet with id=AB4, first strand: chain 'B' and resid 2052 through 2053 removed outlier: 3.546A pdb=" N TRP B2053 " --> pdb=" O GLY B2083 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 2122 through 2124 removed outlier: 3.564A pdb=" N GLY B2151 " --> pdb=" O LEU B2123 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1731 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: 4.25 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4046 1.34 - 1.46: 1942 1.46 - 1.57: 6206 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 12270 Sorted by residual: bond pdb=" C ILE B1642 " pdb=" N PRO B1643 " ideal model delta sigma weight residual 1.335 1.364 -0.028 1.36e-02 5.41e+03 4.38e+00 bond pdb=" C ILE A1642 " pdb=" N PRO A1643 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.15e+00 bond pdb=" C SER A2245 " pdb=" N PRO A2246 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.63e+00 bond pdb=" N ALA A1984 " pdb=" CA ALA A1984 " ideal model delta sigma weight residual 1.459 1.480 -0.021 1.15e-02 7.56e+03 3.44e+00 bond pdb=" C SER B2245 " pdb=" N PRO B2246 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.35e+00 ... (remaining 12265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 15971 1.89 - 3.78: 541 3.78 - 5.67: 86 5.67 - 7.56: 26 7.56 - 9.45: 10 Bond angle restraints: 16634 Sorted by residual: angle pdb=" N ILE A1828 " pdb=" CA ILE A1828 " pdb=" C ILE A1828 " ideal model delta sigma weight residual 108.96 103.28 5.68 1.42e+00 4.96e-01 1.60e+01 angle pdb=" C ILE A1998 " pdb=" CA ILE A1998 " pdb=" CB ILE A1998 " ideal model delta sigma weight residual 111.71 115.05 -3.34 8.50e-01 1.38e+00 1.55e+01 angle pdb=" CA ILE A1998 " pdb=" C ILE A1998 " pdb=" N MET A1999 " ideal model delta sigma weight residual 117.37 120.14 -2.77 7.40e-01 1.83e+00 1.40e+01 angle pdb=" CB ARG B2224 " pdb=" CG ARG B2224 " pdb=" CD ARG B2224 " ideal model delta sigma weight residual 111.30 119.84 -8.54 2.30e+00 1.89e-01 1.38e+01 angle pdb=" C GLU A1997 " pdb=" N ILE A1998 " pdb=" CA ILE A1998 " ideal model delta sigma weight residual 122.97 119.38 3.59 9.80e-01 1.04e+00 1.34e+01 ... (remaining 16629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.34: 6749 14.34 - 28.67: 532 28.67 - 43.01: 131 43.01 - 57.35: 26 57.35 - 71.68: 2 Dihedral angle restraints: 7440 sinusoidal: 3052 harmonic: 4388 Sorted by residual: dihedral pdb=" CA THR B2236 " pdb=" C THR B2236 " pdb=" N ALA B2237 " pdb=" CA ALA B2237 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA THR A2236 " pdb=" C THR A2236 " pdb=" N ALA A2237 " pdb=" CA ALA A2237 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA VAL B2052 " pdb=" C VAL B2052 " pdb=" N TRP B2053 " pdb=" CA TRP B2053 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 7437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1395 0.057 - 0.115: 338 0.115 - 0.172: 86 0.172 - 0.229: 9 0.229 - 0.286: 2 Chirality restraints: 1830 Sorted by residual: chirality pdb=" CB ILE A2247 " pdb=" CA ILE A2247 " pdb=" CG1 ILE A2247 " pdb=" CG2 ILE A2247 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE B2247 " pdb=" CA ILE B2247 " pdb=" CG1 ILE B2247 " pdb=" CG2 ILE B2247 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ILE A1828 " pdb=" N ILE A1828 " pdb=" C ILE A1828 " pdb=" CB ILE A1828 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1827 not shown) Planarity restraints: 2186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B2132 " -0.062 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO B2133 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO B2133 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B2133 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A2132 " 0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A2133 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A2133 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2133 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1650 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C VAL B1650 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL B1650 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU B1651 " 0.017 2.00e-02 2.50e+03 ... (remaining 2183 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3455 2.83 - 3.35: 10360 3.35 - 3.87: 19124 3.87 - 4.38: 23297 4.38 - 4.90: 39520 Nonbonded interactions: 95756 Sorted by model distance: nonbonded pdb=" OG SER A1759 " pdb=" OD1 ASN A1761 " model vdw 2.314 3.040 nonbonded pdb=" OD1 ASP B1991 " pdb=" NH2 ARG B2281 " model vdw 2.352 3.120 nonbonded pdb=" O PRO B1960 " pdb=" NH1 ARG B2281 " model vdw 2.365 3.120 nonbonded pdb=" OD1 ASP A1991 " pdb=" NH2 ARG A2281 " model vdw 2.366 3.120 nonbonded pdb=" OG SER B1759 " pdb=" OD1 ASN B1761 " model vdw 2.381 3.040 ... (remaining 95751 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: 5.900 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: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.230 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12270 Z= 0.289 Angle : 0.854 9.455 16634 Z= 0.486 Chirality : 0.055 0.286 1830 Planarity : 0.010 0.094 2186 Dihedral : 11.332 71.683 4616 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1512 helix: -0.90 (0.17), residues: 718 sheet: 1.37 (0.41), residues: 180 loop : -1.78 (0.21), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B2081 HIS 0.011 0.002 HIS A1918 PHE 0.014 0.002 PHE A1733 TYR 0.022 0.002 TYR B1893 ARG 0.004 0.000 ARG B1977 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.3595 time to fit residues: 104.4137 Evaluate side-chains 122 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1724 ASN B1724 ASN B1761 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.100446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078496 restraints weight = 23139.179| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.70 r_work: 0.3027 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12270 Z= 0.218 Angle : 0.574 6.961 16634 Z= 0.301 Chirality : 0.046 0.188 1830 Planarity : 0.006 0.065 2186 Dihedral : 4.560 18.186 1690 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.55 % Allowed : 4.36 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1512 helix: 0.52 (0.19), residues: 740 sheet: 1.15 (0.39), residues: 200 loop : -1.36 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1704 HIS 0.003 0.001 HIS B1918 PHE 0.015 0.001 PHE B2389 TYR 0.011 0.001 TYR B1872 ARG 0.006 0.000 ARG A1717 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2250 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7819 (pt0) REVERT: A 2389 PHE cc_start: 0.8640 (t80) cc_final: 0.8250 (t80) REVERT: B 1917 MET cc_start: 0.8142 (mmt) cc_final: 0.7338 (mmt) REVERT: B 2032 GLN cc_start: 0.8916 (mt0) cc_final: 0.8640 (mt0) REVERT: B 2391 ARG cc_start: 0.8582 (ptp-110) cc_final: 0.8378 (ptp-110) outliers start: 7 outliers final: 3 residues processed: 132 average time/residue: 0.3542 time to fit residues: 62.3788 Evaluate side-chains 112 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain B residue 2053 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 143 optimal weight: 0.0030 chunk 14 optimal weight: 0.0370 chunk 60 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 103 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.3268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.077631 restraints weight = 23484.380| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.70 r_work: 0.3060 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12270 Z= 0.129 Angle : 0.493 7.926 16634 Z= 0.251 Chirality : 0.043 0.145 1830 Planarity : 0.005 0.056 2186 Dihedral : 4.142 16.126 1690 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.63 % Allowed : 5.55 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1512 helix: 1.16 (0.20), residues: 742 sheet: 1.28 (0.40), residues: 200 loop : -1.14 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1704 HIS 0.002 0.000 HIS A1918 PHE 0.011 0.001 PHE B2389 TYR 0.008 0.001 TYR B1872 ARG 0.006 0.000 ARG A1785 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1730 MET cc_start: 0.8777 (mmp) cc_final: 0.8357 (mmp) REVERT: A 1785 ARG cc_start: 0.9080 (mtt90) cc_final: 0.8387 (mtm-85) REVERT: A 1788 ARG cc_start: 0.8901 (mmt90) cc_final: 0.8470 (mtt-85) REVERT: A 2185 ARG cc_start: 0.7095 (tpm170) cc_final: 0.6501 (tpm170) REVERT: A 2250 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7672 (pt0) REVERT: A 2389 PHE cc_start: 0.8436 (t80) cc_final: 0.8028 (t80) REVERT: B 1917 MET cc_start: 0.8159 (mmt) cc_final: 0.7608 (mmt) REVERT: B 2391 ARG cc_start: 0.8476 (ptp-110) cc_final: 0.8275 (ptp-110) outliers start: 8 outliers final: 3 residues processed: 123 average time/residue: 0.3119 time to fit residues: 51.8462 Evaluate side-chains 101 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2053 TRP Chi-restraints excluded: chain B residue 2053 TRP Chi-restraints excluded: chain B residue 2231 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 27 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 114 optimal weight: 0.2980 chunk 120 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 0.0000 chunk 129 optimal weight: 1.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.075997 restraints weight = 23425.265| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.74 r_work: 0.3038 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12270 Z= 0.146 Angle : 0.483 6.861 16634 Z= 0.246 Chirality : 0.043 0.148 1830 Planarity : 0.004 0.050 2186 Dihedral : 4.003 15.491 1690 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.19 % Allowed : 6.50 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1512 helix: 1.46 (0.20), residues: 742 sheet: 1.25 (0.40), residues: 200 loop : -1.00 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2346 HIS 0.002 0.000 HIS B2259 PHE 0.008 0.001 PHE B1776 TYR 0.010 0.001 TYR B2248 ARG 0.004 0.000 ARG A1785 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 1730 MET cc_start: 0.8776 (mmp) cc_final: 0.8303 (mmp) REVERT: A 1785 ARG cc_start: 0.9122 (mtt90) cc_final: 0.8367 (mtm-85) REVERT: A 1788 ARG cc_start: 0.8964 (mmt90) cc_final: 0.8481 (mtt-85) REVERT: A 2091 MET cc_start: 0.9361 (tpp) cc_final: 0.9079 (mmm) REVERT: A 2185 ARG cc_start: 0.7152 (tpt170) cc_final: 0.6584 (tpm170) REVERT: A 2250 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7718 (pt0) REVERT: A 2389 PHE cc_start: 0.8602 (t80) cc_final: 0.8171 (t80) REVERT: B 1917 MET cc_start: 0.8101 (mmt) cc_final: 0.7652 (mmt) REVERT: B 2389 PHE cc_start: 0.8502 (t80) cc_final: 0.8071 (t80) outliers start: 15 outliers final: 5 residues processed: 112 average time/residue: 0.3355 time to fit residues: 50.7167 Evaluate side-chains 101 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2053 TRP Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 2053 TRP Chi-restraints excluded: chain B residue 2390 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1761 ASN B2385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.096777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075096 restraints weight = 23309.878| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.64 r_work: 0.3006 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12270 Z= 0.235 Angle : 0.517 5.897 16634 Z= 0.267 Chirality : 0.045 0.164 1830 Planarity : 0.004 0.047 2186 Dihedral : 4.117 15.454 1690 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.87 % Allowed : 7.53 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1512 helix: 1.49 (0.20), residues: 744 sheet: 1.02 (0.41), residues: 188 loop : -0.87 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1704 HIS 0.003 0.001 HIS B2249 PHE 0.007 0.001 PHE A1776 TYR 0.013 0.001 TYR A2248 ARG 0.006 0.000 ARG B2391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: A 2185 ARG cc_start: 0.7223 (tpt170) cc_final: 0.6675 (tpm170) REVERT: A 2250 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7963 (pt0) REVERT: A 2389 PHE cc_start: 0.8645 (t80) cc_final: 0.8248 (t80) REVERT: B 1917 MET cc_start: 0.8449 (mmt) cc_final: 0.7820 (mmt) outliers start: 11 outliers final: 7 residues processed: 115 average time/residue: 0.3430 time to fit residues: 52.9615 Evaluate side-chains 109 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 2053 TRP Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 2053 TRP Chi-restraints excluded: chain B residue 2390 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1698 ASN B1698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.072992 restraints weight = 24007.729| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.76 r_work: 0.3008 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12270 Z= 0.198 Angle : 0.505 6.367 16634 Z= 0.260 Chirality : 0.044 0.154 1830 Planarity : 0.004 0.048 2186 Dihedral : 4.073 15.777 1690 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.63 % Allowed : 8.16 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1512 helix: 1.50 (0.20), residues: 744 sheet: 1.00 (0.41), residues: 188 loop : -0.82 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1704 HIS 0.002 0.001 HIS A2249 PHE 0.007 0.001 PHE B1776 TYR 0.011 0.001 TYR A2248 ARG 0.006 0.000 ARG B2391 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 1785 ARG cc_start: 0.9133 (mtt90) cc_final: 0.8516 (mtm-85) REVERT: A 2091 MET cc_start: 0.9359 (tpp) cc_final: 0.9039 (mmm) REVERT: A 2185 ARG cc_start: 0.7183 (tpt170) cc_final: 0.6646 (tpm170) REVERT: A 2250 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7747 (pt0) REVERT: A 2389 PHE cc_start: 0.8635 (t80) cc_final: 0.8269 (t80) REVERT: B 1917 MET cc_start: 0.8244 (mmt) cc_final: 0.7687 (mmt) outliers start: 8 outliers final: 6 residues processed: 108 average time/residue: 0.3294 time to fit residues: 48.1726 Evaluate side-chains 105 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2053 TRP Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 2053 TRP Chi-restraints excluded: chain B residue 2093 GLU Chi-restraints excluded: chain B residue 2390 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 24 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.094490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.072486 restraints weight = 23813.478| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.73 r_work: 0.2992 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12270 Z= 0.215 Angle : 0.513 6.733 16634 Z= 0.264 Chirality : 0.044 0.158 1830 Planarity : 0.004 0.048 2186 Dihedral : 4.078 15.849 1690 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.63 % Allowed : 8.24 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1512 helix: 1.49 (0.20), residues: 744 sheet: 0.93 (0.41), residues: 188 loop : -0.76 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1704 HIS 0.002 0.001 HIS A2249 PHE 0.007 0.001 PHE B1776 TYR 0.012 0.001 TYR A2248 ARG 0.013 0.000 ARG B2391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 1785 ARG cc_start: 0.9142 (mtt90) cc_final: 0.8505 (mtm-85) REVERT: A 2091 MET cc_start: 0.9355 (tpp) cc_final: 0.9036 (mmm) REVERT: A 2185 ARG cc_start: 0.7180 (tpt170) cc_final: 0.6639 (tpm170) REVERT: A 2389 PHE cc_start: 0.8725 (t80) cc_final: 0.8321 (t80) REVERT: B 1917 MET cc_start: 0.8280 (mmt) cc_final: 0.7761 (mmt) REVERT: B 2389 PHE cc_start: 0.8554 (t80) cc_final: 0.8216 (t80) outliers start: 8 outliers final: 7 residues processed: 112 average time/residue: 0.3320 time to fit residues: 50.1699 Evaluate side-chains 103 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2053 TRP Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1951 THR Chi-restraints excluded: chain B residue 2053 TRP Chi-restraints excluded: chain B residue 2093 GLU Chi-restraints excluded: chain B residue 2390 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 46 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.096066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.074341 restraints weight = 23674.087| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.66 r_work: 0.2988 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12270 Z= 0.230 Angle : 0.529 7.094 16634 Z= 0.272 Chirality : 0.044 0.160 1830 Planarity : 0.004 0.048 2186 Dihedral : 4.105 15.924 1690 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.87 % Allowed : 8.24 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1512 helix: 1.56 (0.20), residues: 732 sheet: 0.84 (0.41), residues: 188 loop : -0.74 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1704 HIS 0.002 0.001 HIS A2249 PHE 0.006 0.001 PHE B1776 TYR 0.012 0.001 TYR A2248 ARG 0.013 0.000 ARG B2391 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 1785 ARG cc_start: 0.9232 (mtt90) cc_final: 0.8592 (mtm-85) REVERT: A 2091 MET cc_start: 0.9407 (tpp) cc_final: 0.9103 (mmm) REVERT: A 2185 ARG cc_start: 0.7157 (tpt170) cc_final: 0.6607 (tpm170) REVERT: B 1917 MET cc_start: 0.8457 (mmt) cc_final: 0.8029 (mmt) REVERT: B 1962 ASP cc_start: 0.8853 (t0) cc_final: 0.8588 (t0) REVERT: B 2389 PHE cc_start: 0.8612 (t80) cc_final: 0.8364 (t80) outliers start: 11 outliers final: 10 residues processed: 105 average time/residue: 0.3319 time to fit residues: 47.2278 Evaluate side-chains 105 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1951 THR Chi-restraints excluded: chain A residue 2053 TRP Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1951 THR Chi-restraints excluded: chain B residue 2053 TRP Chi-restraints excluded: chain B residue 2093 GLU Chi-restraints excluded: chain B residue 2390 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.072475 restraints weight = 23869.417| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.74 r_work: 0.3001 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12270 Z= 0.208 Angle : 0.520 8.008 16634 Z= 0.267 Chirality : 0.044 0.155 1830 Planarity : 0.004 0.050 2186 Dihedral : 4.069 16.163 1690 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.79 % Allowed : 8.56 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1512 helix: 1.58 (0.20), residues: 732 sheet: 0.84 (0.41), residues: 188 loop : -0.71 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1704 HIS 0.003 0.001 HIS B2249 PHE 0.007 0.001 PHE B1776 TYR 0.011 0.001 TYR A2248 ARG 0.015 0.000 ARG B2391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 1785 ARG cc_start: 0.9224 (mtt90) cc_final: 0.8571 (mtm-85) REVERT: A 2091 MET cc_start: 0.9382 (tpp) cc_final: 0.9080 (mmm) REVERT: A 2185 ARG cc_start: 0.7125 (tpt170) cc_final: 0.6566 (tpm170) REVERT: B 1917 MET cc_start: 0.8357 (mmt) cc_final: 0.7936 (mmt) REVERT: B 1962 ASP cc_start: 0.8857 (t0) cc_final: 0.8597 (t0) REVERT: B 2389 PHE cc_start: 0.8563 (t80) cc_final: 0.8320 (t80) outliers start: 10 outliers final: 10 residues processed: 105 average time/residue: 0.3426 time to fit residues: 48.7067 Evaluate side-chains 104 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1951 THR Chi-restraints excluded: chain A residue 2053 TRP Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1951 THR Chi-restraints excluded: chain B residue 2053 TRP Chi-restraints excluded: chain B residue 2093 GLU Chi-restraints excluded: chain B residue 2390 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 135 optimal weight: 2.9990 chunk 118 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072364 restraints weight = 23591.861| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.73 r_work: 0.3007 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12270 Z= 0.208 Angle : 0.522 8.431 16634 Z= 0.267 Chirality : 0.044 0.155 1830 Planarity : 0.004 0.048 2186 Dihedral : 4.048 15.964 1690 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.03 % Allowed : 8.40 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1512 helix: 1.61 (0.20), residues: 732 sheet: 0.87 (0.41), residues: 188 loop : -0.68 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1704 HIS 0.002 0.001 HIS A2249 PHE 0.007 0.001 PHE B1776 TYR 0.012 0.001 TYR A2248 ARG 0.008 0.000 ARG A2391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: A 1785 ARG cc_start: 0.9216 (mtt90) cc_final: 0.8563 (mtm-85) REVERT: A 2091 MET cc_start: 0.9380 (tpp) cc_final: 0.9085 (mmm) REVERT: A 2185 ARG cc_start: 0.7133 (tpt170) cc_final: 0.6573 (tpm170) REVERT: B 1917 MET cc_start: 0.8365 (mmt) cc_final: 0.7951 (mmt) REVERT: B 1962 ASP cc_start: 0.8863 (t0) cc_final: 0.8610 (t0) REVERT: B 2389 PHE cc_start: 0.8558 (t80) cc_final: 0.8316 (t80) outliers start: 13 outliers final: 11 residues processed: 107 average time/residue: 0.3221 time to fit residues: 47.1457 Evaluate side-chains 105 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1951 THR Chi-restraints excluded: chain A residue 2053 TRP Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1826 ASP Chi-restraints excluded: chain B residue 1951 THR Chi-restraints excluded: chain B residue 2053 TRP Chi-restraints excluded: chain B residue 2093 GLU Chi-restraints excluded: chain B residue 2390 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 125 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 150 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.072786 restraints weight = 23878.522| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.74 r_work: 0.3004 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12270 Z= 0.194 Angle : 0.518 8.066 16634 Z= 0.265 Chirality : 0.044 0.153 1830 Planarity : 0.004 0.056 2186 Dihedral : 4.024 17.520 1690 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.87 % Allowed : 8.40 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1512 helix: 1.63 (0.20), residues: 732 sheet: 0.90 (0.41), residues: 188 loop : -0.66 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1704 HIS 0.002 0.001 HIS B2249 PHE 0.007 0.001 PHE B1776 TYR 0.011 0.001 TYR A2248 ARG 0.015 0.000 ARG B2391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5808.25 seconds wall clock time: 103 minutes 33.58 seconds (6213.58 seconds total)